Contacts of the strand formed by residues 88 - 92 (chain B) in PDB entry 3E7O
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 LEU 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.7 3.4 - - + -
77B LEU* 3.9 37.0 + - + +
78B LYS* 3.8 30.3 - - + -
86B ILE 3.8 3.4 + - - -
87B SER* 1.3 72.8 - - - +
89B LEU* 1.3 64.1 + - - +
90B ASN 3.5 24.7 - - - +
91B VAL* 4.6 13.5 - - + -
106B LEU* 4.0 29.4 - - + -
107B VAL 3.6 7.4 - - - +
108B MET* 4.1 8.9 - - + +
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Residues in contact with LEU 89 (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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48B LEU* 4.8 13.0 - - + -
50B ILE* 4.6 11.0 - - + -
52B VAL* 3.7 31.0 - - + -
87B SER* 4.6 13.5 - - - +
88B LEU* 1.3 79.3 - - - +
90B ASN* 1.3 61.2 + - + +
107B VAL* 2.6 20.2 + - + +
108B MET 3.9 2.2 - - - -
109B GLU* 3.8 30.7 - - + +
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Residues in contact with ASN 90 (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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23B LEU* 3.9 23.2 - - - +
25B ARG* 4.1 13.6 - - - +
26B TYR* 2.9 30.2 + - - +
88B LEU* 3.5 9.3 - - - +
89B LEU* 1.3 80.5 - - + +
91B VAL* 1.3 76.8 + - - +
92B PHE* 4.2 2.6 - - - +
107B VAL* 2.7 39.3 + - + +
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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
----------------------------------------------------------
74B LEU* 3.8 31.9 - - + -
78B LYS* 5.0 6.5 - - + -
88B LEU* 4.6 11.0 - - + -
90B ASN* 1.3 86.3 + - - +
92B PHE* 1.3 66.6 + - - +
104B VAL* 4.2 3.6 - - + -
105B TYR 3.4 14.1 - - - +
106B LEU* 4.2 6.7 - - + -
359B GLU 4.6 7.9 - - - +
360B VAL* 4.0 38.7 - - + +
362B ASP 5.7 2.5 - - - +
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Residues in contact with PHE 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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10B PHE* 3.8 17.3 - + + -
21B THR 3.9 2.2 - - - -
22B VAL* 3.7 40.6 - - + -
23B LEU* 3.7 28.5 - - + -
26B TYR* 3.6 22.9 - + - -
54B VAL* 4.9 1.6 - - + -
90B ASN* 4.2 4.0 - - - +
91B VAL* 1.3 77.2 - - - +
93B THR* 1.3 65.8 + - - +
104B VAL* 4.0 2.1 - - - +
105B TYR* 3.0 64.3 + + + +
107B VAL* 3.7 21.1 - - + -
360B VAL* 3.7 11.9 - - - +
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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