Contacts of the helix formed by residues 89 - 106 (chain A) in PDB entry 4HI7
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 ASP 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 4.5 1.2 + - - -
87A PRO* 3.4 2.3 - - + +
88A LYS* 1.3 76.6 - - - +
90A LEU* 1.3 60.3 + - - +
91A VAL* 3.1 13.6 + - - +
92A LYS* 2.9 51.0 + - + +
93A ARG* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS 3.2 12.3 + - - +
89A ASP* 1.3 75.6 - - - +
91A VAL* 1.3 59.2 + - + +
93A ARG* 3.8 12.4 - - + +
94A ALA* 2.9 30.0 + - - +
74B TYR* 3.6 21.1 - - + +
77B SER* 3.7 24.9 - - - +
78B LYS* 3.7 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP* 3.1 9.4 + - - +
90A LEU* 1.3 72.9 - - + +
92A LYS* 1.3 68.8 + - + +
94A ALA* 3.3 6.4 + - + +
95A LEU* 3.2 19.9 + - - +
63B ALA* 3.9 31.6 - - + -
64B ASN 5.8 0.7 - - - +
65B ILE* 5.6 2.9 - - + +
74B TYR* 4.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 3.8 26.0 - - + -
89A ASP* 2.9 32.0 + - + +
91A VAL* 1.3 75.8 - - + +
93A ARG* 1.3 63.5 + - - +
95A LEU* 3.2 15.2 + - - +
96A VAL* 3.2 19.0 + - - +
153A ALA 5.3 0.7 - - - +
155A ASN* 5.8 4.4 + - - +
156A GLN* 5.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 4.0 12.5 + - - -
86A TYR* 3.2 69.3 + - + +
87A PRO* 2.8 24.9 + - - +
88A LYS* 3.6 26.6 - - - +
89A ASP 2.8 17.7 + - - +
90A LEU* 3.8 14.6 - - + +
92A LYS* 1.3 75.1 - - - +
94A ALA* 1.3 56.1 + - - +
96A VAL* 3.2 8.0 + - - +
97A ASP* 2.8 35.0 + - - +
86B TYR* 6.1 0.7 - - - -
90B LEU* 6.3 1.0 - - - +
93B ARG* 4.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 2.9 19.0 + - - +
91A VAL 3.5 6.5 - - - +
92A LYS 3.3 0.4 - - - -
93A ARG* 1.3 76.2 - - - +
95A LEU* 1.3 58.0 + - - +
97A ASP* 3.7 9.7 - - - +
98A ASN* 2.9 28.9 + - - +
65B ILE* 3.8 37.2 - - + +
70B ALA* 3.8 7.6 - - - +
74B TYR* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL 3.2 8.2 + - - +
92A LYS* 3.2 10.1 + - - +
93A ARG 3.1 0.8 - - - -
94A ALA* 1.3 77.4 - - - +
96A VAL* 1.3 65.6 + - - +
98A ASN* 3.3 7.6 + - + +
99A ARG* 3.0 64.4 + - - +
149A GLN* 5.2 3.4 - - - +
152A VAL 4.8 1.3 - - - +
153A ALA* 3.7 34.5 - - + +
154A GLY* 4.0 5.6 - - - +
64B ASN 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.8 25.1 - - + -
87A PRO* 4.1 14.8 - - + -
92A LYS 3.2 12.8 + - - +
93A ARG 3.2 6.4 + - - +
95A LEU* 1.3 76.9 - - - +
97A ASP* 1.3 63.6 + - - +
99A ARG* 3.2 3.3 + - - +
100A MET* 3.0 24.9 + - + +
153A ALA* 3.8 16.8 - - + +
158A THR* 3.8 26.2 - - + +
159A ILE* 3.9 7.6 - - + -
160A ALA* 3.8 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 2.7 34.3 + - - -
93A ARG* 2.8 30.7 + - - +
94A ALA* 3.7 7.7 - - - +
96A VAL* 1.3 71.6 - - - +
98A ASN* 1.3 65.0 + - - +
100A MET* 3.1 7.9 + - - +
101A TYR* 2.9 39.7 + - + -
70B ALA* 3.9 15.7 - - + +
73B ALA* 4.4 17.7 - - - +
86B TYR* 5.0 3.6 + - - -
101B TYR* 4.4 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 2.9 19.1 + - - +
95A LEU* 3.5 11.0 - - + +
97A ASP* 1.3 76.7 - - - +
99A ARG* 1.3 89.3 + - - +
101A TYR* 3.3 1.7 + - - +
102A PHE* 2.9 27.6 + - - +
52B GLN* 3.7 12.9 + - - +
65B ILE* 5.6 0.9 - - + -
66B ALA* 2.9 47.5 + - - +
