Contacts of the helix formed by residues 94 - 109 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C HIS* 3.0 27.2 + - - -
82C MET* 5.0 1.9 - - - +
83C ASP* 3.7 9.9 - - - +
93C LEU* 1.3 80.1 - - - +
95C TYR* 1.3 60.1 + - - +
96C LEU* 3.1 4.7 + - - +
97C ALA* 2.8 34.1 + - - +
98C TYR* 3.1 21.7 + - - +
336C ASP* 3.4 24.5 - - + +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 3.9 30.5 + - + -
94C ASP* 1.3 68.6 - - - +
96C LEU* 1.3 57.3 + - - +
98C TYR* 3.5 36.5 - + + +
99C ALA* 2.9 27.7 + - - +
120C ASN* 4.4 5.1 + - + -
121C SER* 2.9 31.9 + - - -
125C GLY* 5.6 0.3 - - - -
270C MET* 3.7 30.0 - - + +
273C ILE* 4.1 16.8 - - + -
332C ALA* 3.7 14.6 - - + +
335C LYS* 3.6 37.0 - - + -
336C ASP* 2.7 23.2 + - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.9 11.9 - - + -
35C PRO* 4.6 8.5 - - + -
38C HIS* 3.8 22.2 - - + +
94C ASP* 3.1 8.7 + - - +
95C TYR* 1.3 73.5 - - - +
97C ALA* 1.3 60.2 + - - +
99C ALA* 3.1 4.9 + - - +
100C ILE* 2.9 34.9 + - + +
329C TRP* 3.8 35.4 - - + +
332C ALA* 3.8 8.7 - - + +
333C MET* 3.6 42.8 - - + -
336C ASP* 3.0 14.9 + - - +
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C HIS* 3.5 15.8 - - + +
41C LEU* 3.3 33.2 - - + +
82C MET* 4.5 1.8 - - + -
93C LEU* 4.0 22.4 - - + -
94C ASP* 2.8 26.0 + - - +
96C LEU* 1.3 72.0 - - - +
98C TYR* 1.3 57.3 + - - +
100C ILE* 3.3 2.3 + - - +
101C ALA* 2.8 27.4 + - - +
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Residues in contact with TYR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C MET* 3.8 25.3 - - + -
83C ASP* 5.7 0.7 - - + +
94C ASP 3.1 10.5 + - - +
95C TYR* 3.5 45.3 - + + +
97C ALA* 1.3 79.0 - - - +
99C ALA* 1.3 56.5 + - - +
101C ALA* 3.8 0.2 - - - +
102C MET* 2.8 57.3 + - + +
116C MET* 4.4 1.6 - - + -
117C SER* 3.1 29.1 + - - -
120C ASN* 3.5 36.0 - - + +
121C SER* 2.9 28.9 + - - -
273C ILE* 5.2 1.3 - - + -
274C GLY* 3.8 14.6 - - - -
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TYR 2.9 15.4 + - - +
96C LEU* 3.1 11.6 + - - +
98C TYR* 1.3 79.5 - - - +
100C ILE* 1.3 62.0 + - - +
102C MET* 4.4 0.2 - - - -
103C GLU* 3.2 21.7 + - - +
273C ILE* 4.6 4.3 - - + -
277C SER* 3.4 28.2 - - - +
280C LEU* 5.7 0.9 - - - +
328C THR* 4.3 14.6 - - + -
329C TRP* 4.5 12.1 - - + +
332C ALA* 4.3 8.5 - - + -
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.4 39.0 - - + -
38C HIS* 3.9 22.9 - - + +
41C LEU* 4.6 3.1 - - + -
42C LEU* 3.8 44.9 - - + +
96C LEU* 2.9 20.2 + - + +
97C ALA* 3.6 6.5 - - - +
99C ALA* 1.3 73.7 - - - +
101C ALA* 1.3 66.7 + - - +
103C GLU* 3.4 8.8 + - - +
104C GLU* 3.3 22.7 + - - +
329C TRP* 4.2 24.0 - - + +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.6 2.0 - - + -
45C CYS* 3.5 31.0 - - - -
79C LEU* 4.0 5.6 - - + -
82C MET* 3.6 26.0 - - + -
97C ALA 2.8 21.3 + - - +
98C TYR 3.8 0.2 - - - +
100C ILE* 1.3 70.3 - - - +
102C MET* 1.3 66.9 + - - +
104C GLU* 3.2 3.6 + - - +
105C ILE* 3.0 26.7 + - + +
116C MET* 4.0 5.2 - - + -
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Residues in contact with MET 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TYR* 2.8 45.7 + - + +
101C ALA* 1.3 73.6 - - - +
