Contacts of the helix formed by residues 96 - 122 (chain A) in PDB entry 1GRB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 3.9 29.2 - - + -
94A PHE* 3.4 29.4 + + + -
95A ASN* 1.3 74.3 + - - +
97A ARG* 1.3 58.8 + - - +
98A VAL 3.2 0.3 + - - -
99A ILE* 3.3 4.8 + - + +
100A LYS* 2.8 34.3 + - + +
103A ARG* 4.8 5.8 - - - +
180A PHE* 3.9 30.3 - + - -
183A LEU* 3.0 42.0 + - + -
184A GLU* 3.3 25.1 - - - -
185A GLU* 4.1 6.7 - - - -
186A LEU* 3.6 56.8 - - + +
187A PRO* 4.8 0.4 - - + -
206A LEU* 4.2 7.6 - - + -
209A LEU* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 3.3 14.3 + - - +
96A TRP* 1.3 79.1 - - + +
98A VAL* 1.3 63.0 + - + +
100A LYS* 3.9 6.7 - - + +
101A GLU* 2.7 65.2 + - + +
184A GLU* 3.6 41.4 + - - +
185A GLU* 5.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 3.5 36.6 - - + +
96A TRP 3.2 0.4 - - - -
97A ARG* 1.3 80.2 - - + +
99A ILE* 1.3 64.5 + - + +
101A GLU* 4.0 8.0 - - - +
102A LYS* 3.3 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 4.5 17.3 - - + -
69A MET* 4.3 20.0 - - + -
72A THR* 3.5 25.4 - - + +
94A PHE* 3.7 29.6 - - + -
95A ASN 3.8 1.0 + - - -
96A TRP* 3.3 10.7 + - + +
98A VAL* 1.3 79.8 - - + +
100A LYS* 1.3 72.6 + - + +
102A LYS* 3.2 19.8 + - + -
103A ARG* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 2.8 30.9 + - + +
97A ARG* 3.9 7.9 - - + +
98A VAL 3.2 0.2 - - - -
99A ILE* 1.3 80.9 - - + +
101A GLU* 1.3 67.9 + - + +
103A ARG* 3.3 22.0 + - - +
104A ASP* 3.0 43.1 + - - +
181A PHE 3.9 18.6 - - - -
182A GLN* 4.2 8.4 + - - +
183A LEU 3.5 22.9 - - - +
184A GLU* 4.3 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 2.7 72.2 + - + +
98A VAL* 4.0 7.8 - - - +
100A LYS* 1.3 84.1 - - + +
102A LYS* 1.3 61.7 + - + +
104A ASP* 3.5 7.3 + - - +
105A ALA* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 5.9 0.4 - - - -
98A VAL* 3.3 36.2 - - - +
99A ILE* 3.2 20.8 + - + +
101A GLU* 1.3 75.3 - - + +
103A ARG* 1.3 64.4 + - - +
105A ALA* 3.5 7.1 + - - +
106A TYR* 3.2 23.0 + - - +
109A ARG* 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.6 39.8 - - + +
68A VAL* 3.9 29.8 - - + +
69A MET* 3.5 34.6 - - - +
96A TRP* 4.8 8.5 - - - +
99A ILE 2.9 17.8 + - - +
100A LYS* 3.6 29.8 - - - +
102A LYS* 1.3 75.2 - - - +
104A ASP* 1.3 82.1 + - - +
106A TYR* 3.1 7.1 + - - +
107A VAL* 3.0 26.9 + - + +
180A PHE* 4.9 1.6 + - - -
181A PHE* 2.8 44.9 + - - +
183A LEU 5.1 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.0 47.2 + - - +
101A GLU* 3.8 8.0 - - - +
103A ARG* 1.3 97.2 + - - +
105A ALA* 1.3 59.9 + - - +
107A VAL* 3.4 10.2 + - - +
108A SER* 3.0 24.4 + - - -
181A PHE 4.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU 3.2 15.1 + - - +
102A LYS* 3.8 8.3 - - - +
103A ARG 3.2 0.2 - - - -
104A ASP* 1.3 75.7 - - - +
106A TYR* 1.3 60.5 + - - +
108A SER* 3.0 11.4 + - - -
109A ARG* 2.9 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.4 31.2 - - + +
68A VAL* 4.0 20.4 - - + -
102A LYS 3.2 14.8 + - - +
103A ARG* 3.1 6.6 + - + +
105A ALA* 1.3 78.7 - - - +
107A VAL* 1.3 63.0 + - + +
109A ARG* 3.2 38.6 + - + +
110A LEU* 3.1 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 6.0 2.5 - - - +
59A VAL* 3.4 23.6 - - + +
60A ASN* 3.7 29.2 - - - +
64A VAL* 4.9 6.7 - - + -
65A PRO* 4.4 22.9 - - + -
103A ARG* 3.0 17.7 + - + +
104A ASP* 3.6 12.1 - - - +
106A TYR* 1.3 78.1 - - + +
108A SER* 1.3 55.8 + - - +
110A LEU* 3.2 8.7 + - - +
111A ASN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP 3.0 14.4 + - - -
105A ALA* 3.0 14.3 + - - -
107A VAL* 1.3 71.4 - - - +
109A ARG* 1.3 67.0 + - - +
111A ASN* 3.3 12.3 + - - +
