Contacts of the helix formed by residues 101 - 116 (chain B) in PDB entry 2ZXI
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B THR 3.1 21.4 + - - +
80B ILE* 4.0 12.4 - - + +
99B GLN 4.3 0.2 + - - -
100B ALA* 1.3 69.7 - - - +
102B LYS* 1.3 63.5 + - - +
103B LYS* 3.2 10.8 + - - +
104B ARG* 3.0 43.9 + - + -
105B TYR* 2.8 22.8 + - - +
307B GLU 3.6 4.3 - - - -
308B GLY* 3.6 12.1 - - - -
309B LEU* 2.9 33.3 + - - +
310B ASP* 4.5 2.1 + - - -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET* 3.2 46.0 + - + +
47B SER* 4.2 0.6 - - - +
48B CYS 3.2 23.3 + - - -
50B PRO* 3.7 20.6 - - + -
100B ALA 3.1 5.8 + - - -
101B ASP* 1.3 69.4 - - - +
103B LYS* 1.3 62.4 + - - +
105B TYR* 3.4 7.0 + - - +
106B ARG* 3.0 24.9 + - - +
205B ARG* 3.5 16.8 - - - +
307B GLU* 2.9 54.7 + - + +
345B ARG* 6.0 2.2 - - - +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.2 56.3 + - + +
111A LYS* 6.3 0.4 - - - +
101B ASP* 3.2 7.9 + - - +
102B LYS* 1.3 79.5 - - - +
104B ARG* 1.3 88.8 + - - +
106B ARG* 3.2 27.8 + - - +
107B GLU* 3.1 33.4 + - - +
307B GLU 4.5 1.0 + - - -
310B ASP* 3.2 28.0 + - - +
311B THR* 6.5 0.9 - - + -
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 4.7 7.7 - - - +
107A GLU* 3.9 4.6 + - - -
77B GLN 5.8 0.4 - - - +
78B THR* 3.4 20.1 - - + +
101B ASP* 3.0 38.2 + - + +
103B LYS* 1.3 106.1 - - - +
105B TYR* 1.3 58.1 + - - +
107B GLU* 2.5 41.0 + - - +
108B TYR* 2.9 30.0 + - - +
309B LEU* 6.2 0.4 - - - +
310B ASP* 3.9 11.9 + - - -
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 4.3 8.5 - + - -
44B GLY 3.5 20.4 - - - -
46B MET* 3.7 42.0 - - + -
52B ILE* 4.3 7.6 - - + -
71B MET* 3.4 31.6 - - + +
74B ALA* 3.5 24.5 - - + -
75B ILE* 4.0 9.4 - - + -
78B THR* 3.4 25.5 - - - +
100B ALA* 4.6 4.3 - - + -
101B ASP 2.8 16.8 + - - +
102B LYS 3.6 5.2 - - - +
104B ARG* 1.3 77.8 - - - +
106B ARG* 1.3 61.6 + - - +
108B TYR* 3.3 3.9 + - - +
109B MET* 3.1 44.9 + - + +
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 4.9 20.0 + - - +
103A LYS* 6.2 0.4 - - - +
106A ARG* 5.3 9.6 - - - +
107A GLU* 5.0 1.8 + - - -
41B ASP 3.4 25.3 + - - -
42B THR* 4.2 0.4 - - - +
43B ILE 3.1 28.0 - - - +
44B GLY 3.6 9.6 - - - +
45B GLN* 3.5 42.0 + - - +
102B LYS 3.0 12.7 + - - +
103B LYS* 3.6 33.5 + - - +
105B TYR* 1.3 76.6 - - - +
107B GLU* 1.3 77.6 + - - +
109B MET* 3.2 2.4 + - - +
110B LYS* 2.9 22.7 + - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.7 49.1 + - + +
104A ARG* 3.0 10.4 + - - -
107A GLU* 2.6 22.2 - - - +
103B LYS* 3.1 15.1 + - - +
104B ARG* 2.5 38.9 + - - +
106B ARG* 1.3 87.5 - - - +
108B TYR* 1.3 58.4 + - - +
110B LYS* 3.2 6.8 + - - +
111B LYS* 2.8 33.0 + - - +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU* 2.9 28.9 + - - -
73B LYS* 3.4 16.7 - - - +
74B ALA* 3.5 37.0 - - + -
77B GLN* 4.0 34.7 + - + -
78B THR* 4.0 9.4 - - + -
104B ARG 2.9 19.6 + - - +
105B TYR* 3.4 4.5 - - - +
107B GLU* 1.3 78.0 - - - +
109B MET* 1.3 65.3 + - - +
111B LYS* 3.3 6.6 + - + +
112B VAL* 3.0 44.4 + - + +
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Residues in contact with MET 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B HIS* 6.1 0.9 - - + -
