Contacts of the strand formed by residues 710 - 718 (chain B) 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 VAL 710 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B ARG* 3.9 26.0 - - - +
702B GLU* 3.6 28.9 - - + +
703B VAL 3.9 4.0 - - - +
704B PRO* 4.5 1.3 - - - -
708B GLY 5.0 0.7 - - - +
709B SER* 1.3 76.4 + - - +
711B ILE* 1.3 60.0 + - - +
712B PHE 3.4 18.4 - - - +
713B THR* 3.2 27.1 - - - +
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Residues in contact with ILE 711 (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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683B HIS* 3.6 54.3 - - + +
703B VAL 3.0 17.7 + - - +
704B PRO 3.9 14.6 - - - +
705B ALA* 4.0 20.9 - - + -
709B SER* 3.4 1.8 + - - -
710B VAL* 1.3 74.3 - - - +
712B PHE* 1.3 58.8 + - + +
728B ALA 5.1 0.4 - - - -
729B GLY* 3.5 5.9 - - - -
730B GLU* 3.0 42.5 + - + +
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Residues in contact with PHE 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B PHE* 3.8 31.4 - + - -
703B VAL* 2.7 45.8 + - + -
710B VAL* 3.4 6.3 - - - +
711B ILE* 1.3 84.0 - - + +
713B THR* 1.3 66.8 + - - +
714B LEU* 3.9 19.7 - - + -
727B GLY* 3.8 20.0 - - - -
728B ALA 3.8 17.7 - - - -
729B GLY* 3.8 7.2 - - - -
730B GLU 3.5 27.4 - - - +
731B ALA* 3.6 28.3 - - + -
734B TRP* 4.1 14.4 - + - -
766B ASN* 6.0 1.1 - - - -
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Residues in contact with THR 713 (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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700B VAL* 3.6 28.0 - - + -
701B CYS 3.4 2.7 - - - -
702B GLU* 3.9 12.1 + - + +
710B VAL* 3.2 23.2 - - - +
712B PHE* 1.3 75.4 - - - +
714B LEU* 1.3 62.4 + - - +
715B LYS* 3.8 19.9 - - - +
726B THR 3.8 1.4 - - - +
727B GLY* 3.7 1.9 - - - -
728B ALA* 3.1 39.9 + - - +
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Residues in contact with LEU 714 (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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668B LEU* 3.2 27.9 - - + +
688B PHE* 4.4 21.5 - - + -
700B VAL* 3.3 3.6 - - - +
701B CYS 2.8 36.4 + - - +
712B PHE* 3.9 22.0 - - + -
713B THR* 1.3 73.6 - - - +
715B LYS* 1.3 81.2 + - - +
716B ALA* 5.0 0.7 - - + -
725B VAL* 3.4 23.8 - - + -
726B THR 3.3 15.7 - - - +
727B GLY* 3.8 13.2 - - - -
734B TRP* 3.9 20.9 - - + -
736B LEU* 5.5 4.7 - - + -
766B ASN* 5.1 0.2 - - - +
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Residues in contact with LYS 715 (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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698B GLU* 3.3 28.6 + - - +
699B ALA 3.3 6.3 - - - +
700B VAL* 3.8 20.0 - - + -
713B THR* 3.8 22.9 - - + +
714B LEU* 1.3 84.4 - - - +
716B ALA* 1.3 60.0 + - - +
717B ALA* 3.9 0.9 - - + +
724B THR 3.5 2.0 - - - +
725B VAL* 3.2 6.9 - - - +
726B THR* 3.0 46.2 + - - +
728B ALA* 6.4 2.0 - - - -
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Residues in contact with ALA 716 (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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668B LEU* 4.1 9.4 - - + +
690B LEU* 3.8 23.6 - - + -
693B LEU* 2.9 30.1 - - + +
698B GLU* 3.5 0.7 - - - -
699B ALA 2.8 28.8 + - - +
714B LEU* 5.0 0.2 - - + -
715B LYS* 1.3 72.7 - - - +
717B ALA* 1.3 59.3 + - - +
723B ILE* 5.3 2.0 - - + -
724B THR 3.8 4.0 - - - -
725B VAL* 4.4 15.7 - - + +
736B LEU* 6.3 0.9 - - + -
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Residues in contact with ALA 717 (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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693B LEU* 4.3 0.2 - - - -
697B HIS 3.5 5.4 - - - +
698B GLU* 3.9 25.6 - - + +
715B LYS* 3.9 1.3 - - + -
716B ALA* 1.3 73.4 - - - +
718B ARG* 1.3 60.4 + - - +
719B THR 3.9 0.4 + - - -
722B THR 3.6 1.6 - - - +
723B ILE* 3.0 3.1 - - - -
724B THR* 2.7 47.9 + - - +
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Residues in contact with ARG 718 (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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693B LEU* 3.3 37.3 + - + -
694B GLN* 3.7 4.6 - - - +
695B ASP* 3.1 39.0 - - - +
696B GLY* 2.7 32.6 + - - -
697B HIS 3.0 8.8 + - - -
716B ALA 4.0 0.6 + - - -
717B ALA* 1.3 73.2 - - - +
719B THR* 1.3 58.9 + - - +
720B GLY 3.9 11.9 + - - -
721B ASN* 3.8 13.5 + - - +
722B THR 3.6 6.7 - - - +
723B ILE* 3.3 22.9 - - + -
772B LEU* 3.0 34.1 - - - +
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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