Contacts of the helix formed by residues 89 - 102 (chain B) in PDB entry 1V8O
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 THR 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.8 11.7 - - - -
44A TRP* 3.5 28.5 - - + -
83B ALA* 4.3 0.9 - - - -
88B LEU* 1.3 76.4 - - - +
90B PHE* 1.3 65.8 + - - +
91B TYR* 3.1 8.9 + - - +
92B ASP* 3.2 30.9 + - - +
93B ALA* 2.9 20.6 + - - +
48D ARG* 6.2 1.6 - - - +
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Residues in contact with PHE 90 (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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36A ILE* 4.0 8.3 - - + -
37A TYR* 3.7 40.4 - + + -
40A GLY* 3.5 25.4 - - - +
41A ASN* 3.2 28.3 - - + +
44A TRP* 4.2 8.5 - - + -
74B PRO 6.1 0.2 - - - -
76B LEU* 3.7 25.8 - - + -
79B VAL* 3.5 32.3 - - + +
80B MSE 3.7 25.1 - - + -
83B ALA* 4.4 3.8 - - + -
89B THR* 1.3 73.9 - - - +
91B TYR* 1.3 56.8 + - - +
93B ALA* 4.4 3.6 - - - -
94B SER* 2.7 45.9 + - - -
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Residues in contact with TYR 91 (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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34A LEU* 5.0 3.2 - - + +
37A TYR* 3.4 32.3 - - + -
38A GLU* 3.6 28.9 - - + +
41A ASN* 3.6 33.0 - - + +
91A TYR* 5.4 14.0 - + - -
34B LEU* 3.6 29.1 - - + +
38B GLU* 3.6 19.3 - - + +
89B THR* 3.1 8.0 + - - +
90B PHE* 1.3 78.0 - - - +
92B ASP* 1.3 66.2 + - - +
94B SER* 3.2 17.4 + - - -
95B TYR* 3.3 15.7 - - - -
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Residues in contact with ASP 92 (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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38B GLU* 5.3 2.3 - - - +
88B LEU* 4.0 22.4 - - + +
89B THR* 3.2 24.1 + - - +
91B TYR* 1.3 82.5 - - - +
93B ALA* 1.3 62.9 + - - +
95B TYR* 2.9 20.8 + - - +
96B ALA 3.2 8.7 + - - -
110B ASP* 4.0 14.6 - - - +
112B GLU* 5.9 0.3 - - - +
113B LEU* 3.7 30.9 - - + +
48D ARG* 4.3 12.6 + - - -
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Residues in contact with ALA 93 (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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79B VAL* 3.7 14.5 - - + +
82B VAL* 4.2 5.2 - - + +
83B ALA* 3.6 35.7 - - + +
88B LEU* 3.9 15.4 - - + +
89B THR 2.9 18.0 + - - +
92B ASP* 1.3 76.8 - - - +
94B SER* 1.3 57.6 + - - +
96B ALA* 3.7 2.2 - - - +
97B TYR* 2.9 31.2 + - - +
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Residues in contact with SER 94 (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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37A TYR* 3.5 35.2 - - - -
32B LEU* 4.2 9.0 - - - -
34B LEU* 4.6 0.4 - - - -
74B PRO* 4.2 3.5 - - - +
79B VAL* 3.2 19.1 - - - +
90B PHE* 2.7 21.4 + - - -
91B TYR 3.2 11.2 - - - -
92B ASP 3.0 0.8 - - - -
93B ALA* 1.3 75.4 - - - +
95B TYR* 1.3 65.8 + - - +
97B TYR* 3.8 0.7 - - - +
98B VAL* 3.0 29.5 + - - +
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Residues in contact with TYR 95 (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 LEU* 3.7 18.6 - - + +
7B VAL 4.0 3.6 - - - -
8B ASP* 3.4 35.8 - - + -
32B LEU* 3.5 23.6 - - + -
34B LEU* 3.8 10.2 - - + -
35B THR* 2.8 35.9 + - - +
38B GLU* 2.7 31.4 + - - -
