Contacts of the helix formed by residues 104 - 115 (chain M) in PDB entry 2VGL
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 ASN 104 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93M PHE* 3.2 35.7 - - + +
100M ASN* 2.3 35.5 + - - +
101M ILE 3.0 6.6 + - - +
103M ASN* 1.3 91.6 - - - +
105M PHE* 1.3 65.5 + - - +
106M VAL 3.1 3.5 + - - +
107M LEU* 3.3 9.9 + - + +
108M ILE* 2.9 23.2 + - + +
136M GLN 4.6 0.3 - - - +
137M GLY* 3.1 13.3 - - - -
138M ILE* 3.0 29.2 + - - +
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Residues in contact with PHE 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA* 4.4 20.4 - - + +
42B THR* 4.0 31.6 - - + +
43B VAL* 4.2 21.1 - - + -
15M LEU* 3.9 26.5 - - + -
16M ILE* 3.8 22.8 - - + +
101M ILE* 3.3 21.8 + - + -
102M LYS* 3.7 32.8 - - + +
103M ASN 3.5 2.4 + - - -
104M ASN* 1.3 76.5 - - - +
106M VAL* 1.3 63.1 + - + +
108M ILE* 3.7 2.0 - - - +
109M TYR* 2.9 36.9 + - + -
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Residues in contact with VAL 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 4.0 23.1 - - + +
38B ILE* 3.8 32.5 - - + -
39B ALA* 4.7 4.0 - - + +
68B LEU* 3.4 31.2 - - + -
71B LEU* 3.5 14.8 - - + +
103M ASN 5.4 0.4 + - - -
104M ASN 3.2 0.8 - - - -
105M PHE* 1.3 74.1 - - + +
107M LEU* 1.3 72.0 + - - +
109M TYR* 3.3 6.0 + - - +
110M GLU* 3.1 16.1 + - - +
135M GLN* 4.2 12.3 - - + -
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Residues in contact with LEU 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M TYR* 3.3 57.7 - - + -
93M PHE* 3.7 16.6 - - + -
104M ASN* 3.3 12.0 + - + +
106M VAL* 1.3 76.0 - - - +
108M ILE* 1.3 54.0 + - - +
110M GLU* 2.4 38.3 + - - +
111M LEU* 3.0 19.8 + - + -
133M ILE* 3.8 16.2 - - + -
135M GLN* 4.0 20.9 - - + +
136M GLN 5.2 1.8 - - - +
137M GLY* 3.6 18.2 - - - +
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Residues in contact with ILE 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M ILE* 4.4 2.7 - - + -
16M ILE* 3.9 23.1 - - + -
89M MET* 3.9 21.1 - - + -
93M PHE* 4.2 14.4 - - + -
101M ILE* 3.5 50.5 - - + +
104M ASN* 2.9 27.8 + - + +
105M PHE* 3.7 6.1 - - - +
107M LEU* 1.3 74.6 - - - +
109M TYR* 1.3 64.9 + - - +
110M GLU 3.1 0.2 + - - -
111M LEU* 3.5 7.4 + - - -
112M LEU* 2.9 47.3 + - + +
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Residues in contact with TYR 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.9 20.6 - - + -
41B MET* 6.0 0.3 - - - +
42B THR* 2.9 45.4 + - - +
71B LEU* 4.4 14.4 - - + +
75B ASN* 3.6 21.4 + - - +
16M ILE* 3.2 31.0 - - + +
17M SER 3.6 18.3 + - - -
18M ARG* 3.2 22.4 - - - +
105M PHE* 2.9 31.0 + - + +
106M VAL 3.8 4.7 - - - +
107M LEU 2.8 0.2 + - - -
108M ILE* 1.3 78.4 - - - +
110M GLU* 1.3 63.1 + - - +
112M LEU* 3.4 7.1 - - + +
113M ASP* 3.2 27.8 + - - +
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Residues in contact with GLU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 2.9 50.7 + - - +
