Contacts of the strand formed by residues 91 - 97 (chain B) in PDB entry 4BHT
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 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLU* 2.6 27.9 + - - +
59B ARG* 3.4 26.3 + - - -
81B ARG* 4.5 0.2 - - - -
83B GLN* 3.5 57.2 - - + -
85B SER 3.4 29.8 - - - -
86B SER* 3.5 10.3 + - - -
89B GLY 3.6 1.2 + - - -
90B PRO* 1.3 70.9 - - - +
92B LYS* 1.3 58.1 + - - +
126B GLY 3.5 13.5 - - - +
127B GLY* 4.5 2.2 - - - -
162B THR* 2.9 34.5 + - + -
163B ASP* 3.1 16.3 - - - +
164B VAL* 3.0 26.9 + - - +
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Residues in contact with LYS 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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81B ARG* 4.0 1.1 - - - +
90B PRO* 3.3 10.6 + - + +
91B TYR* 1.3 75.0 - - - +
93B GLY* 1.3 60.4 + - - +
113B GLN* 3.7 1.6 - - - +
117B ASN* 3.0 30.7 + - - +
124B MET* 3.7 35.0 - - + -
125B GLY 3.7 8.0 + - - +
127B GLY 3.0 20.3 + - - +
164B VAL* 3.1 35.8 + - + +
165B PRO 3.7 4.8 + - - -
166B ALA* 4.0 7.3 - - - +
195B THR* 2.9 40.5 + - - +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 2.9 27.1 + - - +
92B LYS* 1.3 82.4 - - - +
94B GLY* 1.3 61.7 + - - -
113B GLN* 4.1 12.3 - - - -
127B GLY 3.4 13.2 - - - -
164B VAL 3.8 3.8 + - - -
165B PRO* 3.3 9.9 - - - +
166B ALA* 4.2 5.8 - - - -
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Residues in contact with GLY 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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81B ARG* 3.1 4.3 + - - -
93B GLY* 1.3 71.9 - - - -
95B MET* 1.3 61.4 + - - -
113B GLN* 5.4 0.6 - - - +
128B LYS* 3.7 24.5 - - - +
129B GLY 3.0 24.3 + - - +
166B ALA* 3.4 11.3 - - - +
167B GLY 3.4 20.2 - - - -
168B ASP* 4.6 0.2 - - - -
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Residues in contact with MET 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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63B PHE* 5.7 0.9 - - + -
80B TRP 4.0 7.9 - - - +
81B ARG* 3.5 27.8 - - - -
94B GLY* 1.3 73.9 - - - -
96B ARG* 1.3 62.0 + - - +
97B PHE* 4.6 5.2 - - + -
129B GLY* 3.2 14.1 - - - -
130B GLY* 3.8 17.7 - - - +
150B LEU* 4.0 20.4 - - + -
154B LEU* 3.8 25.8 - - + -
165B PRO* 4.0 14.4 - - + -
166B ALA 2.8 17.9 + - - +
167B GLY 4.0 0.2 + - - -
168B ASP* 3.2 14.9 - - - +
171B VAL* 3.2 28.0 - - + +
179B MET* 4.4 17.9 - - + -
194B PHE* 5.0 0.4 - - + -
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Residues in contact with ARG 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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95B MET* 1.3 73.5 - - - +
97B PHE* 1.3 63.5 + - - +
98B HIS* 4.3 7.6 - - + -
101B VAL* 3.5 27.1 - - + +
105B ILE* 4.4 10.8 - - - +
106B LEU* 4.8 5.4 - - + -
108B PHE* 6.0 1.2 - - - -
109B LEU* 3.5 38.6 - - - +
128B LYS* 5.2 3.1 - - - +
129B GLY 2.8 13.9 + - - +
130B GLY* 3.0 3.4 - - - -
131B SER 2.9 25.1 + - - +
168B ASP* 2.8 32.3 + - + +
169B ILE* 3.3 39.1 - - + +
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Residues in contact with PHE 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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95B MET* 4.6 8.3 - - + -
96B ARG* 1.3 77.9 - - - +
98B HIS* 1.3 65.4 + - - +
130B GLY* 4.6 5.2 - - - -
131B SER* 3.5 17.3 - - - -
133B PHE* 3.4 30.3 - + + +
135B PRO* 3.6 17.4 - - + +
143B VAL* 5.6 0.4 - - + -
146B PHE* 3.5 29.4 - + - -
147B CYS* 3.9 18.2 - - - -
150B LEU* 4.0 16.8 - - + -
169B ILE* 2.9 10.2 + - - +
170B GLY* 3.4 27.8 + - - +
171B VAL* 3.6 23.5 - - + +
175B GLU* 4.4 5.8 - - + -
179B MET* 4.2 17.0 - - - -
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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