Contacts of the strand formed by residues 115 - 122 (chain B) in PDB entry 2CVL
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 VAL 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLN 3.9 0.9 - - - +
32B ILE* 3.8 2.3 - - - -
33B PRO* 3.4 20.6 - - + +
45B ILE* 4.0 13.7 - - + -
48B GLN* 4.1 17.0 - - + -
49B THR* 3.9 16.2 - - - +
52B VAL* 3.9 18.8 - - + -
76B PHE 3.3 10.8 - - - +
77B LEU* 4.5 2.7 - - + -
86B PHE* 3.7 31.6 - - + -
109B LEU* 3.6 4.3 - - - -
113B VAL* 3.4 6.4 - - - +
114B ARG* 1.3 83.0 - - - +
116B GLU* 1.3 64.0 + - - +
117B VAL* 3.8 12.3 - - + -
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Residues in contact with GLU 116 (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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30B GLY* 3.5 19.2 - - - +
31B GLN 3.2 11.4 - - - +
32B ILE* 3.9 9.6 - - + -
74B THR 3.8 1.2 - - - +
75B CYS* 3.6 0.3 - - - -
76B PHE* 2.9 38.4 + - + +
109B LEU* 3.7 17.9 - - + +
110B PRO* 3.2 18.9 - - - +
115B VAL* 1.3 75.5 - - - +
117B VAL* 1.3 67.0 + - - +
118B ALA* 4.3 0.4 - - + -
101C ARG 4.7 0.2 - - - +
102C ALA* 3.4 14.6 - - - +
103C THR 2.7 44.3 + - - +
104C VAL* 3.7 5.1 - - - +
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Residues in contact with VAL 117 (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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30B GLY* 3.8 0.9 - - - -
31B GLN* 2.8 33.8 + - - +
52B VAL* 3.8 17.0 - - + -
53B MSE 4.1 6.5 - - + -
56B LEU* 3.5 29.6 - - + +
73B THR* 4.3 9.4 - - + -
74B THR 3.5 2.2 - - - -
75B CYS* 3.9 18.4 - - + -
86B PHE* 3.8 33.7 - - + -
90B TYR* 5.0 0.9 - - + -
115B VAL* 3.8 7.0 - - + -
116B GLU* 1.3 79.5 - - - +
118B ALA* 1.3 70.7 + - - +
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Residues in contact with ALA 118 (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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28B VAL 3.5 15.3 - - - +
29B SER* 3.8 1.1 - - - -
30B GLY* 3.6 18.3 - - - +
56B LEU* 4.9 1.3 - - - -
73B THR* 3.4 1.6 - - - -
74B THR* 2.9 39.7 + - - +
76B PHE* 6.3 0.2 - - + -
116B GLU* 4.3 0.6 - - - +
117B VAL* 1.3 79.0 - - - +
119B CYS* 1.3 66.2 + - - +
72C GLN* 6.1 2.9 - - - +
102C ALA* 4.0 17.9 - - + -
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Residues in contact with CYS 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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27B PHE* 3.8 0.3 - - - -
28B VAL* 2.9 55.9 + - - +
56B LEU* 4.1 17.0 - - + -
60B LEU* 4.3 7.2 - - - -
70B VAL* 4.0 22.9 - - + -
72B GLN* 3.2 15.3 - - - +
73B THR* 3.9 13.7 - - + +
74B THR* 4.8 0.7 - - - +
94B PHE* 5.7 0.7 - - - -
117B VAL* 5.2 0.2 - - + -
118B ALA* 1.3 80.2 - - - +
120B VAL* 1.3 70.1 + - - +
72C GLN* 4.9 2.4 + - - +
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Residues in contact with VAL 120 (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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27A PHE* 4.5 11.0 - - + -
25B PHE* 3.7 31.9 - - + -
26B VAL 3.4 7.0 - - - +
27B PHE* 3.8 17.0 - - + -
70B VAL* 3.6 3.1 - - - +
71B VAL* 2.9 28.6 + - + +
72B GLN* 2.9 37.5 + - + +
119B CYS* 1.3 80.5 - - - +
121B ALA* 1.3 63.1 + - - +
72C GLN* 3.7 22.0 - - - +
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Residues in contact with ALA 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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25B PHE* 3.1 12.6 - - - -
26B VAL* 2.8 33.4 + - + +
60B LEU* 3.7 29.4 - - + -
65B SER* 3.8 8.7 - - - +
69B ARG 3.3 15.9 - - - +
70B VAL* 3.6 11.4 - - + +
71B VAL* 4.1 1.3 - - - +
120B VAL* 1.3 75.6 - - - +
122B LEU* 1.3 61.2 + - - +
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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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1A MSE 4.4 13.9 - - + +
22A ALA* 4.0 15.0 - - + -
23A GLY* 3.8 21.5 - - - +
24B GLY 3.7 8.1 - - - +
25B PHE* 3.8 22.2 - - + -
26B VAL* 4.5 0.2 - - - -
65B SER* 2.9 22.2 + - - -
69B ARG* 2.9 42.5 + - - +
71B VAL* 4.0 15.2 - - + +
121B ALA* 1.3 73.7 - - - +
123B ALA* 1.3 64.0 + - - +
124B GLU* 3.1 14.4 + - - +
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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