Contacts of the strand formed by residues 86 - 93 (chain B) in PDB entry 5ANC
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B ASN* 2.7 49.3 + - - +
80B THR* 3.5 13.5 + - - +
81B GLY* 3.5 15.0 - - - -
85B GLY* 1.3 71.6 - - - -
87B GLU* 1.3 60.4 + - - +
88B TYR* 4.9 2.2 - + + -
145B THR* 3.4 2.1 - - - +
146B GLY 2.8 36.2 + - - +
147B ASN 3.3 19.7 - - - -
149B LEU* 3.3 49.8 - - + -
152B LEU* 3.3 17.0 - - + +
183B ASN* 5.1 10.8 - - - -
184B VAL 3.8 4.3 - - - -
185B LEU* 3.6 20.9 - - + -
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 3.7 10.3 - - - +
86B TYR* 1.3 77.0 - - - +
88B TYR* 1.3 69.1 + - - +
89B LYS* 3.9 17.4 + - - -
133B TYR* 3.7 20.1 + - - -
143B VAL* 4.9 3.6 - - + +
144B LEU 3.8 3.4 - - - -
145B THR* 4.0 20.1 + - + +
181B GLU 3.7 2.8 - - - +
182B ARG* 4.1 0.3 - - - -
184B VAL* 2.8 52.0 + - + +
185B LEU 3.7 2.4 - - - -
186B GLU* 3.0 42.5 + - + +
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 4.9 2.0 - - + -
87B GLU* 1.3 78.0 - - - +
89B LYS* 1.3 62.0 + - - +
90B MET* 3.5 5.2 + - + +
143B VAL* 3.6 0.4 - - - -
144B LEU* 2.8 43.9 + - - +
149B LEU* 4.0 13.2 - - + +
152B LEU* 3.4 18.4 - - + -
153B SER* 2.7 42.2 + - - -
156B CYS* 3.5 36.3 - - + -
179B VAL* 4.0 12.1 - - + -
181B GLU 3.8 3.4 - - - -
182B ARG* 3.3 40.5 - - + +
183B ASN* 3.9 13.6 + - - -
3446N C 5.5 0.7 - - - -
3447N U 3.2 16.6 + - - -
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Residues in contact with LYS 89 (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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87B GLU* 3.9 19.3 + - + -
88B TYR* 1.3 70.5 - - - +
90B MET* 1.3 63.4 + - - +
133B TYR* 5.0 5.6 - - - -
141B GLU* 5.0 13.9 - - + +
142B ILE 3.7 7.6 - - - +
143B VAL* 3.5 26.7 - - + -
179B VAL* 4.1 1.1 - - - -
180B SER* 3.2 8.2 + - - -
181B GLU* 3.2 62.3 + - + +
184B VAL* 4.1 23.0 - - + +
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Residues in contact with MET 90 (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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88B TYR 3.5 4.2 + - - +
89B LYS* 1.3 76.4 - - - +
91B ARG* 1.3 69.2 + - - +
141B GLU* 3.3 4.0 - - - +
142B ILE* 2.8 36.3 + - + +
144B LEU* 3.6 29.2 - - + -
156B CYS* 3.1 35.4 - - + +
159B ILE* 4.1 10.1 - - + -
160B GLN* 4.1 12.6 - - + +
177B ILE* 3.6 34.8 - - + -
178B TYR 3.5 7.2 - - - +
179B VAL* 3.5 29.8 - - + +
180B SER 4.6 0.2 - - - -
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Residues in contact with ARG 91 (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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89B LYS* 5.5 0.4 - - + -
90B MET* 1.3 78.8 - - - +
92B PHE* 1.3 66.7 + - - +
137B LYS* 5.2 14.3 - - - +
140B ASP* 4.4 21.1 + - - +
141B GLU* 3.8 34.4 + - + +
142B ILE 4.7 0.2 - - - +
177B ILE* 4.5 0.2 - - - -
178B TYR* 2.8 37.5 + - - +
180B SER* 3.5 27.5 + - - +
1H ILE* 3.7 35.2 - - - +
4H SER* 6.0 2.2 - - - -
5H LEU* 3.6 26.8 - - + +
8H LEU* 4.9 1.2 - - + +
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Residues in contact with PHE 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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91B ARG* 1.3 74.9 - - - +
93B VAL* 1.3 66.2 + - - +
99B ILE* 3.9 33.0 - - + -
101B VAL* 4.3 19.1 - - + -
134B ARG* 4.1 13.9 - - - -
136B GLU* 3.2 28.7 - - - -
139B LYS* 4.0 10.4 - - + +
140B ASP* 3.5 28.0 - - - +
141B GLU 3.7 10.5 - - - +
142B ILE* 3.5 28.7 - - + -
176B GLY 3.2 14.8 - - - +
177B ILE* 4.0 24.5 - - + -
5H LEU* 3.4 15.3 - - - +
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Residues in contact with VAL 93 (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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92B PHE* 1.3 80.5 - - - +
94B TYR* 1.3 63.4 + - - +
99B ILE* 3.7 4.6 - - - +
174B LEU 3.5 20.6 - - - +
175B ASP* 2.6 34.0 - - - +
176B GLY 3.0 5.9 + - - -
178B TYR* 3.6 27.6 - - + -
2H GLU* 4.1 22.4 - - + +
5H LEU* 3.8 26.5 - - + +
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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