Contacts of the strand formed by residues 125 - 128 (chain R) in PDB entry 6QX2
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 GLU 125 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R TYR* 3.6 33.1 - - + +
65R LYS* 3.2 9.6 - - - +
66R LYS* 3.6 32.2 + - - +
67R SER* 3.8 3.1 - - - -
107R GLN* 2.8 35.3 + - + +
110R PHE* 3.5 6.9 - - - -
124R THR* 1.3 77.1 - - - +
126R ALA* 1.3 62.7 + - - +
150T TYR* 4.9 7.1 + - - -
585U GLU* 2.8 34.7 - - - +
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Residues in contact with ALA 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R LEU* 5.5 0.7 - - + -
58R MET* 4.8 1.6 - - - +
64R TYR* 4.0 4.6 - - - -
65R LYS* 2.9 27.9 + - - +
67R SER* 4.3 0.7 - - - +
70R ILE* 3.8 24.9 - - + +
90R MET* 3.9 23.6 - - + -
104R VAL* 4.0 13.5 - - + -
105R ASP 3.2 11.7 - - - +
110R PHE* 4.5 3.1 - - + -
125R GLU* 1.3 75.6 - - - +
127R ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R LEU* 4.4 10.9 - - - +
58R MET* 4.0 19.5 - - + +
59R THR 3.9 9.4 - - - +
60R PRO* 3.3 17.7 + - - +
61R ASP 4.8 1.2 + - - -
62R LYS 2.9 28.2 + - - +
63R SER* 3.9 12.0 - - - +
64R TYR* 3.2 46.7 + - + +
104R VAL* 3.5 8.3 - - - +
105R ASP* 2.7 56.9 + - - +
126R ALA* 1.3 76.0 - - - +
128R MET* 1.3 63.3 + - - +
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Residues in contact with MET 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R LEU* 3.7 14.6 - - + +
54R ASN* 3.2 50.3 - - + +
58R MET 3.2 21.7 + - - +
59R THR* 3.9 13.9 - - + -
60R PRO* 3.6 20.1 - - + +
103R LEU 4.1 5.6 - - - -
105R ASP* 3.6 4.3 - - - +
127R ARG* 1.3 90.5 - - - +
129R THR* 1.3 69.1 + - - +
132R THR* 3.8 15.3 - - + -
133R LEU* 3.6 23.8 - - - -
136R LEU* 3.7 16.2 - - + -
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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