Contacts of the strand formed by residues 88 - 93 (chain B) in PDB entry 3RC0
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 3.8 13.3 + - - -
86B GLY 3.6 2.2 + - - -
87B GLU* 1.3 78.3 - - - +
89B LEU* 1.3 62.0 + - - +
90B PHE 3.9 10.8 - - - +
91B VAL* 3.6 20.9 - - + -
268B ARG* 3.6 40.8 - - + +
269B MET 3.6 16.4 - - - +
270B VAL* 3.9 8.5 - - + +
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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
----------------------------------------------------------
36B LEU* 3.8 0.3 - - - -
37B SER* 2.8 31.0 + - - +
39B LYS* 6.1 0.2 - - + -
64B VAL* 3.6 30.2 - - + +
77B MET* 6.2 0.2 - - - -
83B VAL* 4.0 30.3 - - + -
88B LEU* 1.3 78.9 - - - +
90B PHE* 1.3 74.4 + - + +
250B LEU* 5.5 0.2 - - + -
258B ALA* 3.9 8.1 - - + -
269B MET* 2.8 20.1 + - + +
270B VAL 3.8 6.1 - - - -
271B ALA* 3.6 27.1 - - + +
275B ILE* 4.9 0.9 - - + -
281B ILE* 3.9 29.6 - - + -
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.6 1.6 - - + -
35B GLU 3.1 16.4 - - - +
36B LEU* 3.7 15.9 - - + +
37B SER 4.6 0.2 - - - +
64B VAL* 5.0 0.4 - - + -
77B MET* 3.7 31.4 - - + -
88B LEU* 3.8 4.1 - - - +
89B LEU* 1.3 89.7 - - + +
91B VAL* 1.3 66.3 + - - +
92B VAL* 3.8 19.1 - - + -
246B ALA* 3.7 13.9 - - + -
247B ALA* 3.7 38.1 - - + -
250B LEU* 4.0 5.8 - - + -
260B LEU* 5.4 1.3 - - + -
268B ARG* 3.4 3.3 - - - -
269B MET* 2.9 61.4 + - + +
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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
----------------------------------------------------------
34B LEU* 3.4 9.9 - - - +
35B GLU* 2.9 38.4 + - + +
88B LEU* 3.6 26.5 - - + -
90B PHE* 1.3 80.3 - - - +
92B VAL* 1.3 66.6 + - - +
93B PRO* 3.7 4.6 - - + +
266B CYS* 3.7 31.6 - - + -
267B LEU 3.4 3.1 - - - +
268B ARG* 3.8 18.8 - - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.9 16.8 - - + -
90B PHE* 3.8 23.3 - - + -
91B VAL* 1.3 77.4 - - - +
93B PRO* 1.3 74.5 - - - +
94B ARG 3.5 0.2 + - - -
96B ALA* 4.1 7.9 - - + -
97B LEU* 3.8 20.9 - - + -
244B VAL* 4.3 7.2 - - + -
245B PRO* 3.6 28.7 - - + +
247B ALA* 5.1 0.2 - - + -
260B LEU* 5.9 0.9 - - + -
266B CYS* 4.1 2.2 - - - -
267B LEU* 2.8 49.8 + - + +
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Residues in contact with PRO 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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32B VAL 3.3 26.5 - - - +
33B GLY* 3.4 25.4 - - - +
34B LEU* 3.8 4.5 - - + -
91B VAL* 3.7 7.4 - - + +
92B VAL* 1.3 91.6 - - + +
94B ARG* 1.3 59.8 + - - +
95B ALA* 3.0 11.7 - - + +
96B ALA* 2.8 30.5 + - + +
97B LEU* 3.8 1.0 + - - +
265B ASN 3.8 9.6 - - - +
266B CYS* 4.1 4.5 - - + -
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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
------------------------------------------------------------
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