Contacts of the helix formed by residues 94 - 109 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G HIS* 3.2 23.7 + - - -
82G MET* 4.9 1.4 - - - +
83G ASP* 3.6 12.3 - - - +
93G LEU* 1.3 79.0 - - - +
95G TYR* 1.3 61.8 + - - +
96G LEU* 3.5 2.9 + - - +
97G ALA* 3.0 22.2 + - - +
98G TYR* 3.0 23.4 + - - +
336G ASP* 3.1 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ASP* 3.4 34.5 - - + -
94G ASP* 1.3 69.2 - - - +
96G LEU* 1.3 54.8 + - - +
97G ALA 3.2 0.2 - - - -
98G TYR* 3.5 29.7 - + + +
99G ALA* 2.7 35.7 + - - +
120G ASN* 4.5 3.7 + - + +
121G SER* 3.2 25.5 + - - -
125G GLY* 5.6 0.5 - - - -
270G MET* 3.5 39.1 - - + +
273G ILE* 3.9 25.1 - - + -
332G ALA* 3.7 16.8 - - + +
335G LYS* 3.4 30.3 - - + -
336G ASP* 2.8 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 4.4 11.2 - - + -
35G PRO* 4.9 9.0 - - + -
38G HIS* 3.7 21.5 - - + +
94G ASP* 3.5 8.7 + - - +
95G TYR* 1.3 73.7 - - - +
97G ALA* 1.3 57.8 + - - +
99G ALA* 3.1 5.4 + - - +
100G ILE* 2.9 36.5 + - + +
329G TRP* 3.8 48.7 - - + +
332G ALA* 3.6 9.7 - - + +
333G MET* 4.3 22.2 - - + -
336G ASP* 3.0 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G HIS* 3.7 16.7 + - + +
41G LEU* 3.4 27.5 - - + +
82G MET* 4.6 2.5 - - + -
93G LEU* 4.0 21.5 - - + -
94G ASP* 3.0 23.1 + - - +
96G LEU* 1.3 74.6 - - - +
98G TYR* 1.3 64.9 + - - +
100G ILE* 3.3 1.5 + - - -
101G ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G MET* 3.9 19.4 - - + -
83G ASP* 5.5 0.4 - - + -
94G ASP 3.0 14.4 + - - +
95G TYR* 3.5 45.3 - + + +
97G ALA* 1.3 73.8 - - - +
99G ALA* 1.3 59.2 + - - +
101G ALA* 3.4 0.9 + - - +
102G MET* 2.8 54.0 + - + +
116G MET* 4.3 6.1 - - + -
117G SER* 2.8 30.7 + - - -
120G ASN* 3.4 37.5 - - + -
121G SER* 2.7 29.3 + - - -
273G ILE* 5.1 1.6 - - + -
274G GLY* 3.7 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TYR 2.7 17.7 + - - +
96G LEU* 3.3 12.1 - - - +
98G TYR* 1.3 76.6 - - - +
100G ILE* 1.3 61.7 + - - +
102G MET* 4.5 0.2 - - - -
103G GLU* 3.1 23.2 + - - +
273G ILE* 4.6 3.8 - - + -
277G SER* 3.4 28.2 + - - +
280G LEU* 5.7 1.1 - - + +
328G THR* 4.4 7.4 - - + -
329G TRP* 4.4 21.1 - - + +
332G ALA* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 3.7 32.8 - - + -
38G HIS* 3.7 27.8 - - + +
41G LEU* 4.7 3.8 - - + -
42G LEU* 3.6 46.9 - - + +
96G LEU* 2.9 21.4 + - + +
97G ALA* 3.7 5.8 - - - +
99G ALA* 1.3 75.4 - - - +
101G ALA* 1.3 59.7 + - - +
103G GLU* 3.3 9.5 + - - +
104G GLU* 3.0 26.7 + - - +
329G TRP* 4.3 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G LEU* 4.6 2.5 - - + -
45G CYS* 3.6 30.5 - - - -
79G LEU* 4.1 2.0 - - + -
82G MET* 3.7 25.1 - - + -
97G ALA 3.0 17.3 + - - +
98G TYR 3.8 0.4 - - - +
100G ILE* 1.3 74.8 - - - +
102G MET* 1.3 56.8 + - - +
104G GLU* 3.0 3.1 + - - +
105G ILE* 2.8 39.8 + - - +
116G MET* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G TYR* 2.8 47.9 + - + +
