Contacts of the helix formed by residues 80 - 96 (chain A) in PDB entry 2VGZ
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 ILE 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ARG* 3.9 11.0 - - - +
75A SER* 4.1 22.9 - - - +
76A PRO* 4.6 2.7 - - + -
79A GLY* 1.3 73.0 - - - -
81A PRO* 1.4 75.2 - - + +
82A GLU* 3.6 10.3 - - - +
83A LEU* 3.1 20.4 + - + +
84A LEU* 3.0 20.4 + - - +
297A THR* 4.2 14.8 - - + -
300A GLN* 2.9 29.5 + - + +
301A LEU* 3.7 44.6 - - + +
304A SER* 4.0 12.1 - - - +
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Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 4.0 7.9 - - - +
76A PRO* 4.7 13.2 - - + -
79A GLY 3.7 4.4 - - - +
80A ILE* 1.4 85.8 - - + +
82A GLU* 1.3 72.8 + - + +
84A LEU* 3.8 10.2 - - + +
85A SER* 2.9 29.5 + - - -
88A LYS* 5.2 0.7 + - - -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 2.8 45.2 + - - -
80A ILE* 3.6 9.4 - - - +
81A PRO* 1.3 83.7 - - + +
83A LEU* 1.3 63.0 + - - +
85A SER* 3.4 6.8 + - - -
86A TRP* 3.2 13.3 + - - +
301A LEU* 5.4 1.1 - - - -
304A SER* 3.8 12.3 - - - +
308A HIS* 3.1 29.2 + - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.1 19.8 + - + +
82A GLU* 1.3 75.8 - - - +
84A LEU* 1.3 58.8 + - - +
86A TRP* 3.1 6.0 + - + +
87A LEU* 2.9 53.9 + - + +
113A VAL* 4.2 13.9 - - + -
261A PHE* 5.2 0.7 - - + -
271A ILE* 4.5 9.4 - - + -
300A GLN* 3.8 44.4 - - + +
303A ILE* 4.2 10.5 - - + -
304A SER* 3.6 16.1 + - - +
307A LEU* 4.1 25.4 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.4 38.6 - - + +
79A GLY 3.7 15.7 - - - +
80A ILE 3.0 15.7 + - - +
81A PRO* 3.8 8.1 - - + +
83A LEU* 1.3 75.9 - - - +
85A SER* 1.3 58.1 + - - +
87A LEU* 3.3 4.7 + - + +
88A LYS* 2.9 50.3 + - - +
111A LEU* 3.7 35.0 - - + +
112A CYS 4.5 0.2 - - - -
113A VAL* 3.8 15.5 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO 2.9 18.9 + - - -
82A GLU* 3.4 10.2 + - - -
84A LEU* 1.3 76.5 - - - +
86A TRP* 1.3 63.2 + - - +
88A LYS* 3.3 15.9 + - - +
89A GLN* 3.0 31.3 + - - +
308A HIS* 5.1 3.1 - - - -
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU 3.2 17.6 + - - +
83A LEU* 3.1 7.8 + - + +
85A SER* 1.3 78.1 + - - +
87A LEU* 1.3 67.5 + - + +
89A GLN* 3.5 5.6 + - - +
90A LEU* 3.1 53.4 + - + -
261A PHE* 5.8 0.4 - + - -
307A LEU* 3.3 57.7 + - + -
308A HIS* 3.6 36.6 - + + +
311A GLY* 4.0 24.0 - - - -
312A GLU* 4.1 13.3 - - + +
315A PHE* 4.1 24.2 - + + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 2.9 40.3 + - + +
84A LEU* 3.9 3.4 - - + +
86A TRP* 1.3 93.9 - - + +
88A LYS* 1.3 59.4 + - - +
90A LEU* 3.3 6.8 + - + +
91A GLN* 2.9 34.5 + - - +
111A LEU* 3.9 16.2 - - + -
113A VAL* 4.0 17.9 - - + -
261A PHE* 3.6 30.3 - - + -
273A PHE* 3.8 35.7 - - + -
307A LEU* 4.6 1.6 - - + -
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO 5.2 0.4 + - - -
84A LEU* 2.9 53.6 + - - +
85A SER* 3.8 15.4 - - - +
87A LEU* 1.3 76.9 - - - +
89A GLN* 1.3 71.3 + - - +
