Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 3E2A
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 HIS 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B HIS* 4.0 12.8 - - + +
37B TYR* 3.5 32.7 - + + -
38B LEU 3.0 24.3 + - - +
90B ILE* 3.1 7.8 - - - +
91B GLU* 1.3 88.0 + - + +
93B ILE* 1.3 63.0 + - - +
94B ILE* 5.1 1.3 - - + -
173B LYS* 4.2 19.2 + - - -
175B SER* 2.7 29.7 + - - +
177B HIS* 3.3 18.3 + + + +
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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
----------------------------------------------------------
38B LEU* 3.4 35.4 - - + +
40B ILE* 4.0 11.4 - - + -
81B VAL* 4.1 17.3 - - + -
84B ALA* 5.7 0.7 - - + -
85B VAL* 3.9 26.9 - - + -
90B ILE* 5.1 2.7 - - + -
92B HIS* 1.3 76.5 - - - +
94B ILE* 1.3 60.9 + - - +
158B LEU* 3.5 27.9 - - + +
164B VAL* 4.5 0.9 - - + -
174B LEU* 3.8 17.7 - - + -
175B SER 3.0 7.3 + - - -
176B LEU* 3.4 15.7 - - + +
177B HIS* 2.8 32.7 + - - +
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Residues in contact with ILE 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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37B TYR* 3.9 35.2 - - + -
38B LEU 2.8 9.5 + - - +
39B TRP* 3.4 41.9 - - + -
40B ILE* 2.8 32.7 + - - +
60B LEU* 5.1 0.9 - - + -
92B HIS* 5.1 0.7 - - + -
93B ILE* 1.3 75.6 - - - +
95B ILE* 1.3 67.2 + - - +
96B CYS* 4.0 0.6 + - + -
177B HIS* 3.8 13.2 - - + +
179B TRP* 3.7 46.0 - - + -
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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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40B ILE* 3.3 23.3 - - + +
68B ASN* 3.9 28.3 - - - +
70B VAL* 3.7 17.3 - - + -
93B ILE 4.0 0.2 + - - -
94B ILE* 1.3 77.0 - - - +
96B CYS* 1.3 62.4 + - - +
151B VAL* 4.2 10.9 - - + +
154B GLN* 3.5 40.6 - - + +
155B VAL* 3.5 13.2 - - + +
158B LEU* 3.8 18.2 - - + -
177B HIS 2.9 12.7 + - - +
178B GLY* 3.4 1.7 - - - -
179B TRP 3.0 25.6 + - - +
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Residues in contact with CYS 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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39B TRP* 3.5 37.0 - - + +
40B ILE 2.9 9.5 + - - -
41B GLY* 3.5 18.9 - - - -
42B CYS* 4.0 2.9 + - - +
45B SER* 5.1 1.6 + - - -
52B LEU* 4.9 1.3 - - - -
68B ASN* 3.6 10.4 - - - +
94B ILE* 4.0 2.8 + - + -
95B ILE* 1.3 72.8 - - - +
97B GLY* 1.3 78.6 + - - +
179B TRP* 3.3 8.7 - - - -
181B PHE* 3.9 11.4 - - - -
188B LEU* 3.7 29.8 - - - -
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Residues in contact with GLY 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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45B SER* 5.7 0.2 - - - -
68B ASN* 3.3 17.3 - - - -
96B CYS* 1.3 80.7 - - - +
98B HIS* 1.3 64.7 + - - +
147B THR* 4.9 3.1 - - - -
151B VAL* 3.5 22.5 - - - +
179B TRP 2.9 9.5 + - - -
180B VAL* 4.1 5.2 - - - -
181B PHE* 2.9 21.3 + - - +
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Residues in contact with HIS 98 (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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42B CYS* 3.8 14.1 - - + -
44B ASP* 3.6 5.8 - - + -
45B SER* 3.6 22.9 + - - +
97B GLY* 1.3 76.8 - - - +
99B THR* 1.3 75.6 + - - +
100B ASN 4.0 4.0 - - - -
101B CYS* 3.5 19.7 - - + +
147B THR* 3.1 24.1 - - - +
180B VAL* 4.0 3.4 - - - -
181B PHE* 3.2 20.2 - - + +
230B ZN 2.1 36.3 - - - -
232B SO4 2.9 39.8 + - - +
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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