Contacts of the helix formed by residues 131 - 147 (chain B) in PDB entry 1VLP
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 TYR 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 6.5 0.2 - - + -
60B LEU* 4.1 16.8 - - + -
95B LEU* 3.6 26.4 - - + +
96B HIS 3.1 17.7 + - - -
97B PRO* 3.0 29.9 - - + +
100B GLN* 3.6 20.3 - - + +
101B ILE* 3.6 27.8 - - + -
121B VAL* 3.5 18.6 - - + -
127B ASP 3.4 20.2 - - - -
128B THR* 3.2 23.3 + - - +
130B LEU* 1.3 78.1 - - - +
132B GLU* 1.3 65.6 + - - +
133B ILE 3.2 0.5 + - - -
134B PRO* 3.4 4.2 - - - +
135B LEU* 3.0 38.1 + - + +
378B ILE* 6.3 0.4 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.1 23.0 + - - -
16B LYS* 2.8 30.7 + - + +
34B TYR* 5.1 7.0 - - + -
128B THR 4.6 1.0 + - - -
129B ILE 4.0 1.6 + - - -
130B LEU 3.3 2.2 - - - -
131B TYR* 1.3 76.1 - - - +
133B ILE* 1.3 65.8 + - + +
135B LEU* 4.1 1.2 - - - +
136B LEU* 3.0 43.2 + - + +
180B ARG* 3.6 16.6 + - - -
233B GLU* 3.4 6.9 - - - +
378B ILE* 3.6 41.9 + - + +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP 4.7 0.7 - - - +
12B THR* 3.2 22.2 - - - +
13B ASP* 2.9 29.6 - - - +
15B TYR* 3.3 17.3 - - + +
16B LYS* 3.3 28.3 - - + -
130B LEU 4.1 0.4 + - - -
132B GLU* 1.3 73.8 - - - +
134B PRO* 1.3 69.7 - - + +
136B LEU* 3.2 3.1 + - - +
137B SER* 2.8 23.0 + - - -
179B THR* 3.2 34.3 - - + -
180B ARG* 3.1 30.0 - - + +
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Residues in contact with PRO 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.2 25.8 - - + -
11B ASP 4.5 8.3 - - - +
12B THR* 4.0 7.9 - - - +
60B LEU* 4.4 18.6 - - + -
95B LEU* 6.0 4.3 - - + -
130B LEU* 3.1 26.5 - - + +
131B TYR* 3.4 8.3 - - + +
133B ILE* 1.3 91.0 - - + +
135B LEU* 1.3 55.3 + - - +
137B SER* 2.9 10.1 + - - +
138B LEU* 2.9 35.7 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.5 36.1 - - + -
60B LEU* 3.8 14.6 - - + -
101B ILE* 3.8 22.0 - - + -
119B ILE* 4.5 9.2 - - + -
121B VAL* 3.8 29.2 - - + -
131B TYR* 3.0 33.1 + - + +
132B GLU* 5.4 0.2 - - - -
134B PRO* 1.3 77.3 - - - +
136B LEU* 1.3 59.3 + - - +
138B LEU* 3.6 1.2 - - - +
139B ILE* 2.9 38.1 + - + +
378B ILE* 3.6 20.2 - - + -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 5.0 2.0 - - + -
132B GLU* 3.0 42.1 + - + +
133B ILE 3.6 2.9 - - - +
135B LEU* 1.3 77.6 - - - +
137B SER* 1.3 62.6 + - - +
139B ILE* 3.3 2.2 + - + -
140B SER* 3.0 25.8 + - - -
180B ARG* 3.5 36.9 - - + +
376B ILE* 3.6 45.6 - - + +
377B VAL* 3.9 8.7 - - - -
378B ILE* 3.9 29.8 - - + +
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Residues in contact with SER 137 (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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6B ILE* 3.8 4.2 - - - +
11B ASP 5.5 0.7 + - - -
133B ILE 2.8 17.5 + - - -
134B PRO* 2.9 21.7 + - - +
136B LEU* 1.3 73.0 - - - +
138B LEU* 1.3 55.9 + - - +
140B SER* 3.9 3.8 - - - -
141B GLU* 3.0 29.5 + - - +
179B THR* 3.7 16.7 - - - +
180B ARG 3.5 8.0 + - - -
182B ARG* 3.5 43.1 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.9 20.6 - - + -
6B ILE* 4.0 21.1 - - + -
52B TRP* 3.5 11.4 - - + -
53B LEU* 3.4 12.7 - - + +
56B GLN* 3.7 43.1 - - + +
57B PHE* 3.8 25.1 - - + -
60B LEU* 4.5 8.1 - - + -
134B PRO 2.9 26.8 + - - +
135B LEU* 3.6 3.8 - - - +
136B LEU 3.2 0.2 - - - -
137B SER* 1.3 75.3 + - - +
139B ILE* 1.3 59.5 + - - +
141B GLU* 3.4 3.0 + - - -
142B ALA* 2.8 31.2 + - - +
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Residues in contact with ILE 139 (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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36B TYR* 3.8 25.6 - - + +
