Contacts of the helix formed by residues 94 - 109 (chain H) in PDB entry 2VIG
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 94 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H HIS* 3.1 25.0 + - - -
82H MET* 5.0 1.0 - - - +
83H ASP* 3.6 12.8 - - - +
93H LEU* 1.3 80.3 - - - +
95H TYR* 1.3 59.3 + - - +
96H LEU* 3.3 3.0 + - - +
97H ALA* 2.9 22.5 + - - +
98H TYR* 3.1 24.4 + - - +
336H ASP* 3.3 24.7 - - - +
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Residues in contact with TYR 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ASP* 3.4 37.9 + - + -
94H ASP* 1.3 70.1 - - - +
96H LEU* 1.3 57.8 + - - +
98H TYR* 3.4 32.8 - + - +
99H ALA* 2.9 29.6 + - - +
120H ASN* 4.7 3.8 + - + -
121H SER* 2.7 34.7 + - - -
125H GLY* 5.9 0.3 - - - -
270H MET* 3.4 27.7 - - + +
273H ILE* 4.1 17.9 - - + -
332H ALA* 3.8 14.1 - - - +
335H LYS* 3.4 35.9 - - + -
336H ASP* 2.8 23.6 + - - +
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Residues in contact with LEU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 4.4 14.6 - - + -
35H PRO* 4.8 9.4 - - + -
38H HIS* 3.9 21.1 - - + +
94H ASP* 3.3 8.2 + - - +
95H TYR* 1.3 74.8 - - - +
97H ALA* 1.3 58.3 + - - +
99H ALA* 3.2 3.4 + - + +
100H ILE* 2.9 37.0 + - + +
329H TRP* 3.6 50.0 - - + +
332H ALA* 3.8 10.0 - - + +
333H MET* 4.4 25.8 - - + -
336H ASP* 3.0 14.6 + - - +
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H HIS* 3.5 16.2 + - + +
41H LEU* 3.3 31.7 - - + +
82H MET* 3.8 3.4 - - + -
93H LEU* 3.8 22.0 - - + -
94H ASP* 2.9 22.8 + - - +
96H LEU* 1.3 72.6 - - - +
98H TYR* 1.3 61.0 + - - +
100H ILE* 3.5 2.0 + - - +
101H ALA* 2.9 26.2 + - - +
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Residues in contact with TYR 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H MET* 3.8 24.1 - - + +
83H ASP* 5.7 0.7 - - + -
94H ASP 3.1 13.3 + - - +
95H TYR* 3.4 45.3 - + + +
96H LEU 3.3 0.2 - - - -
97H ALA* 1.3 76.7 - - - +
99H ALA* 1.3 54.6 + - - +
101H ALA* 3.4 0.9 + - - +
102H MET* 2.7 59.9 + - + +
116H MET* 4.4 1.1 - - + -
117H SER* 3.0 28.4 + - - -
120H ASN* 3.5 36.3 - - + -
121H SER* 2.6 29.2 + - - -
273H ILE* 5.3 1.3 - - + -
274H GLY* 3.8 14.2 - - - -
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Residues in contact with ALA 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TYR 2.9 17.2 + - - +
96H LEU* 3.2 8.0 + - - +
98H TYR* 1.3 79.6 - - - +
100H ILE* 1.3 60.2 + - - +
102H MET* 4.4 0.4 - - - -
103H GLU* 3.2 23.4 + - - +
273H ILE* 4.7 4.7 - - + -
277H SER* 3.4 27.9 - - - +
280H LEU* 5.7 0.9 - - + +
328H THR* 4.4 14.1 - - + -
329H TRP* 4.5 14.8 + - + +
332H ALA* 4.5 6.5 - - + -
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Residues in contact with ILE 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 3.9 25.1 - - + -
38H HIS* 3.6 43.1 - - + +
41H LEU* 4.5 5.4 - - + -
42H LEU* 3.8 44.4 - - + +
96H LEU* 2.9 18.2 + - + +
97H ALA* 3.6 5.2 - - - +
99H ALA* 1.3 73.6 - - - +
101H ALA* 1.3 65.4 + - - +
103H GLU* 3.4 7.9 + - - +
104H GLU* 3.2 23.7 + - - +
329H TRP* 4.2 22.2 - - + +
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Residues in contact with ALA 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LEU* 4.6 2.2 - - + -
45H CYS* 3.6 29.2 - - - -
79H LEU* 4.0 2.7 - - + -
82H MET* 3.5 27.4 - - + -
97H ALA 2.9 20.6 + - - +
98H TYR 3.8 0.2 - - - +
100H ILE* 1.3 70.9 - - - +
102H MET* 1.3 65.2 + - - +
104H GLU* 3.2 3.1 + - - +
105H ILE* 3.0 27.7 + - - +
116H MET* 3.9 8.7 - - + -
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Residues in contact with MET 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H TYR* 2.7 46.2 + - + +
101H ALA* 1.3 72.6 - - - +
