Contacts of the strand formed by residues 91 - 94 (chain B) in PDB entry 1ESQ
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 VAL 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.1 18.8 - - + +
64B LEU* 3.8 21.3 - - + -
84B ALA* 3.5 22.0 - - + -
85B ASN* 4.1 6.7 - - - +
89B VAL 3.4 15.7 - - - +
90B PRO* 1.3 72.9 - - - +
92B ILE* 1.3 71.2 + - - +
115B VAL* 4.0 8.3 - - + -
116B ARG 4.0 20.8 + - - +
117B LEU* 3.7 20.2 - - + -
118B ALA* 2.9 29.0 + - - +
119B ALA 3.6 0.3 + - - -
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Residues in contact with ILE 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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61B ALA* 5.2 0.2 - - + -
62B LEU 2.7 16.3 + - - +
63B VAL* 3.2 11.0 - - + +
64B LEU* 2.7 34.8 + - - +
90B PRO* 4.6 3.1 - - + +
91B VAL* 1.3 92.3 - - - +
93B LEU* 1.3 61.6 + - - +
117B LEU* 4.7 0.4 - - - -
118B ALA* 4.2 9.2 - - + -
119B ALA* 3.6 17.5 - - + +
120B ILE 4.9 0.2 - - - +
121B ARG* 5.1 3.6 - - + +
201B THR* 3.8 19.3 - - + +
204B VAL* 3.9 17.9 - - + -
205B GLY* 3.7 22.9 - - - -
208B CYS* 3.7 33.0 - - + -
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Residues in contact with LEU 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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64B LEU* 3.4 21.3 - - + +
66B ILE* 5.0 4.7 - - + -
92B ILE* 1.3 74.9 - - - +
94B ASP* 1.3 73.3 + - - +
95B PRO* 3.4 20.0 - - + +
108B ALA* 4.2 11.2 - - + +
111B ILE* 4.3 21.1 - - + -
112B ILE* 4.0 28.5 - - + -
117B LEU* 4.0 24.4 - - + +
119B ALA 3.1 10.2 + - - +
120B ILE* 3.3 16.9 - - + -
121B ARG* 3.0 25.3 + - - +
130B THR* 5.6 0.2 - - + -
201B THR* 4.5 3.3 - - - +
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Residues in contact with ASP 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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64B LEU 2.8 13.6 + - - +
65B ASN* 3.2 29.1 + - - +
66B ILE* 3.5 19.9 + - - +
93B LEU* 1.3 75.4 - - - +
95B PRO* 1.3 60.6 - - - +
96B VAL* 2.8 22.9 + - - +
121B ARG* 2.8 30.3 + - - +
126B GLU* 4.7 3.8 - - - +
197B GLY 3.7 2.8 - - - +
198B SER* 3.7 2.1 + - - -
201B THR* 2.7 33.5 + - + +
305B ATP 4.9 0.5 + - - -
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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