Contacts of the strand formed by residues 90 - 95 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU 3.3 4.5 + - - +
89A ASP* 1.3 73.2 - - - +
91A VAL* 1.3 61.6 + - - +
113A ASN* 3.3 18.9 - - - +
115A HIS* 2.8 31.6 + - + +
137A VAL* 4.4 11.8 - - + +
138A LYS 4.6 3.2 - - - +
139A PRO* 3.6 18.3 - - + +
140A LYS* 3.1 25.0 + - - +
141A ILE 3.4 5.9 + - - -
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Residues in contact with VAL 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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81A LEU* 5.6 0.9 - - + -
85A ILE* 4.0 8.1 - - + -
89A ASP* 4.0 4.0 - - + +
90A ASP* 1.3 79.9 - - - +
92A LEU* 1.3 57.9 + - - +
93A ILE* 3.7 26.0 + - + -
107A ALA* 4.2 8.5 - - + -
112A ALA* 3.5 29.8 - - + -
113A ASN 3.1 7.0 + - - +
114A VAL* 3.5 5.2 - - - +
115A HIS* 2.8 34.7 + - - +
141A ILE* 3.3 43.1 - - + +
143A ALA* 4.4 5.2 - - + -
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Residues in contact with LEU 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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91A VAL* 1.3 69.5 - - - +
93A ILE* 1.3 69.6 + - - +
94A PRO* 3.8 3.9 - - + +
115A HIS* 3.3 29.6 - - + +
116A MET 4.9 0.4 - - - -
117A LEU* 4.3 17.9 - - + -
130A ILE* 4.2 13.2 - - + +
133A GLU* 4.0 23.6 - - + +
134A ILE* 3.6 41.3 - - + +
137A VAL* 5.0 4.9 - - + -
139A PRO* 4.0 16.2 - - + +
141A ILE 2.9 10.7 + - - +
142A VAL* 3.4 9.2 - - + +
143A ALA 3.0 24.8 + - - +
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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 VAL* 3.7 25.1 - - + +
92A LEU* 1.3 81.2 - - - +
94A PRO* 1.3 65.0 - - - +
95A ILE* 3.4 21.9 + - + +
100A GLY* 3.8 11.4 - - - +
103A LEU* 3.8 19.7 - - + +
104A THR* 3.5 39.3 - - + +
107A ALA* 4.2 4.0 - - + -
114A VAL* 3.8 11.4 - - + -
115A HIS 2.8 9.9 + - - +
116A MET* 3.4 4.3 - - - -
117A LEU 3.2 18.7 + - - +
143A ALA* 3.4 19.3 - - + +
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Residues in contact with PRO 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 LEU* 3.8 8.5 - - + +
93A ILE* 1.3 86.9 - - - +
95A ILE* 1.3 59.1 + - - +
96A TYR* 4.1 7.1 + - - -
100A GLY* 5.2 1.7 - - - -
117A LEU* 3.6 16.6 - - + +
125A PHE* 3.6 20.0 - - + -
130A ILE* 3.7 41.7 - - + -
142A VAL* 4.6 5.2 - - + -
143A ALA 3.4 13.5 - - - +
144A MET* 3.8 28.6 - - + +
145A VAL* 5.1 1.0 + - - +
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Residues in contact with ILE 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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93A ILE* 3.7 7.2 - - + +
94A PRO* 1.3 73.9 - - - +
96A TYR* 1.3 62.7 + - - +
97A GLY 3.5 22.2 - - - +
100A GLY* 3.6 21.3 - - - +
101A TYR* 3.5 37.2 - - + +
104A THR* 3.2 29.8 - - + -
116A MET* 3.6 30.1 - - + -
117A LEU 2.8 12.0 + - - +
118A GLU* 3.4 5.7 - - + +
119A CYS 3.2 24.8 + - - +
121A TRP* 5.1 1.3 + - - +
125A PHE* 3.6 2.3 - - - -
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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