112A ALA* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS 4.8 1.6 + - - -
105A ALA* 2.9 25.1 + - + +
106A TYR* 3.2 58.2 + - + +
108A SER* 1.3 76.4 - - - +
110A LEU* 1.3 63.9 + - + +
112A ALA* 3.2 8.1 + - - +
113A ILE* 3.0 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.7 20.4 - - + -
64A VAL* 3.8 38.6 - - + -
106A TYR* 3.1 38.2 + - + +
107A VAL* 3.2 8.0 + - - +
109A ARG* 1.3 75.4 - - + +
111A ASN* 1.3 69.0 + - - +
113A ILE* 3.2 16.2 + - + -
114A TYR* 2.8 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 4.3 18.2 + - + +
54A LEU* 2.9 36.0 + - + +
59A VAL* 3.7 9.3 - - - +
60A ASN* 3.0 23.5 + - - +
107A VAL* 3.0 23.6 + - - +
108A SER* 3.8 12.4 + - - +
109A ARG 3.3 0.2 - - - -
110A LEU* 1.3 78.1 - - - +
112A ALA* 1.3 61.0 + - - +
114A TYR* 3.7 3.9 - - - +
115A GLN* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER 3.2 9.7 + - - +
109A ARG* 3.2 10.9 + - - +
110A LEU 3.2 0.4 - - - -
111A ASN* 1.3 78.4 - - - +
113A ILE* 1.3 63.2 + - + +
115A GLN* 3.5 8.8 + - - +
116A ASN* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.0 21.6 + - + +
110A LEU* 3.5 23.1 - - + +
112A ALA* 1.3 79.0 - - + +
114A TYR* 1.3 67.5 + - + +
116A ASN* 3.2 7.9 + - - +
117A ASN* 2.8 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 6.5 0.4 - - - -
33A LEU* 3.5 27.8 - - + +
54A LEU* 4.4 15.3 - - + -
55A GLY* 4.1 9.0 - - - +
58A CYS* 5.5 3.6 - - - -
59A VAL* 3.9 21.5 - - + +
110A LEU* 2.8 50.4 + - + +
111A ASN* 3.7 6.1 - - - +
113A ILE* 1.3 82.6 - - + +
115A GLN* 1.3 67.2 + - - +
117A ASN* 3.2 14.6 + - + +
118A LEU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.9 23.0 - - + +
111A ASN 3.1 14.6 + - - +
112A ALA* 3.7 8.1 - - - +
114A TYR* 1.3 79.4 - - - +
116A ASN* 1.3 63.8 + - - +
118A LEU* 3.0 14.2 + - - +
119A THR* 3.0 24.0 + - + +
125A ILE* 4.1 14.6 - - + +
127A ARG* 3.7 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 3.0 14.9 + - - +
113A ILE* 3.2 10.5 + - - +
115A GLN* 1.3 79.0 - - - +
117A ASN* 1.3 62.4 + - - +
119A THR* 3.2 15.5 + - - -
120A LYS* 3.0 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.8 34.7 + - - +
113A ILE* 2.8 35.0 + - - +
114A TYR* 3.6 17.2 - - + +
115A GLN 3.2 0.8 - - - -
116A ASN* 1.3 77.6 + - - +
118A LEU* 1.3 64.9 + - - +
120A LYS* 3.8 24.1 + - - +
121A SER* 3.4 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.0 31.4 - - + +
36A ALA* 5.3 0.2 - - + -
37A ARG* 3.9 17.3 - - + -
48A VAL* 4.3 16.2 - - + -
54A LEU* 4.3 11.4 - - + -
114A TYR 3.1 14.8 + - - +
115A GLN 3.0 9.6 + - - +
117A ASN* 1.3 75.7 - - - +
119A THR* 1.3 64.0 + - - +
121A SER* 2.9 13.3 + - - -
122A HIS 3.1 8.3 + - - -
123A ILE* 3.1 39.1 + - + +
125A ILE* 3.4 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 3.0 23.0 + - + +
116A ASN* 3.2 21.7 + - - -
118A LEU* 1.3 74.9 - - - +
120A LYS* 1.3 65.2 + - - +
122A HIS* 2.9 23.2 + - - +
123A ILE 4.7 5.8 - - - +
125A ILE* 4.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 3.0 40.9 + - - +
117A ASN* 4.1 21.2 - - - +
119A THR* 1.3 82.8 + - - +
121A SER* 1.4 56.0 + - - +
122A HIS* 3.3 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 4.5 15.8 + - - +
40A ALA* 3.7 20.7 - - - +
41A GLU* 5.8 2.6 - - - +
117A ASN 3.4 12.3 + - - -
118A LEU 2.9 10.1 + - - -
120A LYS* 1.4 74.8 - - - +
122A HIS* 1.3 78.0 + - - +
123A ILE* 3.5 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 5.6 0.7 - - - +
45A ARG* 3.2 22.5 + - - -
46A ALA 4.3 0.9 + - - +
119A THR* 2.9 17.0 + - - +
120A LYS* 3.4 18.1 + - - -
121A SER* 1.3 87.6 + - - +
123A ILE* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il