Contacts of the strand formed by residues 530 - 534 (chain A) in PDB entry 4COO
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 VAL 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A PRO* 3.4 30.6 - - + +
424A THR* 4.7 8.7 - - + -
447A PRO* 4.5 12.6 - - + -
449A VAL* 4.6 15.7 - - + -
455A ILE* 4.0 28.5 - - + -
510A LEU* 4.5 11.0 - - + -
511A VAL 3.5 7.2 - - - +
512A VAL* 4.8 2.0 - - + -
528A GLN 4.7 3.8 - - - +
529A MET* 1.3 89.1 - - - +
531A PHE* 1.3 62.9 + - - +
532A GLY 3.5 21.8 - - - +
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Residues in contact with PHE 531 (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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419A LEU* 3.8 16.3 - - + +
420A SER 3.3 18.9 - - - +
421A ALA* 3.9 3.0 + - - +
422A PRO* 3.8 3.2 - - - +
492A LEU* 3.9 29.8 - - + -
511A VAL* 2.8 26.1 + - + +
512A VAL 4.3 0.7 - - - -
513A HIS* 3.6 33.7 - - + -
529A MET* 3.9 41.7 - - + -
530A VAL* 1.3 73.2 - - - +
532A GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 532 (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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419A LEU* 4.5 10.5 - - - -
420A SER 3.9 10.5 - - - -
422A PRO* 4.2 3.4 - - - -
510A LEU* 3.6 1.6 - - - -
511A VAL* 3.0 35.0 + - - +
530A VAL* 3.4 12.4 - - - +
531A PHE* 1.3 82.9 - - - +
533A VAL* 1.3 63.4 + - - -
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Residues in contact with VAL 533 (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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419A LEU* 5.3 0.9 - - - +
420A SER 5.0 1.2 + - - -
422A PRO* 4.4 10.0 - - + +
445A GLN* 3.4 28.7 + - + +
447A PRO* 3.8 30.3 - - + -
458A MET* 3.9 14.1 - - + -
508A PHE* 3.7 26.9 - - + -
509A ALA 3.5 6.7 - - - +
510A LEU* 4.3 9.0 - - + -
530A VAL* 4.8 0.2 - - + -
532A GLY* 1.3 75.7 - - - +
534A VAL* 1.3 68.7 + - - +
535A THR* 4.9 1.3 - - + -
538A ASP* 3.7 9.4 - - - +
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Residues in contact with VAL 534 (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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414A VAL* 5.1 1.1 - - + -
417A LEU* 3.9 14.4 - - + -
419A LEU* 3.6 29.6 - - + -
490A ILE* 6.0 0.2 - - + -
499A LEU* 3.7 28.0 - - + -
503A LEU* 4.1 2.1 - - - +
508A PHE* 3.8 0.5 - - - -
509A ALA* 2.8 46.3 + - + +
511A VAL* 4.1 15.5 - - + -
533A VAL* 1.3 79.2 - - - +
535A THR* 1.3 78.2 + - - +
538A ASP* 3.5 13.2 - - + -
539A LEU 4.6 2.0 - - - +
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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