20B ILE* 3.7 40.4 - - + -
21B GLU* 4.0 8.7 - - - +
24B LEU* 5.3 0.9 - - - -
43B ILE* 4.5 1.3 - - - -
44B GLY* 3.9 6.1 - - - -
70B GLU* 4.1 9.4 - - + -
71B MET* 3.9 21.1 - - + +
74B ALA* 3.7 12.8 - - + -
105B TYR* 3.1 47.6 + - + +
106B ARG 3.7 6.7 - - - +
108B TYR* 1.3 97.4 - - + +
110B LYS* 1.3 63.3 + - - +
112B VAL* 3.5 3.2 + - - +
113B CYS* 3.0 30.2 + - - -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 5.3 1.0 + - - -
313A GLU* 4.2 14.7 + - - -
345A ARG* 4.5 0.2 - - - +
40B ALA* 3.1 31.2 + - - +
41B ASP* 3.8 18.1 + - - +
43B ILE* 3.7 34.2 - - + +
106B ARG* 2.9 17.9 + - - +
107B GLU* 3.7 7.4 - - - +
109B MET* 1.3 76.0 - - - +
111B LYS* 1.3 63.8 + - - +
113B CYS* 3.9 1.0 - - - +
114B GLU* 2.9 63.6 + - + +
121B ILE* 4.3 2.9 - - - -
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 6.0 1.6 - - - +
310A ASP* 3.3 43.7 + - + +
107B GLU 2.8 18.1 + - - +
108B TYR* 3.6 6.7 - - + +
110B LYS* 1.3 78.4 - - - +
112B VAL* 1.3 63.6 + - + +
114B GLU* 3.4 4.2 + - - -
115B ASN* 2.9 46.5 + - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.9 16.6 - - + -
28B ARG* 3.3 30.3 - - - +
70B GLU* 3.9 10.3 - - + +
108B TYR* 3.0 48.3 + - + +
109B MET* 4.0 5.8 - - - +
111B LYS* 1.3 76.9 - - + +
113B CYS* 1.3 64.4 + - - +
115B ASN* 3.4 2.7 + - - +
116B GLN* 3.1 22.6 + - + +
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 3.7 31.4 - - - -
24B LEU* 4.0 15.7 - - - -
35B MET* 4.1 17.9 - - - -
43B ILE* 4.5 6.1 - - + -
109B MET 3.0 20.9 + - - +
110B LYS* 3.9 4.9 - - - +
112B VAL* 1.3 77.3 - - - +
114B GLU* 1.3 60.1 + - - +
115B ASN 3.4 0.3 + - - -
116B GLN* 3.5 6.6 + - - +
119B LEU* 3.5 33.5 - - + +
121B ILE* 4.3 15.9 - - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG* 3.9 8.8 + - - -
310A ASP* 4.7 1.9 - - - +
311A THR* 2.5 40.6 + - - -
312A ILE* 2.8 51.1 + - + +
313A GLU* 4.2 5.1 + - - +
110B LYS* 2.9 60.0 + - - +
111B LYS* 3.9 4.9 + - - +
112B VAL 3.4 0.2 - - - -
113B CYS* 1.3 78.1 - - - +
115B ASN* 1.3 64.5 + - - +
116B GLN 3.8 0.3 + - - -
119B LEU 5.0 0.7 - - - +
121B ILE* 3.9 13.7 - - + -
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG* 4.7 4.7 + - - +
310A ASP 3.4 21.7 + - - +
312A ILE* 3.3 23.9 - - - +
111B LYS* 2.9 40.8 + - - +
112B VAL* 3.8 2.7 - - - +
114B GLU* 1.3 77.5 - - - +
116B GLN* 1.3 63.1 + - - +
117B GLU* 3.4 4.0 + - - +
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG* 3.0 16.3 + - - -
24B LEU* 3.9 16.8 - - + -
27B ALA* 3.8 8.5 + - + -
28B ARG* 2.9 51.8 + - + +
112B VAL 3.1 16.7 + - - +
113B CYS 3.8 7.9 - - - +
114B GLU 3.4 1.6 - - - -
115B ASN* 1.3 74.9 - - - +
117B GLU* 1.3 97.3 + - - +
118B ASN* 5.4 0.2 - - - +
119B LEU* 3.1 22.7 + - + +
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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
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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) + - + + + + + -
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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