Contacts of the strand formed by residues 523 - 527 (chain X) in PDB entry 6KW5
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 523 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521X ASP 4.2 7.9 - - - +
522X THR* 1.3 71.4 - - - +
524X THR* 1.3 58.2 + - - +
525X LEU* 3.9 14.6 + - + +
605X ARG 3.6 2.1 - - - +
606X CYS* 3.5 7.3 - - - -
607X GLU* 2.9 57.1 + - + +
609X LYS* 4.2 23.4 - - + +
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Residues in contact with THR 524 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513X SER* 6.0 1.3 - - - +
515X LEU* 4.6 7.9 - - + -
522X THR* 3.5 18.8 + - - +
523X GLU* 1.3 74.8 - - - +
525X LEU* 1.3 60.8 + - - +
533X VAL 5.0 0.5 - - - +
534X LYS 5.0 1.9 - - - +
589X GLU* 2.3 36.7 + - - +
591X PHE* 3.8 22.4 - - - -
604X PHE* 4.4 7.4 - - + -
605X ARG 3.7 7.2 - - - -
606X CYS* 3.7 24.7 - - + -
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Residues in contact with LEU 525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523X GLU* 4.7 18.4 - - + +
524X THR* 1.3 75.1 - - - +
526X LEU* 1.3 64.1 + - - +
527X THR* 4.3 16.4 - - + -
532X PRO* 5.3 9.4 - - + -
533X VAL 5.1 2.7 - - - -
603X MET 4.1 0.3 - - - +
604X PHE* 3.6 15.9 - - - -
605X ARG* 3.7 47.2 + - + +
607X GLU* 5.7 2.9 - - - +
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Residues in contact with LEU 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511X LEU* 3.6 31.2 - - + -
525X LEU* 1.3 80.1 - - - +
527X THR* 1.3 59.9 + - - +
528X ILE* 4.4 13.7 - - + -
531X GLU 3.5 1.6 - - - +
532X PRO* 3.3 1.2 - - - +
533X VAL* 2.8 58.3 + - + +
591X PHE* 4.0 22.2 - - + -
593X ILE* 4.6 14.1 - - + -
602X LEU* 4.7 17.7 - - + -
603X MET 3.3 11.4 - - - +
604X PHE* 3.7 18.6 - - + -
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Residues in contact with THR 527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525X LEU* 4.3 15.7 - - + -
526X LEU* 1.3 75.1 - - - +
528X ILE* 1.3 60.6 + - - +
529X ASN 4.5 4.2 + - - -
530X LYS* 3.5 33.7 - - - +
531X GLU 3.4 3.8 - - - -
532X PRO* 4.0 13.9 - - + -
601X HIS* 4.8 0.5 + - - -
602X LEU* 3.3 1.2 - - - -
603X MET* 2.7 58.9 + - - +
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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