Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 3RLG
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A TRP* 3.8 17.3 - - + +
10A MET* 4.2 13.0 - - + -
29A ASN 3.5 2.8 + - - -
30A SER* 3.0 30.3 - - - -
31A ILE 3.1 3.6 + - - -
85A LEU* 3.8 2.4 - - - +
86A VAL* 1.4 79.1 - - - +
88A VAL* 1.3 74.5 + - - +
89A VAL* 3.7 28.0 - - + +
127A ALA* 4.0 0.6 - - - +
128A TYR* 3.3 14.8 - - + +
130A VAL* 4.1 15.5 - - + -
193A TRP* 3.7 19.7 - - + -
279A PRO* 3.7 35.2 - - + -
280A TRP* 4.5 0.4 - - + -
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Residues in contact with VAL 88 (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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31A ILE* 3.3 22.0 - - + +
33A THR* 4.4 4.7 - - - +
70A LEU* 3.7 33.9 - - + -
85A LEU* 4.8 3.6 - - + -
87A LEU* 1.3 80.8 - - - +
89A VAL* 1.3 72.3 + - - +
90A PHE* 3.8 34.5 + - + -
127A ALA* 4.3 9.4 - - + -
128A TYR 2.9 5.1 + - - -
129A ILE* 3.3 19.1 - - + +
130A VAL* 2.9 23.6 + - - +
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Residues in contact with VAL 89 (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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10A MET* 3.4 33.4 - - + -
31A ILE 2.8 10.2 + - - +
32A GLU* 3.2 17.4 - - + -
33A THR* 2.9 26.9 + - - +
87A LEU* 3.7 12.1 - - + -
88A VAL* 1.3 76.1 - - - +
90A PHE* 1.3 63.0 + - - +
91A ASP* 3.7 1.5 + - + +
130A VAL* 3.4 19.1 - - + +
132A SER* 3.6 27.8 - - - -
193A TRP* 5.1 1.3 - - + -
228A TYR* 3.7 18.2 - - + +
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Residues in contact with PHE 90 (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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33A THR* 3.4 21.5 - - + -
35A VAL* 3.6 18.6 - - + -
63A PHE* 3.9 17.3 - + - -
66A PHE* 4.6 2.9 - + - -
67A LEU* 3.6 23.6 - - + -
70A LEU* 3.9 10.8 - - + -
88A VAL* 3.8 22.9 - - + -
89A VAL* 1.3 71.7 - - - +
91A ASP* 1.3 59.9 + - - +
92A LEU* 3.3 23.8 + - + +
109A LEU* 6.0 0.9 - - + -
113A LEU* 3.8 19.5 - - + -
129A ILE* 3.5 36.1 - - + -
130A VAL 2.9 11.0 + - - +
131A LEU* 4.3 8.7 - - + -
132A SER* 2.9 29.5 + - - -
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Residues in contact with ASP 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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32A GLU* 3.2 20.8 - - + +
33A THR 2.8 9.7 + - - +
34A ASP* 3.1 10.2 - - - +
35A VAL 2.9 23.5 + - - -
89A VAL* 3.7 2.4 + - + -
90A PHE* 1.3 67.6 - - - +
92A LEU* 1.4 65.9 + - - +
93A LYS* 3.1 26.3 + - - +
132A SER* 3.9 13.4 + - - +
134A PRO* 4.9 4.5 - - - +
166A SER* 4.6 11.3 + - - -
286A MG 2.3 25.5 - - - -
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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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35A VAL* 4.0 12.8 - - + -
37A PHE* 4.0 3.8 - - + -
90A PHE* 3.7 27.1 - - + +
91A ASP* 1.4 68.4 - - - +
93A LYS* 1.3 58.4 + - - +
94A THR* 2.8 25.0 + - + -
109A LEU* 3.6 43.3 - - + -
131A LEU* 4.1 20.2 - - + -
132A SER 3.0 20.0 + - - +
133A ILE* 4.2 5.2 - - + -
134A PRO* 2.9 23.5 - - + +
141A LEU* 3.9 22.2 - - + -
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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