Contacts of the strand formed by residues 132 - 137 (chain F) in PDB entry 5B6N
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 ARG 132 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F SER 3.6 4.5 - - - -
40F PRO* 3.8 18.8 - - + +
46F VAL* 3.5 27.7 - - - +
47F CSD 2.8 39.3 + - - -
50F GLU* 2.6 40.4 + - - -
131F ALA* 1.3 68.8 - - - +
133F VAL* 1.3 60.3 + - - +
147F ILE 4.0 0.5 - - - +
148F LEU* 3.8 0.3 - - - -
149F TYR* 2.6 52.6 + - + +
150F PRO* 3.0 23.6 + - - +
151F ALA* 3.8 14.8 - - - +
152F THR 4.2 2.8 - - - +
153F THR 3.1 19.2 + - - -
155F ARG* 3.5 19.9 - - - +
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU 4.7 0.9 - - - +
37F PHE* 3.2 0.7 - - - -
38F SER* 3.0 38.9 + - - +
116F MET* 3.5 43.1 - - + +
131F ALA* 3.8 10.3 - - + +
132F ARG* 1.3 77.2 - - - +
134F VAL* 1.3 65.8 + - - +
135F PHE* 3.8 18.8 - - + -
147F ILE 3.5 11.2 - - - +
148F LEU* 4.0 21.5 - - + -
155F ARG* 2.7 21.3 + - - +
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ILE* 3.6 28.5 - - + -
36F LEU 3.5 3.8 - - - -
37F PHE* 4.0 5.6 - - + -
133F VAL* 1.3 82.1 - - - +
135F PHE* 1.3 76.1 + - - +
136F VAL* 4.5 7.4 - - + +
145F LEU* 3.9 2.2 - - + +
146F SER* 3.7 4.0 - - - -
147F ILE* 3.4 52.2 + - + +
155F ARG* 3.6 17.7 - - - +
157F PHE* 5.6 3.1 - - + -
160F ILE* 4.0 22.7 - - + -
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Residues in contact with PHE 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 4.3 24.2 - - + -
34F GLY 3.3 2.6 - - - +
35F ILE* 3.2 4.4 - - - -
36F LEU* 2.7 63.6 + - + +
114F LEU* 4.1 27.8 - - + -
116F MET* 3.8 27.6 - - + -
133F VAL* 3.8 14.4 - - + -
134F VAL* 1.3 80.6 - - - +
136F VAL* 1.3 61.8 + - - +
137F PHE* 3.5 25.2 - + + -
143F LEU* 3.6 17.5 - - + -
145F LEU 3.9 1.3 - - - -
146F SER* 4.7 13.0 - - - -
147F ILE 6.1 0.2 - - - -
148F LEU* 5.7 6.3 - - + -
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Residues in contact with VAL 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F TRP* 5.3 3.8 - - + -
34F GLY 3.5 2.9 - - - +
35F ILE* 3.6 30.1 - - + -
134F VAL* 4.5 9.6 - - + -
135F PHE* 1.3 73.9 - - - +
137F PHE* 1.3 57.9 + - - +
143F LEU* 3.5 6.6 - - - +
144F LYS* 2.7 42.2 + - + -
145F LEU* 3.2 48.6 + - + +
160F ILE* 5.2 4.3 - - + -
163F VAL* 5.3 3.4 - - + -
164F VAL* 5.0 7.2 - - + -
167F LEU* 3.7 12.1 - - + -
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Residues in contact with PHE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 4.5 10.3 - - + -
9F ASP 4.6 1.1 - - - -
11F ALA* 3.6 29.4 - - + -
12F PRO* 5.4 0.9 - - + -
25F PHE* 3.9 32.5 - + - -
29F LEU* 4.7 10.3 - - + -
33F TRP* 3.3 11.4 - - - -
34F GLY 3.0 41.1 + - - +
36F LEU* 4.1 9.0 - - + -
114F LEU* 6.0 1.1 - - + -
135F PHE* 3.5 33.2 - + + -
136F VAL* 1.3 74.9 - - - +
138F GLY* 1.3 66.7 + - - +
141F LYS 4.6 4.3 - - - -
142F LYS 3.3 6.7 - - - +
143F LEU* 3.5 39.9 - - + -
144F LYS* 4.3 0.4 - - - -
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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