Contacts of the strand formed by residues 93 - 99 (chain B) in PDB entry 4GWO
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 GLY 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP 4.2 0.4 + - - -
92B LYS* 1.3 82.6 - - - +
94B SER* 1.3 60.8 + - - -
121B ARG 3.7 3.6 + - - +
122B VAL* 3.2 5.4 - - - +
123B SER* 2.9 24.9 + - - -
281B ARG* 4.4 2.0 - - - -
283B TYR* 3.4 17.7 - - - -
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Residues in contact with SER 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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93B GLY* 1.3 75.1 - - - -
95B LEU* 1.3 60.8 + - - +
96B TYR* 3.5 25.1 - - - -
122B VAL* 4.4 0.4 - - - -
123B SER* 3.3 21.8 - - - +
144B ASP* 3.6 8.9 + - - +
283B TYR* 2.8 22.7 + - - -
284B MET* 3.8 4.7 - - - +
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Residues in contact with LEU 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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94B SER* 1.3 75.5 - - - +
96B TYR* 1.3 61.5 + - - +
97B ILE* 3.7 26.0 + - + -
115B PHE* 3.6 32.8 - - + -
122B VAL* 4.2 9.4 - - + +
123B SER 2.9 8.8 + - - +
124B LEU* 3.6 7.0 - - + +
125B HIS 2.9 27.9 + - - +
144B ASP* 3.4 4.7 - - - +
145B PHE* 3.5 39.0 - - + -
283B TYR* 4.1 9.6 - - + -
284B MET* 4.4 11.2 - - + -
287B PHE* 4.2 14.4 - - + -
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Residues in contact with TYR 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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94B SER* 3.5 30.3 - - - -
95B LEU* 1.3 75.4 - - - +
97B ILE* 1.3 62.3 - - - +
125B HIS* 3.3 51.4 + + + -
142B ASN 3.8 15.3 - - - -
143B ALA* 3.5 19.2 - - + +
144B ASP* 2.6 46.4 + - - +
145B PHE 3.1 8.0 + - - -
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Residues in contact with ILE 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 LEU* 3.8 27.4 - - + -
96B TYR* 1.3 75.6 - - - +
98B ALA* 1.3 69.7 + - - +
99B THR* 4.4 8.7 - - + +
108B LEU* 4.9 2.5 - - + -
112B ILE* 4.0 7.4 - - + -
124B LEU* 3.8 15.5 - - + -
125B HIS 2.8 12.0 + - - +
126B MET* 3.1 18.0 - - + +
127B HIS* 2.8 26.0 + - - +
143B ALA* 4.6 1.3 - - - -
145B PHE* 3.7 10.5 - - + +
147B ILE* 4.2 20.9 - - + -
287B PHE* 3.4 37.5 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR 4.0 0.4 + - - -
97B ILE* 1.3 75.4 - - - +
99B THR* 1.3 60.5 + - - +
127B HIS* 3.2 14.8 - - + +
134B ILE* 3.3 32.2 - - + +
137B ALA* 4.4 5.8 - - + -
143B ALA* 3.8 22.0 - - + -
145B PHE 2.9 11.7 + - - +
146B ALA* 3.3 2.6 - - - -
147B ILE 3.1 22.3 + - - -
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Residues in contact with THR 99 (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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222A PHE* 5.6 1.6 - - + -
97B ILE* 4.4 4.3 - - + +
98B ALA* 1.3 75.7 - - - +
100B THR* 1.3 71.5 + - - +
103B GLN* 3.1 16.6 - - - +
104B ALA* 4.1 10.5 - - + -
108B LEU* 3.9 23.8 - - + -
126B MET* 4.4 12.8 - - + -
127B HIS 2.8 12.6 + - - +
128B GLN* 3.2 6.4 - - - -
129B GLY 2.9 25.3 + - - -
134B ILE* 3.2 10.5 - - - +
147B ILE* 2.6 27.5 + - - +
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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