Contacts of the helix formed by residues 101 - 113 (chain B) in PDB entry 2GZD
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP* 2.8 41.5 + - - +
70B LEU* 4.5 9.8 - - + +
97B LEU* 2.9 38.2 + - - +
98B THR 4.1 1.6 - - - +
99B TYR 3.3 0.4 - - - -
100B GLU* 1.3 75.5 - - - +
102B VAL* 1.3 64.2 + - - +
103B GLU 3.3 1.1 - - - -
104B ARG* 3.0 41.9 + - + +
105B TRP* 3.2 15.8 - - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.7 28.4 - - + +
91B TYR* 4.0 8.7 - - + -
98B THR 3.8 12.5 + - - +
99B TYR* 3.1 28.3 + - + +
100B GLU 3.1 1.8 + - - -
101B ASN* 1.3 76.3 - - - +
103B GLU* 1.3 57.6 + - - +
105B TRP* 3.2 10.9 + - - +
106B LEU* 2.9 32.3 + - + +
121B LEU* 3.9 21.8 - - + -
142B PHE* 3.7 28.3 - - + -
148B LEU* 5.1 1.6 - - + -
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Residues in contact with GLU 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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100B GLU* 3.8 14.9 + - - +
101B ASN 3.3 0.2 - - - -
102B VAL* 1.3 76.6 - - - +
104B ARG* 1.3 61.9 + - + +
106B LEU* 3.5 12.5 + - + +
107B LYS* 3.1 22.5 + - - +
110B ARG* 4.1 5.7 + - - +
142B PHE* 3.9 31.4 - - + -
145B LYS* 5.5 1.6 + - - +
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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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70B LEU* 6.4 1.6 - - - -
100B GLU 5.1 0.7 - - - +
101B ASN* 3.0 39.4 + - + +
103B GLU* 1.3 76.0 - - + +
105B TRP* 1.3 62.4 + - + +
107B LYS* 3.1 10.1 + - - +
108B GLU* 3.1 29.3 + - + +
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Residues in contact with TRP 105 (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 ILE* 3.9 20.6 - - + +
18B GLY* 3.5 29.8 - - - -
19B ASP* 2.9 29.5 + - - +
68B ALA 5.4 0.2 - - - -
69B GLY 3.3 27.6 - - - -
70B LEU* 3.7 12.1 - - + -
71B GLU* 3.3 44.6 - - + -
81B TYR* 4.5 0.9 - - - -
89B LEU* 3.5 20.6 - - + -
90B VAL 5.4 0.2 - - - -
98B THR 5.2 2.0 - - - -
101B ASN* 3.2 25.6 + - + +
102B VAL* 3.2 9.8 + - - +
104B ARG* 1.3 76.2 - - + +
106B LEU* 1.3 64.7 + - - +
108B GLU* 3.2 34.2 + - + +
109B LEU* 3.4 11.6 + - - +
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Residues in contact with LEU 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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89B LEU* 3.9 14.7 - - + +
102B VAL* 2.9 18.1 + - + +
103B GLU* 3.6 12.8 - - + +
105B TRP* 1.3 75.4 - - - +
107B LYS* 1.3 62.9 + - - +
109B LEU* 3.1 19.3 + - + +
110B ARG* 3.2 33.5 + - - +
119B ILE* 4.3 16.4 - - + -
142B PHE* 4.2 27.6 - - + -
146B ASN* 4.3 18.4 - - + +
148B LEU* 3.8 26.9 - - + -
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Residues in contact with LYS 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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103B GLU 3.1 14.5 + - - +
104B ARG* 3.1 13.0 + - - +
106B LEU* 1.3 76.9 - - - +
108B GLU* 1.3 54.4 + - - +
110B ARG* 3.1 29.3 + - + +
111B ASP* 2.9 62.4 + - - +
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Residues in contact with GLU 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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71B GLU* 2.6 50.0 - - - +
72B ARG 5.1 0.3 - - - -
73B TYR 5.3 0.7 + - - -
77B THR* 5.2 0.7 - - - -
81B TYR* 3.1 32.5 + - - +
104B ARG 3.1 18.1 + - - +
105B TRP* 3.2 21.2 - - + +
107B LYS* 1.3 76.8 - - - +
109B LEU* 1.3 56.2 + - - +
111B ASP* 3.7 4.9 + - - +
112B HIS* 2.8 49.6 + - + +
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Residues in contact with LEU 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 ILE* 3.7 15.5 - - + -
81B TYR* 3.6 24.2 - - + -
87B ALA* 3.8 22.9 - - + -
89B LEU* 4.6 1.3 - - + -
105B TRP 3.6 16.4 - - - +
106B LEU* 3.1 18.0 + - + +
108B GLU* 1.3 75.3 - - - +
110B ARG* 1.3 65.9 + - - +
113B ALA* 3.1 34.0 + - + +
114B ASP 5.1 0.5 - - - +
115B SER* 5.3 2.1 + - - -
117B ILE* 3.8 23.4 - - + +
119B ILE* 4.2 32.3 - - + -
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Residues in contact with ARG 110 (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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103B GLU* 4.1 7.5 + - - +
106B LEU* 3.2 25.1 + - - +
107B LYS* 3.1 47.8 + - + +
109B LEU* 1.3 79.7 - - - +
111B ASP* 1.3 67.0 + - - +
112B HIS 3.4 0.2 + - - -
113B ALA 4.2 5.7 - - - +
115B SER* 6.1 1.5 - - - +
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Residues in contact with ASP 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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107B LYS* 2.9 49.7 + - - +
108B GLU* 3.8 2.9 + - - +
110B ARG* 1.3 82.3 - - - +
112B HIS* 1.3 86.9 + - + +
113B ALA 5.1 0.2 - - - -
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Residues in contact with HIS 112 (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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73B TYR* 4.0 24.1 - + + -
77B THR* 4.0 22.2 + - - +
78B SER* 5.1 11.9 - - - +
81B TYR* 3.4 31.7 - - + +
82B ARG* 5.1 0.9 + - - -
108B GLU* 2.8 45.1 + - + +
111B ASP* 1.3 99.1 - - + +
113B ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 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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81B TYR* 4.1 17.7 - - + +
84B ALA 5.5 0.4 - - - +
109B LEU* 3.1 33.5 + - + +
110B ARG 4.2 5.9 - - - +
112B HIS* 1.3 80.3 - - - +
114B ASP* 1.3 64.9 + - - +
115B SER* 3.3 3.1 + - - -
117B ILE* 3.8 34.1 - - + -
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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
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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