Contacts of the strand formed by residues 132 - 137 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C SER 4.0 0.2 - - - -
40C PRO* 3.8 12.1 - - + +
46C VAL* 3.5 26.1 - - - +
47C CSD 2.4 43.2 + - - -
50C GLU* 3.4 21.4 + - - -
131C ALA* 1.3 69.3 - - - +
133C VAL* 1.3 61.7 + - - +
147C ILE 3.5 3.8 - - - +
149C TYR* 2.8 43.1 + - + +
150C PRO 3.0 17.9 + - - +
151C ALA* 2.4 29.4 + - - +
152C THR* 4.6 0.6 - - - +
153C THR 3.1 24.6 + - - -
154C GLY* 3.8 0.4 - - - -
155C ARG* 3.4 29.6 - - - +
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 4.6 0.7 - - - +
37C PHE* 3.2 1.6 - - - -
38C SER* 3.0 34.2 + - - +
116C MET* 4.1 27.8 - - + +
131C ALA* 4.2 13.9 - - + -
132C ARG* 1.3 72.8 - - - +
134C VAL* 1.3 66.3 + - - +
135C PHE* 3.9 36.6 - - + -
147C ILE 3.2 11.0 - - - +
148C LEU* 3.6 27.6 - - + -
155C ARG* 2.7 20.1 + - - -
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.8 26.0 - - + -
36C LEU 3.6 2.5 - - - -
37C PHE* 4.1 5.2 - - + -
133C VAL* 1.3 74.7 - - - +
135C PHE* 1.3 63.7 + - - +
136C VAL* 3.7 8.3 + - + +
145C LEU* 3.6 2.4 - - + +
146C SER* 3.2 24.4 - - - -
147C ILE* 3.1 26.2 + - + +
155C ARG* 3.1 42.8 - - - +
160C ILE* 3.9 26.0 - - + -
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.9 37.0 - - + -
34C GLY 3.5 2.6 - - - +
35C ILE* 3.6 1.0 - - - -
36C LEU* 2.6 57.5 + - + +
114C LEU* 3.9 24.9 - - + -
115C GLY 4.7 7.0 - - - -
116C MET* 4.0 18.4 - - + -
133C VAL* 3.9 17.0 - - + -
134C VAL* 1.3 71.5 - - - +
136C VAL* 1.3 62.9 + - - +
137C PHE* 3.6 23.3 + + + -
143C LEU* 3.7 11.0 - - + -
145C LEU 3.8 0.2 - - - -
146C SER* 3.5 32.3 - - - -
148C LEU* 5.5 1.8 - - + -
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TRP* 4.1 19.7 - - + -
34C GLY 3.6 5.2 - - - +
35C ILE* 4.1 23.1 - - + -
134C VAL* 4.7 11.0 - - + +
135C PHE* 1.3 71.3 - - - +
137C PHE* 1.3 63.1 + - - +
143C LEU* 3.4 5.9 - - - +
144C LYS* 3.0 27.3 + - + -
145C LEU* 2.9 35.1 + - + +
160C ILE* 5.3 2.9 - - + -
163C VAL* 5.4 2.9 - - + -
164C VAL* 4.3 14.8 - - + -
167C LEU* 4.1 21.3 - - + -
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Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.8 18.2 - - + -
11C ALA* 3.7 27.1 - - + -
25C PHE* 4.0 24.0 - + - -
29C LEU* 4.8 7.6 - - + -
33C TRP* 3.3 15.8 - - - +
34C GLY* 2.8 39.0 + - - +
36C LEU* 3.9 18.8 - - + -
114C LEU* 4.9 2.5 - - + -
135C PHE* 3.6 34.8 - + + -
136C VAL* 1.3 75.2 - - - +
138C GLY* 1.3 65.9 + - - +
141C LYS 4.6 1.8 - - - -
142C LYS 3.4 8.3 - - - +
143C LEU* 3.6 35.7 - - + -
144C LYS* 5.0 0.2 - - - -
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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