Contacts of the strand formed by residues 735 - 739 (chain E) in PDB entry 1XSK
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 THR 735 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686E THR 3.0 11.2 + - - -
687E ALA* 4.5 14.4 - - + -
688E PHE* 2.9 32.1 + - - +
689E HIS* 6.1 0.4 - - + +
733E ASN 4.3 0.2 + - - -
734E TRP* 1.3 76.3 - - - +
736E LEU* 1.3 70.9 + - - +
737E CYS* 4.1 5.6 - - + +
760E VAL* 3.4 31.7 - - + +
761E VAL 3.8 5.9 + - - -
762E LYS* 4.9 9.4 - - - +
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Residues in contact with LEU 736 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E LEU* 3.6 21.8 - - + -
688E PHE* 3.5 25.4 - - + -
689E HIS 4.6 0.4 - - - +
690E LEU* 4.5 7.9 - - + +
714E LEU* 4.3 9.0 - - + -
725E VAL* 5.2 17.5 - - + -
734E TRP* 4.3 12.3 - - + -
735E THR* 1.3 80.1 - - - +
737E CYS* 1.3 63.2 + - - +
738E LEU* 3.4 31.6 - - + -
759E LEU 3.7 0.9 - - - +
760E VAL* 3.6 0.2 - - - -
761E VAL* 2.7 50.0 + - + +
768E LEU* 5.3 4.3 - - + -
770E ILE* 6.3 1.3 - - + -
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Residues in contact with CYS 737 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688E PHE 2.9 11.5 + - - +
689E HIS* 3.6 23.6 - - + +
690E LEU* 3.1 25.1 + - - -
735E THR* 4.1 4.5 - - + +
736E LEU* 1.3 74.6 - - - +
738E LEU* 1.3 62.6 + - - +
739E ARG* 3.1 29.4 + - - +
755E SER* 4.3 4.7 - - - -
757E GLN* 4.4 3.6 - - - -
758E GLY* 3.8 26.5 - - - -
759E LEU 3.3 4.0 - - - +
760E VAL* 4.3 11.4 - - + +
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Residues in contact with LEU 738 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690E LEU* 4.1 23.1 - - + -
723E ILE* 4.7 7.2 - - + -
736E LEU* 3.4 27.1 - - + -
737E CYS* 1.3 69.2 - - - +
739E ARG* 1.3 65.8 + - - +
741E VAL* 3.0 44.7 + - + +
744E VAL* 5.0 0.7 - - + -
758E GLY* 3.1 13.7 - - - -
759E LEU* 2.6 35.0 + - + +
761E VAL* 4.5 9.4 - - + -
770E ILE* 4.1 28.3 - - + -
772E LEU* 4.6 5.6 - - + -
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Residues in contact with ARG 739 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636E THR* 5.8 0.2 - - - +
637E HIS 3.7 6.7 + - - -
638E LEU* 2.9 32.9 + - - +
641E ASN* 2.8 31.1 + - - +
671E LEU* 5.7 1.2 - - - +
689E HIS* 3.0 39.2 + - + -
690E LEU 3.1 23.2 + - - +
691E PHE* 3.2 40.6 - - + -
692E ASN* 4.5 10.7 + - - +
737E CYS* 3.1 20.5 + - - +
738E LEU* 1.3 69.0 - - - +
740E ASN* 1.3 72.9 + - - +
741E VAL* 3.1 8.4 + - - +
757E GLN* 3.4 28.4 + - - +
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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