Contacts of the helix formed by residues 118 - 130 (chain B) 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 ILE 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ILE* 6.6 0.4 - - - -
88B VAL* 6.3 0.7 - - - -
110B MET* 3.0 47.3 - - + +
111B GLY* 4.5 2.2 - - - -
113B ILE* 3.0 38.4 - - + +
115B VAL* 3.6 21.8 + - + +
116B ASP 2.9 3.2 + - - -
117B LYS* 1.3 77.9 - - - +
119B THR* 1.3 73.1 + - + +
120B GLU 3.6 0.2 - - - -
121B TYR* 3.6 2.8 + - - +
122B LEU* 3.2 37.8 + - + +
148B LEU* 4.6 5.8 - - + -
151B ILE* 4.0 23.6 - - + -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASP 3.9 15.3 + - - +
117B LYS* 4.9 0.5 - - - -
118B ILE* 1.3 82.1 - - + +
120B GLU* 1.3 82.9 + - - +
121B TYR 3.1 3.6 + - - -
122B LEU* 4.9 2.5 - - - -
123B CYS* 3.2 28.9 + - - +
148B LEU* 4.8 15.3 - - + -
151B ILE* 5.9 3.1 - - + +
152B ASN 5.4 6.5 - - - +
153B ALA* 6.0 0.2 - - + -
155B MET* 5.0 17.7 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 4.2 23.1 - - - +
118B ILE 3.6 0.2 - - - -
119B THR* 1.3 86.4 + - - +
121B TYR* 1.3 98.8 + - + +
123B CYS* 3.1 17.1 - - - -
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 5.8 2.7 - - + -
88B VAL* 4.2 25.6 - - + -
89B ASN* 4.3 17.7 - - - -
92B VAL* 3.8 26.5 - - + +
110B MET* 4.1 15.2 - - + +
117B LYS* 3.0 41.9 - - + +
118B ILE* 3.6 3.1 + - - +
119B THR 3.1 0.6 - - - -
120B GLU* 1.3 102.9 + - + +
122B LEU* 1.3 59.6 + - - +
123B CYS 3.7 0.2 - - - -
125B PRO* 3.0 28.3 - - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 4.3 13.2 - - + +
110B MET* 3.3 36.3 - - + -
111B GLY* 4.1 17.7 - - - -
118B ILE* 3.2 29.5 + - + +
119B THR* 4.9 1.3 - - - -
121B TYR* 1.3 77.5 - - - +
123B CYS* 1.3 68.9 + - - +
124B GLU 3.5 0.7 - - - -
125B PRO* 3.3 4.8 - - + +
126B LEU* 3.1 33.5 + - + +
144B CYS* 4.2 23.1 - - - -
148B LEU* 4.6 27.6 - - + -
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Residues in contact with CYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR* 3.2 14.6 + - - +
120B GLU* 3.1 29.4 - - - -
121B TYR 4.2 1.1 - - - -
122B LEU* 1.3 80.2 - - - +
124B GLU* 1.3 79.6 + - - +
125B PRO* 4.5 0.2 - - - -
126B LEU* 5.1 0.2 - - - -
127B ARG* 3.1 15.7 + - - +
148B LEU* 5.5 6.3 - - - +
157B GLU* 4.3 17.9 - - - +
161B PHE* 3.3 22.8 - - + -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B CYS* 1.3 87.9 - - - +
125B PRO* 1.4 64.4 - - + +
127B ARG* 2.8 34.7 + - + +
128B LYS* 2.9 38.3 + - + +
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 4.6 13.7 - - + -
95B CYS* 3.9 26.2 - - + -
107B VAL* 5.1 4.5 - - + -
121B TYR 3.0 28.5 - - - +
122B LEU* 3.3 9.4 - - + +
123B CYS* 4.5 0.4 - - - -
124B GLU* 1.4 93.6 - - + +
126B LEU* 1.3 55.5 + - - +
128B LYS* 3.5 11.2 + - + +
129B CYS* 3.1 32.7 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 4.2 8.4 - - + +
122B LEU* 3.1 27.0 + - + +
123B CYS 3.8 3.1 - - - +
125B PRO* 1.3 73.7 - - - +
127B ARG* 1.3 62.8 + - - +
128B LYS 3.2 0.4 - - - -
129B CYS* 3.3 9.4 + - - +
130B LEU* 2.9 28.4 + - + +
141B ALA* 3.1 44.6 - - + +
144B CYS* 3.8 26.7 - - + +
145B VAL* 4.2 20.4 - - + -
148B LEU* 4.9 12.1 - - + -
161B PHE* 3.8 24.7 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B CYS 3.1 13.2 + - - +
124B GLU* 2.8 27.1 + - + +
126B LEU* 1.3 76.6 - - - +
128B LYS* 1.3 61.4 + - + +
130B LEU* 4.1 6.8 + - + +
131B LYS* 3.9 29.3 - - - +
157B GLU* 6.1 0.4 - - - -
161B PHE* 3.9 15.0 - - + -
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU* 5.9 6.0 + - + +
124B GLU* 2.9 36.7 + - + +
125B PRO* 3.5 10.5 + - + +
126B LEU 3.2 0.4 - - - -
127B ARG* 1.3 78.6 - - + +
129B CYS* 1.3 56.7 + - - +
130B LEU 3.5 0.2 - - - -
131B LYS* 2.6 32.3 - - - +
132B ASP* 4.6 1.4 - - - +
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Residues in contact with CYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B CYS* 4.9 13.5 - - - -
103B ARG* 4.8 2.5 - - - -
107B VAL* 3.4 33.9 - - + -
125B PRO 3.1 20.8 + - - +
126B LEU* 3.3 7.2 + - - +
128B LYS* 1.3 75.4 - - - +
130B LEU* 1.3 60.7 + - - +
131B LYS 3.1 6.7 + - - -
132B ASP* 3.3 19.2 - - - +
137B VAL* 3.8 23.1 - - + +
138B ARG* 3.4 7.4 - - - +
141B ALA* 3.4 20.4 - - + -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 2.9 26.6 + - + +
127B ARG* 4.4 7.0 - - - +
128B LYS 3.5 0.2 - - - -
129B CYS* 1.3 75.1 - - - +
131B LYS* 1.3 57.8 + - + +
138B ARG* 2.8 31.9 - - - +
141B ALA* 3.7 8.3 - - + -
142B ALA* 3.9 25.6 - - - +
145B VAL* 4.1 11.9 - - + -
161B PHE* 3.5 31.0 - - + -
164B SER* 4.4 15.9 - - - +
165B LEU* 5.1 4.0 - - + -
168B LEU* 3.5 35.5 - - + +
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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