101G ALA* 1.3 71.4 - - - +
103G GLU* 1.3 57.8 - - - +
105G ILE* 3.9 0.2 - - - +
106G SER* 2.7 64.1 + - - +
113G GLY* 3.3 27.4 - - - +
116G MET* 3.8 19.4 - - + +
117G SER* 3.8 21.1 - - - -
274G GLY 3.8 6.7 - - - +
277G SER* 3.3 19.5 - - - -
278G GLN* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ALA 3.1 12.2 + - - +
100G ILE* 3.5 10.8 - - - +
102G MET* 1.3 80.3 - - - +
104G GLU* 1.3 73.3 + - - +
107G ARG* 3.1 25.1 + - + +
277G SER* 3.4 13.7 + - - +
280G LEU* 3.8 18.4 - - + +
281G GLY* 3.4 21.5 - - - +
284G GLN* 4.1 12.4 - - + +
325G ARG* 2.9 46.9 + - - +
329G TRP* 4.8 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LEU* 4.0 31.2 - - + +
45G CYS* 3.5 24.2 - - + -
46G ARG* 2.9 59.7 + - - +
49G ALA* 3.5 13.4 - - - +
100G ILE 3.0 16.1 + - - +
101G ALA 3.0 4.0 + - - +
103G GLU* 1.3 87.1 - - - +
105G ILE* 1.3 62.8 + - - +
107G ARG* 3.4 29.2 + - - +
108G GLY 3.4 4.2 + - - -
284G GLN* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G CYS* 4.4 15.3 - - + +
48G PHE* 3.9 22.4 - - + -
49G ALA* 4.7 0.7 - - + -
53G LEU* 3.4 10.7 - - + +
74G MET* 4.2 2.9 - - + -
79G LEU* 3.9 24.7 - - + -
101G ALA* 2.8 23.4 + - - +
102G MET 3.9 2.7 - - - +
104G GLU* 1.3 70.7 - - - +
106G SER* 1.3 58.5 + - - +
108G GLY* 2.9 6.4 + - - -
109G CYS 2.9 23.9 + - - -
112G THR* 3.6 29.2 - - + -
113G GLY* 3.7 15.3 - - - +
116G MET* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G MET* 2.7 43.5 + - - +
103G GLU 4.1 2.2 - - - -
105G ILE* 1.3 72.5 - - - +
107G ARG* 1.3 65.8 + - - +
108G GLY 3.4 0.5 + - - -
109G CYS 3.6 9.4 - - - -
110G ALA* 3.5 21.9 + - - +
113G GLY* 3.4 8.5 - - - -
278G GLN* 3.4 34.0 - - - +
281G GLY* 4.2 6.3 - - - -
282G ILE* 4.3 3.6 + - - +
285G THR* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ARG* 3.9 34.4 + - - +
49G ALA* 5.5 0.4 - - - +
50G GLU* 4.7 5.7 - - - +
54G PHE* 3.5 31.3 - - + -
103G GLU* 3.1 19.0 + - - +
104G GLU* 3.4 24.7 + - - +
106G SER* 1.3 78.8 - - - +
108G GLY* 1.3 58.8 + - - +
281G GLY* 3.3 18.1 - - - +
284G GLN* 4.0 18.1 - - - +
285G THR* 3.5 32.6 + - - +
288G ASP* 3.2 27.3 + - - +
380G ARG* 6.0 0.2 + - - -
381G HIS* 5.1 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA* 4.3 3.4 - - - -
53G LEU* 3.9 17.1 - - - +
54G PHE* 3.6 28.6 + - - -
57G ALA* 3.5 18.9 - - - +
104G GLU 3.4 3.6 + - - -
105G ILE 2.9 8.5 + - - -
106G SER 4.1 0.2 - - - -
107G ARG* 1.3 81.2 - - - +
109G CYS* 1.3 60.0 + - - +
380G ARG* 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LEU* 4.0 17.6 - - + +
56G ILE* 5.3 2.5 - - + -
57G ALA* 4.5 13.9 - - + -
60G VAL* 4.1 32.1 - - - -
105G ILE 2.9 16.3 + - - +
106G SER* 3.6 4.1 - - - -
108G GLY* 1.3 77.3 - - - +
110G ALA* 1.3 66.7 + - - +
111G SER* 3.2 5.3 + - - -
112G THR* 3.7 30.0 - - - +
113G GLY 3.1 18.2 + - - -
380G ARG* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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