45B PHE* 3.6 26.6 - - + -
53B LEU* 3.8 21.3 - - + -
57B PHE* 4.1 7.9 - - + -
117B LEU* 4.3 3.1 - - + -
119B ILE* 3.7 27.1 - - + -
135B LEU* 2.9 26.6 + - + +
136B LEU 3.3 0.2 + - - -
138B LEU* 1.3 70.7 - - - +
140B SER* 1.3 59.7 + - - +
142B ALA* 3.3 2.8 + - - +
143B TYR* 2.9 29.3 + - - +
374B LEU* 4.0 2.2 - - + -
376B ILE* 3.6 22.0 - - + -
378B ILE* 4.6 5.6 - - + -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 3.0 16.3 + - - -
137B SER 3.9 2.0 - - - -
139B ILE* 1.3 75.5 - - - +
141B GLU* 1.3 64.8 + - - +
143B TYR* 3.3 1.6 + - - +
144B PHE* 3.1 34.6 + - - -
180B ARG 4.5 7.2 - - - -
181B ARG* 3.9 7.6 + - - -
182B ARG 2.6 29.1 + - - -
183B ARG* 4.0 2.0 - - - -
359B ASN* 3.9 8.8 + - - -
374B LEU* 4.4 15.2 + - - +
376B ILE* 4.2 6.4 - - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.6 32.7 - - + +
52B TRP* 4.2 12.6 - - + -
137B SER 3.0 18.6 + - - +
138B LEU* 3.8 5.2 - - - +
140B SER* 1.3 77.6 - - - +
142B ALA* 1.4 56.0 + - - +
144B PHE* 3.2 2.1 + - - +
145B LYS* 2.9 46.6 + - + +
182B ARG* 4.3 1.9 + - - -
183B ARG 3.3 11.5 + - - +
184B SER* 3.3 22.3 - - - -
185B LEU* 2.9 24.2 + - - +
186B LYS* 5.4 0.7 + - - +
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Residues in contact with ALA 142 (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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45B PHE* 4.7 0.9 - - + -
49B ALA* 4.3 12.3 - - + +
52B TRP* 3.6 18.7 - - + -
53B LEU* 3.6 28.5 - - + -
138B LEU 2.8 20.8 + - - +
139B ILE 3.5 4.9 - - - +
141B GLU* 1.4 67.8 - - - +
143B TYR* 1.3 67.4 + - - +
145B LYS* 3.2 0.8 + - - -
146B PHE* 2.9 35.4 + - + +
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Residues in contact with TYR 143 (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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43B LEU* 3.5 40.1 - - + +
44B THR 3.4 29.8 + - - -
45B PHE* 3.9 20.8 - + + -
139B ILE 2.9 16.7 + - - +
140B SER 3.7 4.3 - - - +
141B GLU 3.3 0.2 - - - -
142B ALA* 1.3 75.8 - - - +
144B PHE* 1.3 85.0 + + + +
147B VAL* 2.9 55.2 + - + +
148B ASP* 3.0 33.9 + - + +
372B GLU 5.4 0.2 - - - -
374B LEU* 3.8 17.9 - - + -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 3.1 34.2 + - - +
141B GLU 3.7 0.4 - - - -
143B TYR* 1.3 97.0 - + - +
145B LYS* 1.3 60.1 + - - +
148B ASP* 3.3 36.2 - - + +
149B ILE* 4.2 3.3 - - - +
151B TRP* 3.0 33.3 + - + +
183B ARG* 3.5 63.3 - - + +
359B ASN* 4.0 12.8 - - - -
371B SER* 4.0 0.2 - - - -
372B GLU 3.3 24.5 - - - -
373B PRO* 4.0 3.1 - - + -
374B LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 145 (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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5B VAL* 6.1 0.4 - - - -
52B TRP* 3.9 35.0 - - + +
141B GLU* 2.9 29.3 + - + +
142B ALA 3.6 4.0 - - - +
144B PHE* 1.3 79.4 - - - +
146B PHE* 1.3 87.3 + - + +
147B VAL 3.9 0.2 - - - -
149B ILE* 3.5 16.2 - - - +
151B TRP* 5.3 0.9 - - - -
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 3.1 15.3 + - - +
48B GLU* 4.0 19.9 - - + +
49B ALA* 3.8 31.9 - - + +
52B TRP* 3.4 49.4 - + + -
142B ALA* 2.9 19.5 + - - +
145B LYS* 1.3 105.1 - - + +
147B VAL* 1.3 62.8 + - - +
149B ILE* 4.6 5.3 - - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR* 3.2 25.1 - - - +
45B PHE* 4.1 2.7 - - + -
46B ASN* 3.8 26.9 - - - +
49B ALA* 4.1 14.1 - - + -
114B HIS* 6.4 0.2 - - - +
143B TYR* 2.9 44.2 + - + +
146B PHE* 1.3 82.6 - - - +
148B ASP* 1.3 58.3 + - - +
149B ILE* 3.8 4.9 + - - +
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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