71B LEU* 3.8 15.9 - - + +
106M VAL 3.1 10.6 + - - +
107M LEU* 2.4 28.2 + - - +
109M TYR* 1.3 66.6 - - - +
111M LEU* 1.3 65.0 + - - +
113M ASP* 3.4 11.4 + - - +
114M GLU* 3.4 12.5 + - - +
133M ILE* 3.5 19.5 - - + +
134M THR* 3.2 19.0 + - - -
135M GLN* 3.3 36.2 + - - +
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Residues in contact with LEU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M VAL* 3.1 36.8 - - + -
89M MET* 5.0 13.7 - - + -
92M TYR* 4.3 9.2 - - + -
93M PHE* 5.4 0.7 - - + -
107M LEU* 3.0 40.3 + - + +
108M ILE* 3.9 10.3 - - - +
110M GLU* 1.3 75.5 - - - +
112M LEU* 1.3 56.0 + - + +
114M GLU* 2.9 6.9 + - - +
115M ILE* 2.6 45.2 + - + +
129M LEU* 3.6 13.5 - - + -
133M ILE* 3.1 33.0 - - + -
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Residues in contact with LEU 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M LEU* 4.4 14.1 - - + +
7M ILE* 5.8 2.7 - - + -
16M ILE* 5.5 3.6 - - + -
17M SER* 5.1 5.4 - - - +
18M ARG* 4.4 17.5 - - + +
20M TYR* 3.5 18.6 + - - +
85M MET* 3.4 30.3 - - + -
89M MET* 4.6 2.5 - - + -
108M ILE* 2.9 40.8 + - + +
109M TYR* 3.4 17.9 - - + +
111M LEU* 1.3 78.9 - - + +
113M ASP* 1.3 61.6 + - - +
114M GLU 3.0 4.5 + - - -
115M ILE* 3.7 6.3 - - + -
116M LEU* 3.1 27.9 + - + +
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Residues in contact with ASP 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 5.3 0.2 - - - +
71B LEU* 4.0 16.7 - - + +
74B MET* 3.4 34.6 - - - +
105B LEU* 6.0 1.2 - - - +
108B ARG* 3.2 41.9 + - - +
18M ARG* 3.0 34.9 + - - -
20M TYR* 5.0 2.5 - - - -
109M TYR 3.2 8.9 + - - +
110M GLU* 3.4 7.8 + - - +
112M LEU* 1.3 73.7 - - - +
114M GLU* 1.3 55.3 + - - +
116M LEU 4.6 4.9 - - - -
117M ASP* 4.8 10.4 - - - +
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Residues in contact with GLU 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 4.6 4.2 + - - -
108B ARG* 2.7 32.0 + - - +
136B TYR* 2.7 34.8 + - - -
139B LYS* 4.4 5.5 + - - -
110M GLU 3.4 9.6 + - - +
111M LEU* 2.9 12.9 + - - +
113M ASP* 1.3 75.6 - - - +
115M ILE* 1.3 60.4 + - + +
116M LEU 3.0 5.7 + - - -
117M ASP* 4.8 1.7 + - - +
122M GLN* 3.9 12.0 - - - +
123M ASN 3.7 12.4 + - - +
129M LEU* 3.6 28.0 - - + +
132M PHE* 3.9 17.3 - - + +
133M ILE* 4.5 6.5 - - + -
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Residues in contact with ILE 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M PHE* 3.7 23.5 - - + -
84M LYS* 5.0 0.7 - - + -
85M MET* 3.7 46.9 - - + +
88M VAL* 4.8 9.0 - - + -
111M LEU* 2.6 28.3 + - + +
112M LEU* 3.7 11.7 - - - -
114M GLU* 1.3 74.2 - - + +
116M LEU* 1.3 73.1 + - + +
121M PRO 3.9 0.2 - - - -
122M GLN 3.2 24.8 + - - +
123M ASN 4.2 7.0 - - - -
124M SER* 3.4 26.5 - - - +
129M LEU* 5.1 7.0 - - + -
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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
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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