Contacts of the helix formed by residues 109 - 122 (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 CYS 109 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H SER* 3.6 12.9 + - - +
109H CYS* 1.3 73.5 - - - +
111H SER* 1.3 57.1 + - - +
113H GLY* 3.4 1.4 + - - -
114H VAL* 3.1 14.0 + - - +
233H ILE* 4.0 7.2 - - + -
278H GLN* 2.9 23.4 + - - +
282H ILE* 4.0 20.0 - - + -
380H ARG* 5.3 3.6 - - - +
384H ASP* 3.5 41.1 + - + +
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Residues in contact with SER 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H VAL* 4.2 4.6 - - - +
67H PRO* 5.4 0.7 - - - -
109H CYS* 3.2 12.4 - - - -
110H ALA* 1.3 76.3 - - - +
112H THR* 1.3 61.4 + - - +
114H VAL* 3.0 13.2 + - - +
115H ILE* 2.9 34.3 + - - +
233H ILE* 3.1 19.7 - - - +
234H ARG 3.5 0.5 + - - -
235H GLY* 3.0 29.9 + - - -
236H SER 3.8 14.6 - - - -
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Residues in contact with THR 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LEU* 3.8 15.4 - - + +
67H PRO* 3.4 20.6 - - - +
70H GLN* 5.1 0.2 - - - +
71H VAL* 4.7 8.7 - - + +
74H MET* 3.0 40.2 - - + -
105H ILE* 3.7 9.6 - - + -
109H CYS* 3.4 23.6 + - - -
111H SER* 1.3 77.3 - - - +
113H GLY* 1.3 60.2 + - - +
115H ILE* 3.8 10.2 - - - +
116H MET* 3.0 24.6 + - - +
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Residues in contact with GLY 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H MET* 3.2 20.5 - - - +
105H ILE* 3.9 9.8 - - - +
106H SER* 3.4 24.0 - - - -
109H CYS 3.1 11.4 + - - -
110H ALA 3.6 3.1 - - - -
111H SER 3.1 0.4 - - - -
112H THR* 1.3 77.5 - - - +
114H VAL* 1.3 55.7 + - - +
116H MET* 3.3 2.0 + - - +
117H SER 2.9 23.6 + - - -
278H GLN* 4.8 0.7 - - - -
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Residues in contact with VAL 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H ALA 3.1 7.9 + - - +
111H SER* 3.0 24.8 + - - +
113H GLY* 1.3 71.3 - - - +
115H ILE* 1.3 66.7 + - - +
117H SER* 3.1 5.5 + - - -
118H VAL* 2.9 42.9 + - + +
187H THR* 4.3 6.1 - - + +
233H ILE* 4.2 8.5 - - + -
236H SER* 3.6 27.4 - - - +
275H ILE* 4.5 7.0 - - + -
278H GLN* 3.7 7.9 - - - +
391H TYR* 3.1 43.1 - - + +
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Residues in contact with ILE 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H PHE* 3.7 14.1 - - + -
67H PRO* 3.6 34.3 - - + -
71H VAL* 4.1 21.8 - - + -
80H LEU* 5.4 1.6 - - + -
111H SER 2.9 27.5 + - - +
112H THR* 3.8 5.8 - - - +
114H VAL* 1.3 78.2 - - - +
116H MET* 1.3 63.1 + - - +
118H VAL* 3.5 0.6 + - - -
119H ASN* 3.3 18.2 + - - +
149H ILE* 3.8 23.3 - - + -
187H THR* 5.1 0.2 - - - -
188H ASN* 3.5 32.6 + - - +
235H GLY 4.3 6.1 - - - +
236H SER* 4.1 10.3 - - - -
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Residues in contact with MET 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H MET* 3.7 27.6 - - + -
79H LEU* 3.6 24.5 - - + +
80H LEU* 4.0 13.0 - - + -
82H MET* 4.1 6.7 - - - -
98H TYR* 4.4 4.0 - - + -
101H ALA* 3.9 16.8 - - + -
