Contacts of the strand formed by residues 90 - 95 (chain B) in PDB entry 3ISL
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B GLU 3.4 4.0 + - - +
89B ASP* 1.3 70.9 - - - +
91B VAL* 1.3 62.0 + - - +
113B ASN* 3.3 17.4 - - - +
115B HIS* 2.9 29.7 - - + +
137B VAL* 4.2 13.7 - - + +
138B LYS 4.5 3.0 - - - +
139B PRO* 3.7 18.7 - - + +
140B LYS* 3.0 29.9 + - - +
141B ILE 3.4 4.7 + - - -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 5.2 0.7 - - + -
85B ILE* 3.9 20.6 - - + -
89B ASP* 3.9 3.6 - - + +
90B ASP* 1.3 77.1 - - - +
92B LEU* 1.3 62.6 + - - +
93B ILE* 3.7 27.9 + - + +
107B ALA* 4.3 8.3 - - + -
112B ALA* 3.5 29.6 - - + -
113B ASN 2.9 10.4 + - - +
114B VAL* 3.5 4.6 - - + -
115B HIS* 2.8 28.3 + - - +
141B ILE* 3.3 32.3 - - + -
143B ALA* 4.4 4.7 - - + -
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Residues in contact with LEU 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 VAL* 1.3 72.6 - - - +
93B ILE* 1.3 61.3 + - - +
94B PRO* 3.9 9.0 - - + +
115B HIS* 3.3 30.1 - - + +
116B MET* 5.0 0.4 - - - -
117B LEU* 4.4 12.3 - - + -
130B ILE* 4.1 11.4 - - + +
133B GLU* 3.8 26.0 - - + +
134B ILE* 3.6 46.2 - - + +
137B VAL* 4.8 2.0 - - + -
139B PRO* 3.9 15.9 - - + +
141B ILE 2.8 11.6 + - - +
142B VAL* 3.2 7.5 - - + -
143B ALA 3.0 24.9 + - - +
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Residues in contact with ILE 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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81B LEU* 6.3 0.2 - - + -
91B VAL* 3.8 27.6 - - + +
92B LEU* 1.3 81.2 - - - +
94B PRO* 1.3 65.9 - - - +
95B ILE* 3.5 7.3 + - + +
100B GLY* 3.8 11.4 - - - +
103B LEU* 3.7 37.9 - - + +
104B THR* 3.7 31.6 - - + -
107B ALA* 4.0 5.2 - - + -
114B VAL* 4.2 6.3 - - + -
115B HIS 2.8 12.0 + - - +
116B MET* 3.4 8.0 - - - +
117B LEU 3.3 18.3 + - - -
143B ALA* 3.4 17.9 - - + +
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Residues in contact with PRO 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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92B LEU* 3.9 7.0 - - + +
93B ILE* 1.3 85.6 - - - +
95B ILE* 1.3 60.1 + - - +
96B TYR* 3.9 12.8 + - - -
100B GLY* 5.1 2.6 - - - -
117B LEU* 3.7 14.1 - - + +
125B PHE* 3.8 12.1 - - + -
130B ILE* 3.7 48.5 - - + -
142B VAL* 4.6 5.4 - - + -
143B ALA 3.3 15.9 - - - +
144B MET* 4.0 24.6 - - + +
145B VAL* 5.3 1.4 + - - +
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Residues in contact with ILE 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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93B ILE* 3.6 9.9 - - + +
94B PRO* 1.3 75.9 - - - +
96B TYR* 1.3 60.1 + - - +
97B GLY 3.3 26.9 - - - +
100B GLY* 3.8 20.2 - - - +
101B TYR* 3.5 42.6 - - + +
104B THR* 3.4 28.7 - - + -
116B MET* 3.9 18.8 - - + -
117B LEU 2.8 13.0 + - - +
118B GLU* 3.2 9.2 - - + +
119B CYS 3.1 24.1 + - - +
121B TRP* 5.1 1.4 + - - +
125B PHE* 3.5 3.1 - - - -
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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