103C GLU* 1.3 55.2 + - - +
105C ILE* 3.5 2.3 + - - +
106C SER* 2.6 57.1 + - - +
113C GLY* 3.1 30.5 - - - +
116C MET* 3.7 26.4 - - + +
117C SER* 3.7 15.9 - - - -
274C GLY* 3.5 22.0 - - - +
277C SER* 3.4 17.9 - - - -
278C GLN* 3.7 8.1 - - + -
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ARG* 5.9 0.3 + - - -
99C ALA 3.2 11.9 + - - +
100C ILE* 3.6 11.3 - - - +
102C MET* 1.3 78.7 - - - +
104C GLU* 1.3 69.3 + - - +
106C SER 3.4 0.3 + - - -
107C ARG* 3.0 28.7 + - + +
277C SER* 3.4 13.4 + - - +
280C LEU* 3.8 16.1 - - + +
281C GLY* 3.3 29.1 - - - +
284C GLN* 4.2 10.8 - - + +
325C ARG* 2.8 47.5 + - - -
329C TRP* 4.8 6.8 + - - -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.9 30.5 - - + +
45C CYS* 3.7 25.6 - - + -
46C ARG* 3.2 57.4 + - - +
49C ALA* 3.2 21.1 - - - +
100C ILE 3.3 12.4 + - - +
101C ALA 3.2 3.5 + - - +
103C GLU* 1.3 89.7 - - - +
105C ILE* 1.3 64.3 + - - +
107C ARG* 3.6 22.1 + - - +
108C GLY 3.6 0.2 + - - -
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C CYS* 4.5 12.6 - - + +
48C PHE* 3.9 21.8 - - + -
49C ALA* 4.7 0.7 - - + -
53C LEU* 3.4 19.1 - - + +
74C MET* 3.7 14.6 - - + -
79C LEU* 4.0 13.5 - - + -
101C ALA 3.0 20.2 + - - +
102C MET 3.9 3.8 - - - +
104C GLU* 1.3 74.4 - - - +
106C SER* 1.3 58.4 + - - +
108C GLY 2.9 5.2 + - - -
109C CYS 2.9 23.6 + - - +
112C THR* 3.6 29.2 - - + -
113C GLY* 3.9 14.8 - - - +
116C MET* 3.8 18.8 - - - -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C MET* 2.6 30.6 + - - +
103C GLU 3.9 2.9 - - - -
105C ILE* 1.3 73.1 - - - +
107C ARG* 1.3 64.7 + - - +
108C GLY 3.4 0.5 + - - -
109C CYS 3.5 10.9 - - - -
110C ALA* 3.4 22.6 + - - +
113C GLY* 3.6 4.6 - - - -
278C GLN* 3.3 49.2 - - - +
281C GLY* 4.2 5.8 - - - -
282C ILE* 4.4 3.5 + - - +
285C THR* 5.1 1.2 - - - +
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ARG* 3.6 39.4 + - - +
49C ALA* 5.4 1.0 - - - +
50C GLU* 4.6 6.3 - - - +
54C PHE* 3.6 31.8 - - + -
103C GLU* 3.0 20.0 + - - +
104C GLU* 3.6 22.5 + - - +
106C SER* 1.3 78.5 - - - +
108C GLY* 1.3 60.1 + - - +
281C GLY* 3.4 16.5 - - - +
284C GLN* 3.9 19.0 - - - +
285C THR* 3.3 36.1 + - - +
288C ASP* 3.1 28.8 + - - +
380C ARG* 5.9 0.3 + - - -
381C HIS* 5.3 1.6 - - - -
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Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 4.4 2.7 - - - -
53C LEU* 3.9 16.5 - - - +
54C PHE* 3.7 27.9 + - - -
57C ALA* 3.4 22.2 - - - +
104C GLU 3.6 4.0 + - - -
105C ILE 2.9 7.7 + - - -
106C SER 4.0 0.4 - - - -
107C ARG* 1.3 81.7 - - - +
109C CYS* 1.3 58.0 + - - +
380C ARG* 4.5 3.9 + - - -
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Residues in contact with CYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 4.0 14.9 - - + +
56C ILE* 5.4 1.3 - - + -
57C ALA* 4.6 13.9 - - + -
60C VAL* 4.1 24.0 - - - -
105C ILE 2.9 14.1 + - - +
106C SER* 3.5 4.8 - - - -
108C GLY* 1.3 77.9 - - - +
110C ALA* 1.3 65.5 + - - +
111C SER* 3.7 14.6 - - - -
112C THR* 3.3 35.9 - - - +
113C GLY 3.1 15.8 + - - -
380C ARG* 5.3 2.0 - - - +
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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