102H MET* 3.8 42.6 - - + +
105H ILE* 3.9 17.0 - - + -
112H THR 3.0 18.4 + - - +
113H GLY 3.6 1.8 - - - +
114H VAL 3.2 0.2 - - - -
115H ILE* 1.3 74.5 - - - +
117H SER* 1.3 62.8 + - - +
119H ASN* 3.5 1.8 + - - +
120H ASN* 2.6 42.6 + - - +
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Residues in contact with SER 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H TYR* 3.0 21.8 + - - -
102H MET* 3.8 13.2 - - - -
113H GLY 2.9 17.2 + - - -
114H VAL* 3.1 8.5 + - - -
116H MET* 1.3 74.2 - - - +
118H VAL* 1.3 61.2 + - - +
121H SER* 3.0 32.1 + - - -
122H LEU* 3.8 2.0 + - - +
271H GLY 4.4 2.6 + - - -
274H GLY* 3.5 20.1 - - - -
275H ILE* 4.0 14.3 + - - +
392H GLU* 4.7 2.2 + - - -
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Residues in contact with VAL 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H VAL* 2.9 27.4 + - + +
116H MET 3.3 0.2 - - - -
117H SER* 1.3 76.4 - - - +
119H ASN* 1.3 60.0 + - - +
122H LEU* 3.0 33.8 + - + -
123H TYR* 2.8 26.5 + - - +
150H GLY 4.0 9.6 - - - +
151H CYS* 4.0 14.4 - - - -
152H PHE* 4.5 2.5 - - + +
187H THR* 3.5 33.7 - - + +
188H ASN* 3.6 22.0 - - - +
392H GLU* 5.4 1.8 - - - +
501H FAD 5.1 1.1 - - - +
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Residues in contact with ASN 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 2.8 35.8 + - + +
115H ILE 3.3 11.4 + - - +
116H MET* 4.0 7.0 - - - +
117H SER 3.4 0.2 - - - -
118H VAL* 1.3 80.4 - - - +
120H ASN* 1.3 56.9 + - - +
123H TYR* 3.7 10.7 - - - +
124H LEU* 2.9 44.4 + - - +
143H PHE* 3.1 23.0 + - - +
149H ILE* 3.5 20.6 - - + +
150H GLY* 2.9 30.5 + - - +
188H ASN* 4.5 0.6 - - - +
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Residues in contact with ASN 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H LEU 3.0 21.2 + - - +
80H LEU* 3.6 10.5 - - - +
81H ALA* 3.4 4.0 + - - -
82H MET* 3.1 33.3 + - - +
83H ASP* 4.6 2.4 + - + -
95H TYR* 4.7 4.9 + - + +
98H TYR* 3.5 28.2 - - + -
116H MET* 2.6 38.2 + - - +
119H ASN* 1.3 75.7 - - - +
121H SER* 1.3 59.0 + - - +
124H LEU* 3.7 6.4 - - - +
125H GLY* 3.0 25.1 + - - -
128H LEU* 6.0 0.2 - - - +
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Residues in contact with SER 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H TYR* 2.7 25.8 + - - -
98H TYR* 2.6 26.9 + - - -
117H SER* 3.0 12.6 + - - -
120H ASN* 1.3 78.2 - - - +
122H LEU* 1.3 63.9 + - - +
125H GLY* 3.4 19.0 - - - -
267H THR* 3.5 10.5 - - - +
270H MET* 3.5 9.4 + - - +
271H GLY* 3.6 27.8 - - - -
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Residues in contact with LEU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H VAL* 3.0 33.7 + - + +
121H SER* 1.3 77.6 - - - +
123H TYR* 1.3 61.0 + - - +
126H PRO* 3.3 15.1 - - - +
152H PHE* 3.1 54.1 - - + +
196H VAL* 4.5 1.6 - - - +
267H THR* 3.6 26.5 - - + +
268H LEU* 4.4 10.8 - - + -
271H GLY* 4.2 3.8 - - - -
392H GLU* 3.5 41.7 - - + +
501H FAD 4.8 9.2 - - + +
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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