Contacts of the strand formed by residues 87 - 97 (chain A) in PDB entry 3B3T
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 ALA 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 1.3 73.4 - - - +
88A PRO* 1.3 61.3 - - - +
89A ASP 3.1 3.4 - - - -
90A GLU* 3.0 56.1 + - + +
140A LYS 2.8 12.5 + - - +
141A ARG* 3.5 7.5 - - + -
290A THR* 3.8 20.2 - - + -
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 3.9 13.2 - - + -
84A GLY 3.4 24.2 - - - +
85A SER 4.8 0.7 - - - -
86A GLU* 3.3 10.3 - - - +
87A ALA* 1.3 88.7 - - - +
89A ASP* 1.3 68.8 + - - +
90A GLU 3.3 0.9 - - - -
91A TRP* 3.6 8.7 + - - -
142A SER* 2.7 32.1 + - - +
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 3.1 1.4 + - - -
88A PRO* 1.3 86.7 - - - +
90A GLU* 1.3 62.4 + - + +
91A TRP* 3.7 14.4 + - - +
171A ASN* 3.5 22.0 + - - +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.0 26.0 + - + +
89A ASP* 1.3 82.3 - - + +
91A TRP* 1.3 60.2 + - - +
141A ARG* 2.8 31.9 + - - +
142A SER* 3.0 27.7 + - - +
171A ASN* 3.7 20.0 - - - +
173A VAL* 4.1 5.8 - - + -
290A THR* 3.6 2.8 - - - -
291A GLY* 2.8 40.0 + - - -
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Residues in contact with TRP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 3.9 26.7 - - + -
82A ILE 5.1 1.6 - - - -
83A THR* 5.6 2.5 - - + -
88A PRO 3.6 10.5 + - - -
89A ASP* 3.7 17.8 + - - +
90A GLU* 1.3 73.7 - - - +
92A ILE* 1.3 63.4 - - - +
93A VAL* 4.9 2.5 - - + -
142A SER* 3.4 37.0 - - - -
143A ILE 3.7 17.9 - - - -
144A ALA* 4.0 18.4 - - + -
165A TYR* 4.7 9.6 - + + -
170A LYS* 3.5 40.9 - - + +
171A ASN 2.8 19.5 + - - +
172A VAL* 3.5 16.6 - - + +
173A VAL* 2.8 32.5 + - - +
174A SER 3.9 1.4 + - - -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 1.3 79.2 - - - +
93A VAL* 1.3 59.1 + - - +
94A ILE* 6.0 0.2 - - + -
141A ARG* 3.7 22.0 - - - -
142A SER 2.9 15.4 + - - +
143A ILE* 3.2 18.9 - - + +
144A ALA 2.8 26.2 + - - -
173A VAL* 3.9 10.1 - - + -
174A SER* 3.9 12.1 - - - +
282A TYR* 3.4 34.3 - - + +
283A ALA* 4.9 4.7 - - - -
286A MET* 3.7 41.5 - - + +
287A GLY* 4.0 6.7 - - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 4.9 3.1 - - + -
92A ILE* 1.3 77.0 - - - +
94A ILE* 1.3 67.2 + - - +
144A ALA* 3.3 20.4 - - + +
146A MET* 4.2 9.4 - - + -
148A TYR* 3.8 22.4 - - - +
165A TYR* 4.9 2.7 - - + -
172A VAL* 4.0 23.8 - - + -
174A SER 3.0 13.2 + - - +
175A ALA* 3.9 15.5 - - + -
176A LEU 2.9 14.0 + - - +
233A TRP* 4.1 20.4 - - + -
282A TYR* 2.7 25.7 + - - -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 1.3 79.1 - - - +
95A GLY* 1.3 61.9 + - - +
125A VAL* 4.2 14.7 - - + +
128A VAL* 4.5 14.6 - - + -
143A ILE* 4.7 5.6 - - + -
144A ALA 2.9 5.9 + - - +
145A PHE* 3.2 35.9 - - + -
146A MET* 2.9 22.3 + - - +
176A LEU* 3.4 32.3 - - + +
178A LEU* 4.3 12.8 - - + -
279A GLY* 4.0 24.2 - - - +
282A TYR* 4.2 9.0 - - + -
283A ALA* 5.6 2.7 - - + -
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 1.3 79.4 - - - +
96A GLY* 1.3 57.6 + - - -
125A VAL* 4.2 12.6 - - - -
146A MET 3.0 15.0 - - - -
148A TYR* 3.9 10.0 + - - -
176A LEU 2.9 8.1 + - - -
177A GLN* 3.2 10.6 - - - +
178A LEU* 2.9 27.2 + - - +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY* 1.3 75.1 - - - -
97A HIS* 1.3 62.1 + - - -
118A ASN* 3.8 2.5 - - - -
121A GLY 5.5 0.2 - - - -
122A ILE* 3.4 7.5 - - - +
125A VAL* 4.6 3.3 - - - +
146A MET 3.0 3.6 + - - -
147A ALA* 3.2 9.4 - - - -
148A TYR* 3.0 25.8 + - - -
177A GLN* 3.6 11.4 - - - -
178A LEU 3.4 18.2 - - - -
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY* 1.3 73.0 - - - -
98A LEU* 1.3 59.2 + - - +
99A ASP* 2.9 32.5 + - - +
117A ASP* 3.0 6.7 + - - -
118A ASN* 3.2 34.3 + - + +
122A ILE* 3.5 7.3 - - - +
148A TYR 3.4 9.6 - - - +
151A GLU* 3.2 37.9 - - + -
152A GLU* 3.3 22.7 - - - -
179A ASP* 3.0 25.0 + - - -
229A ASP* 3.3 11.5 + - - +
293A ZN 2.1 31.2 - - - -
299A ILE* 3.2 1.6 + - - -
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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