Contacts of the strand formed by residues 132 - 137 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ALA* 5.4 0.4 - - - +
38B SER 3.3 1.3 - - - +
40B PRO* 3.9 15.7 - - + +
46B VAL* 3.4 26.6 - - - +
47B CSD 2.3 35.9 + - - -
50B GLU* 2.6 40.9 + - - +
131B ALA* 1.3 78.2 - - - +
133B VAL* 1.3 56.4 + - - +
147B ILE 3.9 1.4 - - - +
148B LEU* 4.8 0.2 - - - -
149B TYR* 2.8 43.1 + - + +
150B PRO 2.9 23.2 + - - +
151B ALA* 2.3 27.2 + - - +
152B THR 4.8 0.4 - - - -
153B THR 3.3 13.8 + - - -
154B GLY* 4.6 0.2 - - - -
155B ARG* 3.1 27.0 + - - +
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Residues in contact with VAL 133 (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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36B LEU 4.5 2.2 - - - +
37B PHE* 3.1 1.9 - - - -
38B SER* 3.0 42.6 + - - +
114B LEU 5.6 0.4 - - - +
116B MET* 3.6 31.6 - - + -
131B ALA 5.2 0.7 - - - -
132B ARG* 1.3 75.6 - - - +
134B VAL* 1.3 64.1 + - - +
135B PHE* 3.9 33.0 - - + -
146B SER* 5.3 0.4 - - - -
147B ILE 3.1 18.4 - - - +
148B LEU* 4.0 24.5 - - + +
155B ARG* 3.1 8.0 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.6 28.5 - - + -
36B LEU 3.5 2.5 - - - -
37B PHE* 3.7 11.4 - - + -
133B VAL* 1.3 80.5 - - - +
135B PHE* 1.3 66.3 + - - +
136B VAL* 4.6 9.7 - - + +
145B LEU* 3.9 2.4 - - + +
146B SER* 3.1 26.5 - - - -
147B ILE* 3.1 35.9 + - + -
155B ARG* 3.7 12.8 - - - +
160B ILE* 3.9 26.7 - - + -
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Residues in contact with PHE 135 (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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5B LEU* 4.2 22.2 - - + -
34B GLY 3.5 1.4 - - - +
35B ILE* 3.4 7.3 - - - +
36B LEU* 2.8 50.7 + - + +
114B LEU* 3.7 44.4 - - + -
116B MET* 3.9 11.9 - - - -
133B VAL* 3.9 20.2 - - + -
134B VAL* 1.3 75.5 - - - +
136B VAL* 1.3 61.6 + - - +
137B PHE* 3.5 30.9 - + + -
143B LEU* 3.7 9.4 - - + -
145B LEU 3.8 0.2 - - - -
146B SER* 3.6 26.7 - - - -
148B LEU* 6.1 1.8 - - + -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 4.4 9.2 - - + -
34B GLY 3.6 5.6 - - - +
35B ILE* 4.8 12.1 - - + -
134B VAL* 4.6 11.2 - - + -
135B PHE* 1.3 76.7 - - - +
137B PHE* 1.3 63.2 + - - +
143B LEU* 3.6 2.1 - - - +
144B LYS* 2.6 36.2 + - + -
145B LEU* 2.9 45.0 + - + +
160B ILE* 5.6 2.7 - - + -
163B VAL* 5.2 5.4 - - + -
164B VAL* 4.9 12.6 - - + -
167B LEU* 3.8 23.6 - - + -
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Residues in contact with PHE 137 (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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5B LEU* 4.1 13.7 - - + -
11B ALA* 3.6 26.9 - - + -
25B PHE* 3.9 31.2 - + + -
29B LEU* 5.7 4.7 - - + -
33B TRP* 3.3 12.4 - - - -
34B GLY* 2.9 42.7 + - - +
36B LEU* 4.1 10.3 - - + -
114B LEU* 5.5 3.1 - - + -
135B PHE* 3.5 37.0 - + + -
136B VAL* 1.3 74.6 - - - +
138B GLY* 1.3 63.8 + - - +
141B LYS* 4.2 7.0 - - + -
142B LYS 3.2 17.5 - - - +
143B LEU* 3.6 24.9 - - + -
144B LYS* 4.1 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
------------------------------------------------------------
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