Contacts of the strand formed by residues 519 - 524 (chain B) in PDB entry 1QCO
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 TYR 519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B LEU* 4.1 12.3 - - + -
518B PRO* 1.3 74.4 - - - +
520B GLY* 1.3 59.2 + - - +
532B ILE* 4.8 4.3 - - + -
533B GLY 3.5 3.1 - - - +
534B VAL* 3.6 24.2 - - + -
543B LEU* 4.2 17.3 - - + -
567B LEU* 3.7 22.2 - - + -
570B PHE* 3.7 28.9 - + - -
578B TRP* 4.4 3.6 + - + +
581B ALA* 3.9 21.2 - - + +
582B ARG* 4.1 11.3 + - - +
585B LEU* 4.1 11.4 - - + +
726B PHE* 3.8 22.0 - + + -
762B TRP* 3.7 3.3 - - - -
763B VAL* 2.8 49.6 + - + +
765B PRO* 4.4 15.7 - - + -
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Residues in contact with GLY 520 (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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519B TYR* 1.3 76.0 - - - +
521B VAL* 1.3 65.3 + - - +
522B PHE* 4.2 0.9 - - - -
532B ILE* 3.4 7.1 - - - +
533B GLY* 2.9 33.2 + - - -
567B LEU* 4.3 5.1 - - - +
615B MET* 4.3 4.3 - - - -
618B PRO* 4.9 0.9 - - - -
761B PRO 3.8 10.8 - - - -
762B TRP* 3.6 16.2 - - - -
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLY* 1.3 75.5 - - - +
522B PHE* 1.3 65.2 + - - +
530B PRO* 3.7 22.0 - - + -
531B ARG 3.3 10.3 - - - +
532B ILE* 4.6 4.5 - - + -
565B THR 3.4 27.8 - - - +
566B THR* 4.2 5.4 - - - -
567B LEU* 4.5 7.2 - - + -
615B MET* 3.6 8.5 - - - +
616B HIS* 2.9 41.2 + - + +
617B LEU 3.8 11.4 - - - +
618B PRO* 3.6 29.7 - - + +
761B PRO 4.8 0.4 + - - -
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Residues in contact with PHE 522 (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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520B GLY 4.7 0.9 - - - -
521B VAL* 1.3 74.8 - - - +
523B SER* 1.3 70.2 + - - +
524B THR* 4.1 7.0 - - + -
529B LYS 3.6 1.2 - - - +
530B PRO* 3.3 1.7 - - - +
531B ARG* 2.8 85.2 + - + +
532B ILE 4.0 2.9 - - - -
533B GLY* 3.8 17.3 - - - -
540B ILE* 3.7 35.2 - - + -
542B ASP* 3.8 18.2 - - + -
608B THR* 4.5 10.8 - - - -
613B ALA* 4.0 14.8 - - + -
614B THR 3.3 12.3 - - - +
615B MET* 3.9 17.5 - - + -
616B HIS* 3.8 5.2 - - - -
762B TRP* 5.7 0.9 - + - -
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Residues in contact with SER 523 (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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522B PHE* 1.3 75.4 - - - +
524B THR* 1.3 71.1 + - - +
527B ASN 3.8 4.0 - - - -
528B PRO* 3.7 25.5 - - - +
529B LYS 3.9 4.0 - - - -
531B ARG* 3.6 8.5 - - - +
613B ALA* 3.4 2.4 - - - +
614B THR* 2.9 36.7 + - - +
616B HIS* 2.8 26.8 + - - -
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Residues in contact with THR 524 (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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522B PHE* 4.1 8.7 - - + -
523B SER* 1.3 79.1 + - - +
525B GLN* 1.3 64.0 + - - +
526B SER* 3.2 21.1 + - - -
527B ASN 3.0 23.1 + - - +
528B PRO* 3.8 4.7 - - - +
531B ARG* 3.0 25.3 + - - +
608B THR* 3.7 29.8 - - + +
612B SER* 3.8 16.4 - - - +
613B ALA* 4.4 1.3 - - - -
614B THR* 5.0 3.6 - - - +
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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