Contacts of the strand formed by residues 698 - 704 (chain D) 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 GLU 698 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666D ASN* 4.4 7.7 - - - +
693D LEU* 4.3 3.6 - - - -
697D HIS* 1.3 78.2 - - - +
699D ALA* 1.3 64.6 + - - +
700D VAL* 4.0 15.7 - - - +
715D LYS* 3.0 35.3 + - - +
716D ALA 3.5 9.0 - - - +
717D ALA* 3.7 22.3 - - + +
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Residues in contact with ALA 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666D ASN 3.8 16.6 - - - +
667D THR 3.9 1.1 - - - -
668D LEU* 3.6 35.1 - - + +
690D LEU* 3.8 17.9 - - + -
693D LEU* 4.5 3.6 - - + -
698D GLU* 1.3 74.1 - - - +
700D VAL* 1.3 62.0 + - - +
715D LYS* 3.3 3.8 - - - -
716D ALA 3.0 32.9 + - - +
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Residues in contact with VAL 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ASN* 5.7 3.1 + - - -
668D LEU* 3.9 9.9 + - - +
698D GLU* 3.8 20.3 + - - +
699D ALA* 1.3 77.3 - - - +
701D CYS* 1.3 66.7 + - - +
702D GLU* 4.2 13.4 + - + -
713D THR* 3.7 24.7 - - + -
714D LEU 3.5 2.2 - - - +
715D LYS* 3.6 26.0 - - + +
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Residues in contact with CYS 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D LEU* 3.2 39.3 - - + +
669D LEU* 4.7 0.2 - - - -
670D ALA* 3.4 36.6 - - - -
688D PHE* 3.7 14.6 - - + -
700D VAL* 1.3 74.3 - - - +
702D GLU* 1.3 66.2 + - - +
703D VAL* 3.7 5.1 + - - +
712D PHE 3.6 1.7 - - - +
713D THR* 3.4 3.1 - - - -
714D LEU* 2.9 32.9 + - + +
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Residues in contact with GLU 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D PRO 4.6 0.9 - - - +
575D ARG* 3.1 49.3 + - + +
579D ARG* 4.1 10.2 + - - -
700D VAL* 4.2 16.4 + - + -
701D CYS* 1.3 77.4 - - - +
703D VAL* 1.3 63.0 + - - +
704D PRO* 3.3 9.2 - - - +
710D VAL* 3.4 33.6 - - + +
712D PHE 3.6 4.9 - - - -
713D THR* 4.1 10.5 + - + +
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Residues in contact with VAL 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D PRO* 4.7 4.7 - - + -
670D ALA* 4.0 14.1 - - + -
682D TRP* 4.2 10.3 - - + +
683D HIS* 4.0 32.3 - - + +
686D THR* 4.5 2.7 - - + +
688D PHE* 3.6 36.6 - - + -
701D CYS* 4.2 1.6 - - - +
702D GLU* 1.3 72.9 - - - +
704D PRO* 1.3 75.4 - - + +
710D VAL* 3.7 1.2 - - - -
711D ILE* 2.9 27.7 + - - +
712D PHE* 2.8 26.9 + - + +
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Residues in contact with PRO 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D PRO* 3.2 27.4 - - + +
574D TYR* 4.0 15.7 - - + -
575D ARG* 3.7 26.7 - - + +
682D TRP* 3.3 24.9 - - + +
683D HIS* 5.1 2.6 + - - -
702D GLU 3.3 7.9 - - - +
703D VAL* 1.3 98.0 - - + +
705D ALA* 1.3 65.1 + - - +
708D GLY 4.2 11.7 - - - +
709D SER 3.2 11.9 - - - +
710D VAL* 4.3 0.9 - - - -
711D ILE* 3.9 5.1 - - - +
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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