Contacts of the strand formed by residues 625 - 630 (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 ASP 625 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619E VAL* 4.0 3.3 - - - +
620E PHE 4.8 1.4 + - - -
621E THR* 2.9 31.1 + - + +
623E ALA* 3.4 22.9 - - - +
624E GLY* 1.3 77.8 - - - +
626E VAL* 1.3 60.9 + - - +
651E LYS* 4.2 20.6 + - - +
652E GLN 3.6 7.6 - - - +
653E GLN* 3.8 14.9 - - - +
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Residues in contact with VAL 626 (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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617E ALA* 4.1 17.7 - - + +
618E PRO 3.8 21.3 - - - +
619E VAL* 4.3 9.2 - - + -
620E PHE* 5.5 2.9 - - + +
624E GLY 3.9 9.0 - - - +
625E ASP* 1.3 76.0 - - - +
627E GLN* 1.3 75.7 + - - +
628E PHE* 4.1 2.1 - - + -
650E HIS 3.7 0.9 - - - +
651E LYS* 3.7 2.7 - - - +
652E GLN* 3.0 29.9 + - + +
654E HIS* 4.1 10.8 - - + -
660E PRO* 3.7 27.4 - - + -
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Residues in contact with GLN 627 (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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606E ARG* 4.8 13.4 + - - +
607E GLN* 4.9 0.3 - - - +
617E ALA* 5.2 0.7 - - - +
626E VAL* 1.3 85.9 - - - +
628E PHE* 1.3 64.8 + - - +
649E TRP* 3.7 19.2 - - + +
650E HIS 3.2 6.8 + - - +
651E LYS* 4.1 37.0 - - + +
597F ASP 4.4 7.1 + - - +
599F PRO* 3.8 34.2 - - + +
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Residues in contact with PHE 628 (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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607E GLN* 3.5 13.7 - - + +
615E MET* 3.6 27.1 - - + -
617E ALA* 3.9 18.8 - - + -
626E VAL* 4.1 6.1 - - + -
627E GLN* 1.3 78.0 - - - +
629E TYR* 1.3 58.5 + - - +
630E LEU* 4.0 24.2 - - + -
644E LEU* 3.9 2.2 - - + -
649E TRP* 3.3 10.0 - - - -
650E HIS* 2.7 67.4 + - + +
652E GLN* 3.6 38.8 - - + -
660E PRO* 3.7 15.3 - - + -
662E TYR* 3.8 14.1 - + - -
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Residues in contact with TYR 629 (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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591E MET* 5.0 0.2 - - + -
598E ASP* 2.5 34.8 + - - -
600E ALA* 3.5 21.0 - - + +
601E CYS* 3.9 11.0 - - - -
604E LEU* 3.9 29.2 - - + -
607E GLN* 2.9 27.3 + - - +
628E PHE* 1.3 74.1 - - - +
630E LEU* 1.3 95.5 + - - +
631E PRO* 3.5 6.5 - - + +
647E SER* 3.3 19.9 + - - -
648E ARG* 3.3 33.9 - - - -
649E TRP* 3.7 32.1 - + + -
649F TRP* 5.6 2.4 - + - -
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Residues in contact with LEU 630 (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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615E MET* 3.5 33.7 - - + -
628E PHE* 4.0 5.2 - - + -
629E TYR* 1.3 96.4 - - - +
631E PRO* 1.3 62.0 - - + +
635E TRP* 3.6 39.5 - - + +
644E LEU* 3.8 26.2 - - + -
645E ASP 4.7 0.7 - - - +
646E GLY* 4.3 4.3 - - - -
647E SER 2.7 27.5 + - - -
648E ARG 3.0 12.0 + - - +
650E HIS* 3.5 27.1 - - + +
662E TYR* 4.6 2.9 - - + -
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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