91A GLN* 3.3 4.4 + - - +
92A ILE* 3.2 28.5 + - + +
109A MET* 4.5 9.4 - - + +
110A ASP* 4.4 17.9 - - - +
111A LEU* 3.4 37.7 - - + +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER* 3.0 21.8 + - - +
86A TRP* 4.0 5.2 - - + +
88A LYS* 1.3 79.9 - - - +
90A LEU* 1.3 64.4 + - - +
92A ILE* 3.4 31.1 + - - +
93A LYS* 3.0 20.4 + - - +
312A GLU* 3.5 18.9 - - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 3.1 40.8 + - + +
87A LEU* 3.5 18.8 - - + +
89A GLN* 1.3 75.3 - - - +
91A GLN* 1.3 70.7 + - - +
92A ILE 3.3 0.2 + - - -
93A LYS* 3.3 6.7 + - + +
94A LEU* 2.9 57.3 + - + +
235A PHE* 4.2 14.4 - - + -
261A PHE* 6.0 0.9 - - + -
273A PHE* 4.8 4.9 - - + -
312A GLU* 3.7 19.1 + - + +
315A PHE* 4.2 12.1 - - + -
316A MET* 4.1 17.3 - - + -
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Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU 2.9 23.9 + - - +
88A LYS 3.7 4.9 - - - +
90A LEU* 1.3 76.9 - - - +
92A ILE* 1.3 54.9 + - - +
94A LEU* 4.2 7.4 - - - +
95A HIS* 2.8 63.8 + - + +
96A ASN 3.4 0.7 + - - -
97A PRO* 3.9 2.3 - - - +
109A MET* 4.5 16.2 - - + -
111A LEU* 4.0 17.7 - - + -
235A PHE* 5.5 0.7 - - - -
247A LEU* 4.3 2.4 - - + +
257A ARG* 4.1 3.8 - - - +
259A ASP* 3.3 20.0 + - - +
273A PHE* 3.6 16.2 - - - -
275A THR* 2.8 28.3 + - + +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.2 16.1 + - + +
89A GLN* 3.7 35.7 - - - +
90A LEU 3.2 0.2 - - - -
91A GLN* 1.3 75.0 - - - +
93A LYS* 1.3 59.4 + - - +
96A ASN* 2.8 44.2 + - - +
97A PRO* 4.2 2.9 - - + -
100A ILE* 4.0 39.3 - - + -
109A MET* 4.6 7.2 - - + -
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLN 3.0 14.0 + - - +
90A LEU* 3.5 10.8 - - + +
92A ILE* 1.3 78.7 - - - +
94A LEU* 1.3 77.0 + - + +
96A ASN* 5.6 0.9 - - - +
242A ARG* 5.7 2.7 - - - +
312A GLU* 3.5 50.3 + - + +
313A GLU* 3.7 20.4 + - - +
316A MET* 4.3 13.9 - - + +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 2.9 44.6 + - + +
91A GLN* 4.2 3.4 - - - +
93A LYS* 1.3 90.5 - - + +
95A HIS* 1.3 87.3 + - + +
234A TYR* 4.2 10.2 + - + +
235A PHE* 3.7 25.8 - - + -
242A ARG* 3.7 35.2 + - - +
316A MET* 4.2 16.6 - - + -
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Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN* 2.8 53.6 + - - +
94A LEU* 1.3 86.4 + - + +
96A ASN* 1.3 72.3 + - - +
97A PRO* 4.0 12.3 - - + -
234A TYR* 3.6 25.2 + + - -
235A PHE* 6.0 0.2 - - - -
245A THR* 3.1 43.9 + - + +
247A LEU* 4.1 11.0 - - + -
248A SER* 3.1 28.8 - - - +
257A ARG* 3.7 15.0 + - - -
259A ASP* 4.9 0.6 + - - -
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 2.8 24.6 + - - +
93A LYS 5.6 0.9 - - - +
94A LEU 3.9 0.4 - - - -
95A HIS* 1.3 78.5 - - - +
97A PRO* 1.3 71.8 - - - +
98A PRO* 3.5 4.9 - - - +
100A ILE* 4.2 16.1 - - - +
101A HIS* 5.6 1.2 + - - -
248A SER 4.4 2.4 - - - +
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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