Contacts of the strand formed by residues 134 - 137 (chain B) in PDB entry 1RQF
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 LYS 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.7 19.3 - - + +
121B PRO* 3.5 5.0 - - - +
122B ILE* 2.9 37.3 + - + +
124B LEU* 3.8 32.1 - - + -
131B ALA* 5.5 1.1 - - - -
132B MET* 3.6 21.6 - - - +
133B VAL* 1.3 84.9 + - - +
135B LEU* 1.3 66.9 + - - +
143B VAL* 3.4 21.3 - - + -
144B TYR 3.5 5.8 - - - +
145B THR* 3.0 31.8 + - - +
146B PRO* 4.3 1.5 - - - +
41J GLU* 4.6 7.1 + - - -
46J TYR* 5.1 7.1 + - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 4.0 18.4 - - + -
106B PHE* 3.4 35.0 - - + +
107B GLY* 5.3 0.4 - - - -
119B MET* 3.6 33.0 - - + -
120B LEU 3.5 9.0 - - - +
121B PRO* 4.0 8.7 - - + -
122B ILE* 4.2 2.7 - - - -
134B LYS* 1.3 83.2 - - - +
136B TYR* 1.3 60.3 + - - +
142B ASP 3.7 0.7 - - - +
143B VAL* 3.3 3.3 - - - -
144B TYR* 2.7 45.5 + - + +
145B THR 4.8 1.1 - - - +
146B PRO* 3.8 35.2 - - + -
147B LYS 5.1 0.7 - - - +
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Residues in contact with TYR 136 (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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119B MET* 3.3 4.2 - - - +
120B LEU* 2.8 40.2 + - + +
122B ILE* 3.9 26.6 - - + +
135B LEU* 1.3 72.1 - - - +
137B CYS* 1.3 63.8 + - - +
138B PRO* 3.4 26.9 + - + +
141B MET* 3.6 42.4 - - + +
142B ASP 3.5 12.3 - - - -
143B VAL* 4.3 11.2 - - + +
164B PRO* 3.8 25.4 - - + -
165B HIS* 3.8 25.7 - + - -
168B PHE* 4.4 8.3 - + - -
175B ARG* 4.4 5.2 + - - -
141D MET* 5.1 4.4 - - + +
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Residues in contact with CYS 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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109B CYS* 3.5 21.5 - - + -
114B CYS* 3.4 6.7 - - - -
117B GLN* 3.6 12.8 - - - -
119B MET* 3.8 10.0 - - + +
135B LEU 4.0 1.6 + - - -
136B TYR* 1.3 72.9 - - - +
138B PRO* 1.3 60.9 - - - +
139B LYS 3.3 16.2 - - - -
140B CYS* 3.5 5.2 - - - -
141B MET* 2.8 32.2 + - - -
142B ASP 3.1 7.1 + - - -
144B TYR* 4.3 3.1 - - + -
179B ZN 2.1 37.2 - - - -
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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