Contacts of the strand formed by residues 91 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLU* 2.6 27.6 + - - +
59A ARG* 3.4 30.6 + - - -
83A GLN* 3.4 46.0 - - + -
85A SER 3.3 35.0 - - - -
86A SER* 3.4 12.0 + - - -
89A GLY 3.7 0.8 + - - -
90A PRO* 1.3 72.3 - - - +
92A LYS* 1.3 59.7 + - - +
126A GLY 3.4 21.5 - - - +
127A GLY* 4.5 2.2 - - - -
162A THR* 2.9 33.8 + - + -
163A ASP* 3.1 18.9 - - - +
164A VAL* 2.9 28.1 + - - +
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Residues in contact with LYS 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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81A ARG* 4.1 1.1 - - - +
90A PRO* 3.1 7.3 + - + +
91A TYR* 1.3 75.3 - - - +
93A GLY* 1.3 60.7 + - - +
113A GLN* 3.4 2.9 - - - +
117A ASN* 3.1 31.9 + - - +
124A MET* 3.8 20.6 - - + -
125A GLY 3.7 6.6 + - - +
127A GLY 2.9 21.3 + - - +
164A VAL* 2.8 34.2 + - + +
165A PRO 3.5 9.3 + - - -
166A ALA* 4.0 4.8 - - - +
195A THR* 2.9 26.5 + - - -
377A VAL* 4.7 3.6 - - + +
380A SER* 3.4 21.2 + - - +
384A MET* 3.5 35.2 - - + -
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Residues in contact with GLY 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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81A ARG* 3.0 24.3 + - - +
92A LYS* 1.3 82.3 - - - +
94A GLY* 1.3 62.1 + - - -
113A GLN* 3.9 13.7 - - - -
127A GLY 3.2 13.0 - - - -
164A VAL 3.8 2.8 + - - -
165A PRO* 3.1 12.7 - - - +
166A ALA* 4.1 5.2 - - - -
377A VAL* 6.0 1.1 - - - -
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Residues in contact with GLY 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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81A ARG* 3.3 0.2 + - - -
93A GLY* 1.3 76.6 - - - +
95A MET* 1.3 61.4 + - - -
113A GLN* 5.3 0.8 - - - +
128A LYS* 3.5 25.8 - - - +
129A GLY 3.1 23.2 + - - +
166A ALA* 3.4 12.2 - - - +
167A GLY 3.3 21.3 - - - -
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Residues in contact with MET 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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63A PHE* 5.6 1.1 - - + -
80A TRP 3.8 8.7 - - - +
81A ARG* 3.7 18.6 - - - -
94A GLY* 1.3 73.0 - - - -
96A ARG* 1.3 60.3 + - - +
97A PHE* 4.6 4.0 - - + -
129A GLY* 3.2 22.2 - - - -
130A GLY* 3.5 22.7 - - - +
150A LEU* 4.0 20.6 - - + -
154A LEU* 3.7 26.5 - - + -
165A PRO* 3.9 13.2 - - + -
166A ALA 2.8 17.1 + - - +
168A ASP* 3.1 15.3 + - - +
171A VAL* 3.2 29.5 - - + +
179A MET* 4.3 19.1 - - + -
194A PHE* 4.9 0.9 - - + -
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Residues in contact with ARG 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 MET* 1.3 73.6 - - - +
97A PHE* 1.3 62.3 + - - +
98A HIS* 4.3 7.2 - - + -
100A SER* 6.0 0.4 + - - -
101A VAL* 3.7 27.0 - - + +
105A ILE* 4.3 11.6 - - - +
106A LEU* 4.8 4.7 - - + -
108A PHE* 6.0 1.0 - - - -
109A LEU* 3.4 39.9 - - - +
128A LYS* 5.0 2.8 - - - +
129A GLY 2.8 13.8 + - - +
130A GLY* 2.9 22.0 - - - -
131A SER 2.9 6.8 + - - +
168A ASP* 2.7 33.1 + - + +
169A ILE* 3.2 42.2 - - + +
324A GLN* 6.2 0.4 - - - +
348A ASN* 4.4 10.3 - - - +
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Residues in contact with PHE 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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95A MET* 4.6 6.1 - - + -
96A ARG* 1.3 78.6 - - - +
98A HIS* 1.3 65.4 + - - +
130A GLY* 4.4 4.7 - - - -
131A SER* 3.5 17.0 - - - -
133A PHE* 3.4 32.3 - + + +
135A PRO* 3.5 18.6 - - + +
143A VAL* 5.4 0.4 - - + -
146A PHE* 3.6 25.4 - + - -
147A CYS* 4.1 16.8 - - - -
150A LEU* 4.0 22.2 - - + -
169A ILE* 3.0 7.4 + - - +
170A GLY* 3.5 30.9 + - - +
171A VAL* 3.6 18.7 - - + +
175A GLU* 4.4 7.4 - - + -
179A MET* 4.4 15.7 - - - -
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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