91B TYR 3.3 26.2 - - - -
92B ASP* 2.9 12.5 + - - +
94B SER* 1.3 77.2 - - - +
96B ALA* 1.3 64.5 + - - +
99B ALA* 2.8 28.4 + - - +
106B LEU* 3.9 20.0 - - + -
113B LEU* 4.3 7.2 - - + -
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Residues in contact with ALA 96 (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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82B VAL* 4.3 2.9 - - + -
86B ARG* 4.2 16.2 - - - +
88B LEU* 4.1 14.4 - - + -
92B ASP 3.2 8.9 + - - +
93B ALA* 3.7 8.1 - - - +
95B TYR* 1.3 78.5 - - - +
97B TYR* 1.3 57.4 + - - +
99B ALA* 3.9 0.2 - - - +
100B GLU* 2.8 36.9 + - - +
106B LEU* 4.0 1.4 - - - +
113B LEU* 4.0 5.2 - - + -
117B THR* 3.7 29.8 - - + +
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Residues in contact with TYR 97 (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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74B PRO* 3.8 18.2 - - + -
75B PRO* 3.6 24.6 - - + +
78B GLU* 3.2 48.6 + - + +
79B VAL* 4.4 8.7 - - + -
82B VAL* 4.1 23.5 - - + +
86B ARG* 6.3 0.2 - - - +
93B ALA 2.9 19.7 + - - +
94B SER 3.8 2.2 - - - +
96B ALA* 1.3 74.4 - - - +
98B VAL* 1.3 62.9 + - + +
100B GLU* 4.7 2.5 - - - -
101B SER* 2.7 63.0 + - - -
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Residues in contact with VAL 98 (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 LEU* 3.6 15.3 - - + -
32B LEU* 3.6 15.5 - - + -
71B LEU* 3.5 33.2 - - + -
72B GLU 4.5 4.7 - - - +
74B PRO* 3.0 39.7 - - + -
94B SER 3.0 17.7 + - - +
97B TYR* 1.3 76.5 - - + +
99B ALA* 1.3 59.7 - - - +
101B SER* 4.6 1.8 - - - -
102B SER* 2.8 39.2 + - - +
104B LEU* 4.7 0.7 - - + -
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Residues in contact with ALA 99 (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 LEU* 3.7 11.0 - - + +
95B TYR 2.8 22.0 + - - +
96B ALA 3.9 1.8 - - - +
98B VAL* 1.3 76.4 - - - +
100B GLU* 1.3 63.4 + - - +
103B GLY 3.2 0.7 + - - -
104B LEU* 2.8 46.6 + - - +
106B LEU* 3.5 34.8 - - + +
117B THR* 4.6 3.6 - - + -
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Residues in contact with GLU 100 (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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86B ARG* 2.6 48.3 + - - -
96B ALA 2.8 21.9 + - - +
97B TYR* 4.0 3.0 - - + +
99B ALA* 1.3 74.2 - - - +
101B SER* 1.3 63.9 + - - +
103B GLY* 3.3 9.7 + - - -
104B LEU 5.0 1.6 - - - -
116B LYS 4.1 0.3 - - - +
117B THR* 3.9 3.7 - - + -
118B LYS* 3.1 61.5 + - + +
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Residues in contact with SER 101 (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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97B TYR* 2.7 53.7 + - - -
98B VAL* 3.9 1.8 - - - -
100B GLU* 1.3 70.0 - - - +
102B SER* 1.3 60.2 + - - +
103B GLY* 2.9 10.0 + - - -
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Residues in contact with SER 102 (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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71B LEU* 5.1 2.1 - - - +
98B VAL* 2.8 28.3 + - - +
101B SER* 1.3 71.6 + - - +
103B GLY* 1.3 62.7 + - - +
104B LEU* 3.1 27.7 + - - +
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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