67B ASP* 3.6 10.1 - - - +
70B ALA* 3.9 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.0 39.7 + - - +
96A VAL 3.2 0.2 + - - -
98A ASN* 1.3 95.5 + - - +
100A MET* 1.3 58.4 + - - +
102A PHE* 3.4 5.9 - - - +
103A GLU* 3.0 25.5 + - - +
145A PHE* 3.6 60.2 + - - +
147A LYS* 5.4 6.7 - - - +
152A VAL* 2.9 29.7 + - + +
153A ALA* 3.9 8.1 - - + -
160A ALA* 3.7 19.1 - - + -
164A LEU* 4.1 15.9 - - + +
52B GLN* 3.8 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 3.6 39.7 + - + +
72A MET* 4.1 14.1 - - - -
73A ALA* 4.8 1.3 - - + -
86A TYR* 4.3 8.3 - - + +
96A VAL* 3.0 18.1 + - + +
97A ASP* 3.1 15.9 + - - +
99A ARG* 1.3 75.4 - - - +
101A TYR* 1.3 59.1 + - - +
103A GLU* 3.2 7.4 + - - +
104A SER* 2.9 25.1 + - - -
159A ILE* 3.6 39.7 - - + +
160A ALA* 3.9 17.0 - - - -
163A SER* 4.3 3.1 - - - -
101B TYR* 3.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 2.9 40.2 + - + +
98A ASN 3.9 0.9 - - - +
100A MET* 1.3 72.8 - - - +
102A PHE* 1.3 64.7 + - - +
104A SER* 2.6 19.5 + - - -
105A GLY* 3.2 6.4 + - - -
67B ASP* 3.3 29.5 - - - +
69B HIS* 3.3 39.7 - + + +
70B ALA 4.2 7.9 - - - -
73B ALA* 6.5 0.4 - - + -
97B ASP* 3.8 5.0 + - - -
100B MET* 3.3 29.1 - - + +
101B TYR* 3.3 60.2 - + - -
104B SER* 3.4 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN* 2.9 20.8 + - - +
99A ARG* 3.4 9.4 - - - +
101A TYR* 1.3 77.8 - - - +
103A GLU* 1.3 64.5 + - - +
106A VAL* 3.0 60.5 + - + +
107A VAL* 3.4 24.7 + - + -
138A ALA 4.3 2.5 - - - -
141A PHE* 3.5 37.0 - + + -
142A VAL* 3.7 15.9 - - + -
145A PHE* 3.6 25.1 - + + -
164A LEU* 4.1 4.9 - - + -
52B GLN* 3.6 24.2 - - - +
67B ASP* 4.5 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 5.6 0.3 - - - +
69A HIS* 2.7 29.8 + - - -
99A ARG 3.0 14.3 + - - +
100A MET* 3.2 8.5 + - - +
102A PHE* 1.3 76.5 - - - +
104A SER* 1.3 56.7 + - - +
105A GLY 3.3 0.3 + - - -
107A VAL* 3.9 9.6 - - + -
108A PHE* 2.7 45.8 + - - +
163A SER* 3.2 28.2 - - - +
164A LEU* 3.6 18.4 - - + -
166A SER* 4.4 2.4 + - - -
167A SER* 2.6 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 3.6 18.6 - - - -
100A MET 2.9 12.9 + - - -
101A TYR* 2.6 23.7 + - - -
103A GLU* 1.3 84.2 + - - +
105A GLY* 1.3 55.8 + - - +
108A PHE* 3.7 7.8 - - - +
109A ALA* 3.1 24.9 + - - +
301A GSH 5.3 4.9 + - - -
101B TYR* 3.8 16.2 - - - -
104B SER* 2.8 25.1 + - - -
105B GLY* 4.0 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR 3.2 4.5 + - - -
103A GLU 3.2 0.2 - - - -
104A SER* 1.3 82.1 + - - +
106A VAL* 1.3 62.0 + - - +
107A VAL 3.3 1.1 - - - -
109A ALA* 3.4 2.8 + - - +
110A ASN* 2.9 31.5 + - - +
104B SER* 3.9 14.4 - - - -
105B GLY* 4.2 0.4 - - - -
109B ALA* 3.8 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR 4.8 0.2 + - - -
102A PHE* 3.0 52.2 + - + +
105A GLY* 1.3 71.9 - - - -
107A VAL* 1.3 63.6 + - + +
110A ASN* 3.3 25.8 + - - +
111A ALA* 3.6 8.1 + - - +
134A ALA 4.8 1.8 - - - +
137A GLU* 6.0 1.1 - - + -
138A ALA* 4.7 9.2 - - + +
141A PHE* 4.1 20.4 - - + -
52B GLN* 5.5 1.8 - - - +
113B ARG* 6.4 2.9 - - - -
----------------------------------------------------------
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