103H GLU* 1.3 57.1 + - - +
105H ILE* 3.6 1.8 + - - +
106H SER* 2.7 59.7 + - - +
113H GLY* 3.2 30.5 - - - +
116H MET* 3.8 26.6 - - + +
117H SER* 3.8 14.8 - - - -
274H GLY* 3.7 20.2 - - - +
277H SER* 3.4 19.1 - - - -
278H GLN* 3.8 8.7 - - + -
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Residues in contact with GLU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ARG* 5.7 1.0 + - - -
99H ALA 3.2 15.4 + - - +
100H ILE* 3.8 6.6 - - - +
101H ALA 3.2 0.4 - - - -
102H MET* 1.3 77.3 - - - +
104H GLU* 1.3 77.4 + - - +
107H ARG* 3.0 27.5 + - + +
277H SER* 3.4 15.5 + - - +
280H LEU* 3.9 15.5 - - + +
281H GLY* 3.3 22.5 - - - +
284H GLN* 4.1 11.5 - - + +
325H ARG* 2.8 46.2 + - - +
329H TRP* 4.9 5.7 + - - -
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Residues in contact with GLU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H LEU* 3.8 37.5 - - + +
45H CYS* 3.5 27.4 - - + -
46H ARG* 3.3 49.7 + - - +
49H ALA* 3.4 19.3 - - - +
100H ILE 3.2 12.2 + - - +
101H ALA 3.2 4.3 + - - +
103H GLU* 1.3 89.0 - - - +
105H ILE* 1.3 62.8 + - - +
107H ARG* 3.4 26.1 + - - +
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Residues in contact with ILE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H CYS* 4.6 15.0 - - + +
48H PHE* 3.8 21.3 - - + -
49H ALA* 4.6 0.4 - - - -
53H LEU* 3.7 21.8 - - + +
74H MET* 4.1 7.9 - - + -
79H LEU* 4.0 16.8 - - + -
101H ALA 3.0 19.6 + - - +
102H MET 4.0 2.9 - - - +
104H GLU* 1.3 75.9 - - - +
106H SER* 1.3 59.4 + - - +
108H GLY* 3.0 5.2 + - - -
109H CYS 2.9 24.4 + - - +
112H THR* 3.7 28.0 - - + -
113H GLY* 3.9 15.0 - - - +
116H MET* 3.9 17.9 - - + -
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Residues in contact with SER 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H MET* 2.7 42.2 + - - +
103H GLU 4.0 2.5 - - - -
105H ILE* 1.3 72.9 - - - +
107H ARG* 1.3 63.8 + - - +
108H GLY 3.5 0.2 + - - -
109H CYS 3.6 15.9 + - - -
110H ALA* 3.6 14.4 + - - +
113H GLY* 3.4 4.9 - - - -
278H GLN* 3.4 37.2 - - - +
281H GLY* 4.1 6.8 - - - -
282H ILE* 4.3 4.4 + - - +
285H THR* 4.9 1.6 - - - +
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Residues in contact with ARG 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ARG* 3.5 42.1 + - - +
49H ALA* 5.7 1.0 - - - +
50H GLU* 6.0 1.2 - - - +
54H PHE* 3.5 37.0 - - + -
103H GLU* 3.0 20.9 + - - +
104H GLU* 3.4 23.4 + - - +
106H SER* 1.3 77.4 - - - +
108H GLY* 1.3 59.7 + - - +
281H GLY* 3.4 16.5 + - - +
284H GLN* 4.0 17.7 - - - +
285H THR* 3.6 28.6 + - - +
288H ASP* 3.1 30.5 + - - +
380H ARG* 5.8 0.2 + - - -
381H HIS* 5.2 1.9 - - - -
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Residues in contact with GLY 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ALA* 4.2 2.9 - - - -
53H LEU* 3.8 16.4 - - - +
54H PHE* 3.7 29.3 + - - -
57H ALA* 3.5 19.8 - - - +
104H GLU 3.4 4.6 + - - -
105H ILE 3.0 7.5 + - - -
106H SER 4.1 0.2 - - - -
107H ARG* 1.3 81.4 - - - +
109H CYS* 1.3 60.9 + - - +
380H ARG* 4.5 3.7 + - - -
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Residues in contact with CYS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H LEU* 4.1 17.2 - - + +
56H ILE* 5.4 2.0 - - + -
57H ALA* 4.6 12.1 - - + -
60H VAL* 4.2 23.1 - - - -
105H ILE 2.9 16.7 + - - +
106H SER* 3.6 5.3 + - - -
108H GLY* 1.3 75.4 - - - +
110H ALA* 1.3 67.6 + - - +
111H SER* 3.3 11.8 + - - -
112H THR* 3.7 33.7 - - - +
113H GLY 3.1 17.0 + - - -
380H ARG* 5.2 2.7 - - - +
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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
------------------------------------------------------------
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