Contacts of the strand formed by residues 625 - 630 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A VAL* 3.9 3.6 - - - +
620A PHE 4.7 1.2 + - - -
621A THR* 2.7 35.7 + - + +
623A ALA* 3.4 22.9 - - - +
624A GLY* 1.3 78.4 - - - +
626A VAL* 1.3 59.7 + - - +
651A LYS* 4.4 21.2 - - - -
652A GLN 3.4 7.6 - - - +
653A GLN* 3.5 24.2 - - - +
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Residues in contact with VAL 626 (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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617A ALA* 4.1 17.3 - - + +
618A PRO 3.6 23.6 - - - +
619A VAL* 4.0 11.7 - - + -
620A PHE* 5.3 2.5 - - + +
624A GLY 4.2 2.0 - - - +
625A ASP* 1.3 76.4 - - - +
627A GLN* 1.3 74.3 + - - +
628A PHE* 4.0 2.8 - - + -
650A HIS 4.0 0.7 - - - +
651A LYS* 3.6 2.7 - - - +
652A GLN 2.9 36.0 + - - +
654A HIS* 4.1 10.3 - - + -
660A PRO* 3.7 29.4 - - + -
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Residues in contact with GLN 627 (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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606A ARG* 4.6 19.0 + - - +
607A GLN* 5.0 0.5 - - - +
617A ALA* 5.3 0.7 - - - +
626A VAL* 1.3 82.0 - - - +
628A PHE* 1.3 62.6 + - - +
649A TRP* 3.7 20.0 - - + -
650A HIS 3.3 6.2 + - - +
651A LYS* 3.7 39.6 - - + +
597D ASP 4.5 4.7 + - - +
599D PRO* 3.6 35.4 - - + +
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Residues in contact with PHE 628 (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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607A GLN* 3.5 12.1 - - + +
615A MET* 3.3 27.8 - - + -
617A ALA* 3.8 12.6 - - + -
626A VAL* 4.0 9.6 - - + -
627A GLN* 1.3 80.0 - - - +
629A TYR* 1.3 61.0 + - - +
630A LEU* 4.1 11.9 - - + -
644A LEU* 3.8 20.0 - - + -
649A TRP* 3.4 10.5 - - - -
650A HIS* 2.9 49.7 + - + +
652A GLN* 3.5 35.9 - - + -
660A PRO* 3.4 26.0 - - + -
662A TYR* 3.9 13.5 - + - -
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Residues in contact with TYR 629 (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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591A MET* 4.9 0.4 - - + -
598A ASP* 2.6 27.7 + - - -
600A ALA* 3.6 20.8 - - + +
601A CYS* 3.9 8.3 - - - -
604A LEU* 3.8 29.4 - - + -
607A GLN* 2.7 31.3 + - - +
615A MET* 3.8 0.2 - - - +
628A PHE* 1.3 74.8 - - - +
630A LEU* 1.3 84.8 + - - +
631A PRO* 3.4 15.5 - - + +
647A SER* 3.2 19.5 + - - -
648A ARG* 3.2 35.2 - - - -
649A TRP* 3.7 32.2 - + + +
649D TRP* 5.7 2.4 - + - -
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Residues in contact with LEU 630 (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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615A MET* 3.5 38.4 - - + -
628A PHE* 4.1 4.7 - - + -
629A TYR* 1.3 78.9 - - - +
631A PRO* 1.3 57.5 - - + +
635A TRP* 3.6 41.1 - - + -
644A LEU* 3.7 29.4 - - + +
645A ASP 4.8 0.2 - - - +
646A GLY* 4.0 9.0 - - - -
647A SER* 2.4 27.4 + - - -
648A ARG 2.9 22.0 + - - +
650A HIS* 3.5 24.0 - - + +
662A TYR* 4.6 6.1 - - + -
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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