Contacts of the strand formed by residues 87 - 95 (chain A) in PDB entry 3RBQ
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 ASP 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LYS 3.5 4.0 + - - +
86A ILE* 1.3 75.9 - - - +
88A PHE* 1.3 63.7 + - - +
89A VAL* 3.3 9.8 + - - +
107A LYS* 2.7 42.0 + - - -
149A PHE* 3.0 3.8 - - - -
150A THR* 2.8 48.1 + - - +
505G SER* 3.4 10.3 + - - -
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Residues in contact with PHE 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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86A ILE* 4.5 3.6 - - + -
87A ASP* 1.3 71.6 - - - +
89A VAL* 1.3 58.6 + - - +
90A ARG 3.6 2.0 - - - +
107A LYS* 3.8 5.2 - - - -
147A VAL* 3.3 33.2 - - + -
148A GLU 3.4 3.4 - - - +
149A PHE* 3.7 19.7 - + + -
159A PHE* 4.2 10.3 - + - -
179A PHE* 4.3 12.8 - + - -
220A TYR* 3.3 44.6 - + - -
228A MET* 3.7 26.2 - - + -
230A ASN* 4.6 0.9 - - - -
502G ALA* 3.7 21.8 - - + +
505G SER* 3.3 34.1 + - - +
506G ALA* 3.2 20.6 + - + -
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Residues in contact with VAL 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 ASP* 3.3 27.5 + - - +
88A PHE* 1.3 76.5 - - - +
90A ARG* 1.3 63.4 + - + +
106A LYS* 3.4 2.1 - - - +
107A LYS* 2.9 50.8 + - + +
148A GLU* 2.8 31.1 + - + +
149A PHE* 4.4 2.9 - - - +
150A THR* 4.5 13.2 - - + -
187A LYS* 4.4 20.6 - - + -
506G ALA* 4.0 5.2 - - - -
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Residues in contact with ARG 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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88A PHE* 3.6 1.8 - - - +
89A VAL* 1.3 83.4 + - + +
91A PHE* 1.3 68.4 + - - +
92A LYS* 3.7 29.4 - - - +
104A GLU* 2.9 28.1 + - - +
105A ILE 3.4 14.4 - - - +
106A LYS* 3.2 28.4 - - + +
146A THR* 4.0 19.4 - - + +
147A VAL* 3.4 6.2 - - - +
148A GLU* 2.7 79.6 + - + +
506G ALA* 4.0 3.6 - - - -
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Residues in contact with PHE 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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90A ARG* 1.3 75.6 - - - +
92A LYS* 1.3 61.6 + - - +
93A ILE* 3.8 26.2 - - + -
103A PHE* 3.9 13.5 - + - -
104A GLU* 3.4 2.8 - - - +
105A ILE* 3.0 34.8 + - + +
131A TYR* 3.4 20.2 - + - -
145A ALA* 3.8 19.5 - - + -
146A THR 3.4 7.2 - - - -
147A VAL* 4.4 9.6 - - + -
192A HIS* 5.7 1.6 - - - -
194A TYR* 4.8 3.6 - - - -
500G DAO 3.7 28.9 - - + -
502G ALA* 3.5 30.1 - - + +
503G GLY* 3.7 28.5 - - - -
506G ALA* 3.9 4.4 - - + +
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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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90A ARG* 3.7 22.7 - - - +
91A PHE* 1.3 75.0 - - - +
93A ILE* 1.3 70.8 + - - +
94A ARG* 4.8 10.6 - - + +
101A VAL* 4.1 26.0 - - + +
103A PHE 3.2 11.2 - - - +
104A GLU* 3.7 30.0 + - + +
144A GLY 3.6 0.9 - - - +
145A ALA* 3.2 4.7 - - - +
146A THR* 2.8 58.9 + - - +
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Residues in contact with ILE 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 PHE* 3.8 19.7 - - + -
92A LYS* 1.3 79.3 - - - +
94A ARG* 1.3 55.2 + - - +
101A VAL* 3.6 4.0 - - - +
102A LEU* 2.8 35.2 + - + -
103A PHE* 2.8 31.7 + - + +
131A TYR* 5.2 0.7 - - + -
133A PHE* 3.6 32.1 - - + -
137A PHE* 4.5 7.6 - - + -
143A VAL* 3.8 18.6 - - + -
144A GLY 3.4 1.3 - - - -
145A ALA* 3.7 22.0 - - + -
194A TYR* 5.1 0.2 - - + -
500G DAO 3.9 22.2 - - + -
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Residues in contact with ARG 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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92A LYS* 4.2 13.0 - - + +
93A ILE* 1.3 76.2 - - - +
95A ASP* 1.3 63.4 + - - +
96A MET* 3.6 37.4 + - - +
99A GLY* 3.1 35.9 + - - +
100A THR 3.3 13.0 - - - +
101A VAL* 4.5 7.6 - - + -
102A LEU* 4.1 4.5 - - - +
143A VAL* 3.5 1.3 - - - -
144A GLY* 2.8 39.1 + - - +
191A GLU* 5.2 4.9 - - - +
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Residues in contact with ASP 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 ARG* 1.3 69.4 + - - +
96A MET* 1.3 59.9 + - - +
97A ASP* 2.9 23.5 + - - +
98A SER* 2.8 29.6 + - - +
99A GLY* 2.9 27.2 + - - -
100A THR* 2.9 14.6 + - - +
102A LEU* 3.8 21.3 - - + +
140A LEU* 3.5 31.4 - - + +
141A ARG 5.4 0.3 + - - -
142A GLN 3.8 9.7 + - - +
143A VAL* 4.3 1.3 - - - -
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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