Contacts of the strand formed by residues 745 - 748 (chain J) in PDB entry 6PSS
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 GLY 745 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690J ASN* 4.1 16.4 - - - -
743J MET* 3.6 14.9 - - - +
744J ARG* 1.3 80.7 - - - +
746J LEU* 1.3 62.1 + - - -
747J MET* 3.7 4.1 + - - +
758J PRO* 3.5 4.4 - - - +
759J ILE* 2.7 39.0 + - - +
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Residues in contact with LEU 746 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683J ILE* 3.5 52.5 - - + +
686J TRP* 3.8 17.7 - - + +
687J ALA* 3.9 17.3 - - + +
690J ASN* 5.1 2.4 - - + +
745J GLY* 1.3 73.2 - - - -
747J MET* 1.3 64.7 + - - +
754J ILE* 3.7 12.3 - - + -
755J ILE 3.9 8.5 - - - +
756J GLU 4.1 6.7 - - - +
758J PRO* 3.7 20.9 - - + -
16N THR* 4.0 14.4 - - - +
20N ILE* 3.8 28.7 - - + +
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Residues in contact with MET 747 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739J GLN* 4.6 2.2 - - - +
744J ARG* 3.8 65.7 - - + +
745J GLY 3.7 5.3 + - - +
746J LEU* 1.3 77.7 - - - +
748J ALA* 1.3 63.9 + - - +
754J ILE* 3.8 2.5 - - - -
755J ILE* 2.8 32.4 + - + +
757J THR 5.5 0.4 + - - -
758J PRO* 5.2 1.4 - - - +
759J ILE* 3.7 26.9 - - + -
774J ILE* 3.8 26.0 - - + +
775J SER* 4.2 12.3 - - - +
778J GLY* 6.1 2.7 - - - +
12N THR* 6.0 4.0 - - - -
13N GLU* 5.9 2.9 - - - +
16N THR* 4.6 8.3 - - - -
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Residues in contact with ALA 748 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747J MET* 1.3 80.5 - - - +
749J LYS* 1.3 75.2 + - - +
753J SER 3.4 11.4 - - - +
754J ILE* 4.0 11.2 - - + -
755J ILE* 3.4 9.5 - - - +
774J ILE 4.8 0.3 - - - +
777J HIS* 4.2 6.1 - - - +
778J GLY* 4.5 15.5 + - - +
12N THR 5.3 0.2 - - - +
15N LEU* 4.3 21.8 - - + -
16N THR* 3.7 25.2 - - + +
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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