Contacts of the strand formed by residues 94 - 102 (chain B) in PDB entry 1B8M
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 GLN 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR* 4.4 7.4 - - - -
56A THR* 5.0 2.9 + - - -
107A THR 5.2 0.9 - - - +
31B VAL* 6.3 0.6 - - - +
92B ALA* 3.6 12.1 - - - +
93B LYS* 1.3 89.5 - - - +
95B SER* 1.3 67.6 + - - +
96B TYR* 6.0 1.3 - - + -
114B ARG* 3.5 48.1 - - + +
115B ILE 3.2 16.4 - - - +
116B ASP* 3.3 18.0 - - - +
117B THR* 4.1 0.2 - - - -
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Residues in contact with SER 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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54A TYR* 3.9 23.8 - - - -
56A THR* 4.8 1.7 + - - -
107A THR* 3.7 16.6 + - - -
94B GLN* 1.3 75.4 + - - +
96B TYR* 1.3 67.5 + - - +
97B VAL* 5.6 2.0 - - - -
113B ILE 3.4 0.7 - - - +
114B ARG* 3.6 2.2 - - - -
115B ILE* 3.0 30.9 + - - +
117B THR* 2.5 38.8 + - - +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 3.9 23.3 - + + -
54A TYR* 3.7 55.1 + + + +
87A VAL* 5.5 1.2 - - - +
32B ASP 4.3 0.7 - - - -
33B LEU* 3.9 38.8 + - + +
94B GLN* 6.1 1.1 - - + -
95B SER* 1.3 76.0 - - - +
97B VAL* 1.3 66.9 + - - +
112B TRP* 3.9 21.8 - - + -
113B ILE 3.1 18.8 - - - -
114B ARG* 3.2 46.8 + - + -
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Residues in contact with VAL 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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87A VAL* 3.9 27.8 - - + -
56B PHE* 4.1 22.9 - - + -
95B SER* 4.9 2.9 - - - +
96B TYR* 1.3 79.1 - - - +
98B ARG* 1.3 65.1 + - - +
112B TRP* 3.4 9.7 - - - -
113B ILE* 2.9 46.7 + - + +
115B ILE* 3.8 33.2 - - + -
117B THR* 6.1 0.2 - - + -
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Residues in contact with ARG 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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42A VAL* 5.9 0.2 - - - +
49A LEU* 3.9 32.3 - - + +
50A LYS 3.0 29.5 + - - +
52A TYR* 4.6 4.0 - - - -
54B GLN* 4.8 0.3 - - - +
56B PHE* 5.2 1.6 - - - -
97B VAL* 1.3 79.2 - - - +
99B ALA* 1.3 63.3 + - - +
110B TRP* 3.5 47.7 + - + -
111B ARG* 3.4 12.3 - - - +
112B TRP* 3.5 52.1 - - + +
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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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40B VAL* 4.8 0.4 - - + -
54B GLN* 3.4 18.8 - - - +
56B PHE* 4.2 9.2 - - + -
97B VAL 3.8 0.2 + - - -
98B ARG* 1.3 77.3 - - - +
100B LEU* 1.3 64.6 + - - +
101B THR* 3.3 11.9 - - + +
110B TRP* 3.7 7.2 - - - -
111B ARG 2.9 30.8 + - - +
113B ILE* 3.6 30.1 - - + -
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Residues in contact with LEU 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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41B LEU* 3.3 34.5 + - + +
43B GLU 4.3 5.8 - - - +
44B VAL* 4.3 10.3 - - + -
45B PRO* 4.1 25.1 - - + -
54B GLN* 2.8 35.7 + - - +
99B ALA* 1.3 70.3 - - - +
101B THR* 1.3 61.8 + - - +
108B VAL* 3.7 8.5 - - + -
109B GLY* 3.3 37.5 - - - +
110B TRP* 3.7 30.8 - - + +
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Residues in contact with THR 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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38B VAL* 3.8 18.3 - - + +
39B GLU 3.0 16.4 - - - +
40B VAL* 4.1 9.2 - - + -
41B LEU* 3.9 7.6 - - - -
99B ALA* 3.3 22.7 - - + +
100B LEU* 1.3 82.5 - - - +
102B ALA* 1.3 59.3 + - - +
108B VAL* 3.3 2.3 - - - +
109B GLY 2.7 35.5 + - - +
111B ARG* 3.0 32.1 + - - +
113B ILE* 4.0 10.5 - - + -
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Residues in contact with ALA 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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38B VAL* 3.4 3.4 - - - +
39B GLU* 2.9 49.9 + - + +
41B LEU* 4.0 13.0 - - + +
101B THR* 1.3 74.1 - - - +
103B ASP* 1.3 66.1 + - - +
106B GLY* 4.3 12.6 - - - +
107B ARG 3.4 7.4 - - - +
108B VAL* 4.2 8.1 - - + +
111B ARG* 3.6 0.9 - - - -
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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
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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