Contacts of the strand formed by residues 625 - 630 (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 ASP 625 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B VAL* 3.9 4.9 - - - +
620B PHE 4.7 1.7 + - - -
621B THR* 3.0 27.6 + - + +
623B ALA* 3.7 19.5 - - - +
624B GLY* 1.3 78.9 - - - +
626B VAL* 1.3 61.8 + - - +
651B LYS* 3.7 24.6 + - - +
652B GLN 3.6 8.6 - - - +
653B GLN* 3.9 17.5 - - - +
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Residues in contact with VAL 626 (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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617B ALA* 4.1 18.8 - - + +
618B PRO 3.6 24.2 - - - +
619B VAL* 4.2 8.7 - - + -
620B PHE* 5.4 1.6 - - + +
624B GLY 4.4 0.9 - - - +
625B ASP* 1.3 77.7 - - - +
627B GLN* 1.3 71.5 + - - +
628B PHE* 4.1 2.6 - - + -
650B HIS 3.7 1.0 - - - +
651B LYS* 3.5 3.1 - - - +
652B GLN* 3.0 36.0 + - + +
654B HIS* 4.0 11.9 - - + -
660B PRO* 3.6 29.4 - - + -
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Residues in contact with GLN 627 (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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606B ARG* 4.8 14.4 + - - +
607B GLN* 4.9 0.2 - - - +
617B ALA* 5.5 0.3 - - - +
626B VAL* 1.3 78.3 - - - +
628B PHE* 1.3 61.7 + - - +
649B TRP* 3.6 20.5 - - + +
650B HIS 3.1 6.6 + - - +
651B LYS* 3.5 48.3 - - + +
597C ASP 4.8 4.3 + - - +
599C PRO* 4.1 32.1 - - + +
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Residues in contact with PHE 628 (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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607B GLN* 3.3 14.8 - - + +
615B MET* 3.6 16.6 - - + -
617B ALA* 3.7 20.6 - - + -
626B VAL* 4.1 5.8 - - + -
627B GLN* 1.3 77.8 - - - +
629B TYR* 1.3 58.0 + - - +
630B LEU* 3.8 22.9 - - + -
644B LEU* 3.9 5.4 - - + -
649B TRP* 3.4 8.1 - - - -
650B HIS* 2.7 59.3 + + + +
652B GLN* 3.4 40.4 - - + -
660B PRO* 3.5 16.2 - - + -
662B TYR* 3.6 20.2 - + - -
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Residues in contact with TYR 629 (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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598B ASP* 2.7 30.6 + - - -
600B ALA* 3.6 20.5 - - + +
601B CYS* 3.9 11.2 - - - -
604B LEU* 3.8 22.0 - - + -
607B GLN* 2.8 36.0 + - - +
628B PHE* 1.3 75.0 - - - +
630B LEU* 1.3 83.4 + - - +
631B PRO* 3.6 8.4 - - + +
647B SER* 3.4 18.0 - - - -
648B ARG* 3.2 36.6 - - - -
649B TRP* 3.6 37.6 - + + -
649C TRP* 5.6 3.2 - + - -
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Residues in contact with LEU 630 (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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615B MET* 3.8 22.0 - - + -
628B PHE* 3.8 16.4 - - + -
629B TYR* 1.3 85.8 - - - +
631B PRO* 1.3 57.2 - - + +
635B TRP* 3.4 42.2 - - + +
644B LEU* 3.7 27.1 - - + +
645B ASP 4.5 0.7 - - - +
646B GLY* 4.2 3.6 - - - -
647B SER* 2.6 29.5 + - - -
648B ARG 2.9 15.0 + - - +
650B HIS* 3.4 34.5 - - + +
662B TYR* 4.6 4.0 - - + -
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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