Contacts of the strand formed by residues 690 - 694 (chain A) in PDB entry 4A0L
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 SER 690 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A HIS* 4.2 14.8 + - - -
681A PRO* 3.8 5.7 - - - +
682A LEU 2.8 30.8 + - - +
687A TYR* 3.5 23.4 + - - +
688A PRO* 3.9 0.9 - - - +
689A ASP* 1.3 79.6 + - - +
691A LEU* 1.3 76.5 + - - +
701A ILE* 4.1 16.8 - - - -
702A GLY* 3.7 13.5 - - - -
703A THR* 4.7 2.9 + - - +
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Residues in contact with LEU 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE* 5.7 3.4 - - + -
641A PHE* 4.4 19.7 - - + -
642A ARG 5.6 2.7 - - - +
650A PHE* 4.6 9.0 - - + -
679A MET* 4.1 24.2 - - + -
680A CYS 3.7 6.3 - - - +
681A PRO* 4.4 1.6 - - + -
682A LEU* 4.1 2.2 - - - +
689A ASP 5.0 0.9 - - - +
690A SER* 1.3 88.8 - - - +
692A ALA* 1.3 60.9 + - - +
693A LEU* 4.1 20.0 - - + +
700A THR 4.2 0.2 - - - +
701A ILE* 3.0 21.5 - - - +
702A GLY 2.9 21.6 + - - +
703A THR 5.3 1.1 - - - +
704A ILE* 3.4 50.3 - - + +
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A LEU* 3.7 7.2 - - + +
425A LEU* 4.7 15.3 - - + -
679A MET* 3.2 4.2 - - - -
680A CYS* 2.9 48.0 + - - +
682A LEU* 4.3 12.3 - - + -
691A LEU* 1.3 74.2 - - - +
693A LEU* 1.3 67.8 + - - +
699A LEU* 4.9 4.5 - - + -
700A THR 3.7 4.9 - - - +
701A ILE* 4.3 8.5 - - + +
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE* 4.9 15.3 - - + -
410A LEU* 4.8 0.2 - - - -
650A PHE* 4.5 11.4 - - + -
673A LEU* 4.2 25.1 - - + -
676A VAL* 4.2 17.0 - - + -
678A TYR 3.7 3.8 - - - +
679A MET* 3.2 26.2 - - + -
691A LEU* 4.1 16.2 - - + +
692A ALA* 1.3 89.8 - - - +
694A ALA* 1.3 61.8 + - - +
695A ASN 4.3 0.2 - - - -
698A THR 3.8 1.3 - - - +
699A LEU* 3.2 6.2 - - - +
700A THR* 2.8 53.6 + - + +
701A ILE 6.3 0.2 - - - -
702A GLY 6.2 0.4 - - - +
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Residues in contact with ALA 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ILE* 3.5 51.4 - - + +
410A LEU* 3.7 8.3 - - + +
676A VAL* 4.9 2.2 - - - -
677A ASN* 3.1 23.6 + - - +
678A TYR 3.1 20.1 + - - +
693A LEU* 1.3 76.8 - - - +
695A ASN* 1.3 61.5 + - - +
698A THR 3.6 4.3 - - - +
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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