Contacts of the helix formed by residues 101 - 114 (chain A) in PDB entry 1D5C
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 ASN 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.4 44.5 + - + +
97A GLN* 2.9 36.7 + - - +
98A SER 3.9 2.2 - - - +
99A PHE 3.0 1.2 - - - -
100A GLU* 1.3 77.4 - - - +
102A THR* 1.3 64.1 + - - +
103A THR 3.2 3.1 - - - -
104A LYS* 3.0 37.0 + - - +
105A TRP* 3.2 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.0 15.0 - - + +
90A VAL 5.0 0.9 - - - +
91A TYR* 3.8 31.0 - - + -
98A SER 3.6 12.8 + - - +
99A PHE* 2.7 25.8 + - + +
101A ASN* 1.3 79.2 - - - +
103A THR* 1.3 59.6 + - - +
105A TRP* 3.1 5.4 + - + +
106A ILE* 2.8 36.1 + - - +
121A LEU* 3.9 20.0 - - + -
142A LYS* 4.1 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU 4.1 10.1 + - - -
101A ASN 3.2 0.4 - - - -
102A THR* 1.3 78.7 + - - +
104A LYS* 1.3 58.2 + - - +
106A ILE* 3.2 10.1 + - - +
107A GLN* 2.9 38.8 + - + +
142A LYS* 3.1 32.1 + - - +
146A TYR* 3.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.1 22.6 + - - -
69A GLY 5.3 2.0 + - - -
71A GLU* 4.8 12.9 + - - +
77A ILE* 6.3 0.9 - - - -
100A GLU 4.9 0.4 + - - -
101A ASN* 3.0 28.3 + - - +
103A THR* 1.3 81.4 - - - +
105A TRP* 1.3 89.8 + - - +
107A GLN* 3.4 5.7 + - - +
108A ASP* 3.1 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 33.2 - - + +
18A GLY* 3.6 34.9 - - - -
19A GLU* 3.0 25.5 + - - +
67A THR* 5.9 0.7 - - - -
68A ALA 5.3 0.9 - - - -
69A GLY* 3.8 33.4 - - - -
77A ILE* 3.7 37.9 - - + -
80A TYR* 5.2 2.5 - + - -
89A VAL* 3.9 18.8 - - + -
90A VAL 5.8 0.2 - - - -
98A SER 5.8 0.7 - - - -
101A ASN* 3.2 26.2 + - + -
102A THR* 3.1 9.6 + - + +
104A LYS* 1.3 88.1 - - - +
106A ILE* 1.3 65.9 + - - +
108A ASP* 3.3 12.9 + - - +
109A ILE* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.1 16.2 - - + -
102A THR 2.8 25.6 + - - +
103A THR* 3.2 5.4 + - - +
105A TRP* 1.3 76.5 - - - +
107A GLN* 1.3 58.7 + - - +
109A ILE* 3.2 10.6 + - - +
110A LEU* 3.0 34.4 + - + +
119A ILE* 4.8 14.8 - - + -
121A LEU* 4.6 15.3 - - + -
142A LYS* 4.4 18.2 - - + +
146A TYR* 3.9 48.2 - - + -
148A THR* 4.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 2.9 29.2 + - + +
104A LYS* 3.7 6.3 - - - +
106A ILE* 1.3 74.8 - - - +
108A ASP* 1.3 65.6 + - - +
110A LEU* 3.2 14.9 + - - +
111A ASN* 2.9 41.8 + - - +
146A TYR* 3.1 36.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 4.0 21.7 - - + +
81A ILE* 3.7 19.0 - - + +
104A LYS* 3.1 28.0 + - - +
105A TRP* 3.3 25.3 + - + +
107A GLN* 1.3 76.5 - - - +
109A ILE* 1.3 62.3 + - - +
111A ASN* 3.8 10.6 + - - +
112A GLU* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.7 18.6 - - + -
81A ILE* 4.0 14.6 - - + -
87A ALA* 3.5 25.8 - - + -
89A VAL* 3.5 27.8 - - + -
105A TRP 3.1 15.5 + - - +
106A ILE* 3.4 9.9 - - - +
107A GLN 3.1 0.6 - - - -
108A ASP* 1.3 77.0 - - - +
110A LEU* 1.3 57.6 + - - +
112A GLU 3.4 1.0 + - - -
113A ARG* 2.9 30.2 + - + +
117A VAL* 3.8 18.6 - - + -
119A ILE* 3.6 29.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
106A ILE* 3.0 23.5 + - + +
107A GLN* 3.2 22.4 + - - +
109A ILE* 1.3 73.0 - - - +
111A ASN* 1.3 64.4 + - - +
114A GLY* 2.8 46.4 + - - +
119A ILE* 4.0 18.8 - - + -
146A TYR* 4.0 29.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
107A GLN* 2.9 34.5 + - - +
108A ASP* 3.8 12.6 + - - +
109A ILE 3.3 0.2 - - - -
110A LEU* 1.3 78.1 - - - +
112A GLU* 1.3 61.5 + - - +
114A GLY 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO* 4.2 21.7 - - + +
81A ILE* 3.7 31.2 - - + -
82A ARG* 3.9 36.1 + - - +
83A ASP 4.7 0.3 + - - -
108A ASP 3.2 14.5 + - - +
111A ASN* 1.3 82.1 - - - +
113A ARG* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.5 37.9 - - + -
83A ASP* 3.8 26.5 + - - +
84A SER* 3.0 26.4 + - - +
85A ALA* 5.3 0.4 - - - +
109A ILE* 2.9 14.0 + - + +
112A GLU* 1.3 86.2 + - - +
114A GLY* 1.3 67.6 + - - +
115A LYS 3.2 0.3 + - - -
116A ASP* 3.0 58.3 + - - +
117A VAL* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 2.8 45.0 + - - +
111A ASN 4.7 0.6 + - - -
112A GLU 3.9 0.4 - - - -
113A ARG* 1.3 72.7 - - - +
115A LYS* 1.3 60.4 + - - -
116A ASP 3.6 0.3 + - - -
117A VAL* 3.9 13.2 - - - +
----------------------------------------------------------
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