Contacts of the helix formed by residues 530 - 539 (chain A) in PDB entry 6WG4
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 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A PRO* 4.4 5.4 - - + -
526A THR* 4.0 5.4 - - - -
527A GLN* 3.5 48.3 + - + +
528A LYS 3.1 1.2 + - - -
529A LYS* 1.3 98.5 + - + +
531A GLN* 1.3 63.8 + - - +
532A ILE 3.4 1.8 - - - -
533A ALA* 3.5 4.3 + - + +
534A VAL* 3.0 26.9 + - + +
592A LYS* 3.5 30.4 + - + +
597A VAL* 3.4 37.9 - - + -
618A VAL* 3.9 22.4 - - + -
619A CYS 6.1 0.2 - - - -
620A ASP* 4.5 5.6 + - - -
641A LEU* 3.7 26.7 - - + -
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Residues in contact with GLN 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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524A GLN* 3.7 10.9 - - - +
525A PRO* 3.6 15.3 + - + +
527A GLN 4.0 2.5 + - - +
528A LYS* 3.0 53.5 + - - +
529A LYS 3.4 0.4 - - - -
530A TYR* 1.3 77.7 - - - +
532A ILE* 1.3 55.9 + - + +
534A VAL 3.8 0.2 - - - -
535A THR* 2.3 39.3 + - - -
663A ALA* 3.7 18.1 - - + +
664A ARG* 5.2 0.2 - - - -
666A TRP* 3.5 35.5 + - + +
667A ASP* 3.2 28.3 + - - +
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Residues in contact with ILE 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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528A LYS 4.8 0.2 + - - -
529A LYS 4.8 2.5 + - - +
530A TYR 3.4 0.4 - - - -
531A GLN* 1.3 76.7 - - + +
533A ALA* 1.3 57.3 + - - +
535A THR* 3.3 7.2 + - - -
536A LYS* 2.9 28.1 + - - +
641A LEU 3.6 21.8 - - - +
642A ASP* 3.7 9.9 - - - +
643A GLY* 3.6 18.4 - - - +
656A ALA* 4.5 6.1 - - + +
659A LEU* 3.8 16.5 - - + +
660A LYS* 3.9 35.0 - - + +
663A ALA* 3.7 18.6 - - + -
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Residues in contact with ALA 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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529A LYS 5.3 0.2 + - - -
530A TYR* 3.5 10.6 + - + +
531A GLN 3.3 0.2 - - - -
532A ILE* 1.3 81.5 - - - +
534A VAL* 1.3 59.0 + - + +
536A LYS* 3.3 2.4 + - - +
537A VAL* 3.0 35.0 + - - +
594A VAL* 5.8 1.3 - - + -
618A VAL* 4.0 23.6 - - + -
639A VAL* 4.0 18.1 - - + +
640A ALA 3.7 20.2 - - - +
641A LEU* 4.3 6.3 + - - -
643A GLY* 4.8 0.2 - - - -
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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
----------------------------------------------------------
525A PRO* 4.1 16.8 - - + -
530A TYR* 3.0 22.3 + - + +
531A GLN 3.9 2.5 - - - +
533A ALA* 1.3 74.4 - - + +
535A THR* 1.3 65.9 + - - +
537A VAL* 4.6 3.8 - - - +
538A LEU* 2.9 49.0 + - + +
594A VAL* 4.6 9.2 - - + -
597A VAL* 4.4 13.9 - - + -
598A ILE* 3.8 32.3 - - + -
666A TRP* 3.8 16.4 - - + -
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Residues in contact with THR 535 (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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531A GLN 2.3 28.7 + - - -
532A ILE* 3.5 8.3 - - - -
534A VAL* 1.3 76.2 - - - +
536A LYS* 1.3 56.0 + - - +
538A LEU* 4.2 0.2 - - - -
539A GLY* 3.0 26.3 + - - +
542A MET* 3.6 26.4 - - + +
659A LEU* 4.4 11.2 - - + +
662A LYS* 3.8 36.8 - - + +
663A ALA* 3.5 8.2 - - - +
666A TRP* 3.1 12.6 + - - -
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Residues in contact with LYS 536 (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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532A ILE 2.9 17.2 + - - +
533A ALA* 3.6 5.4 - - - +
535A THR* 1.3 77.0 - - - +
537A VAL* 1.3 65.2 + - - +
539A GLY* 3.5 8.7 + - - -
639A VAL* 4.5 4.3 - - + -
643A GLY* 2.8 37.8 + - - +
645A LEU* 4.0 30.0 - - + +
653A SER* 3.7 34.4 + - - -
654A GLY* 3.8 5.9 - - - -
659A LEU* 4.1 27.7 - - + +
584B GLU* 4.6 12.4 + - - +
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Residues in contact with VAL 537 (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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533A ALA 3.0 21.0 + - - +
534A VAL 4.1 2.0 - - - +
536A LYS* 1.3 78.1 - - - +
538A LEU* 1.3 63.9 + - + +
539A GLY* 4.4 0.3 - - - -
594A VAL* 3.9 28.3 - - + -
612A ALA 3.7 22.3 - - - +
613A CYS* 4.1 12.1 - - + -
616A ALA* 4.2 12.6 - - + -
637A LYS* 5.2 9.6 + - - +
639A VAL* 3.6 30.3 - - + -
645A LEU* 4.2 14.1 - - + -
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Residues in contact with LEU 538 (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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519A LEU* 4.0 19.3 - - + -
523A CYS* 4.6 1.6 - - - -
534A VAL* 2.9 39.7 + - + +
535A THR 4.3 0.9 - - - +
537A VAL* 1.3 77.0 - - + +
539A GLY* 1.3 65.7 + - - +
540A LYS 3.4 0.3 + - - -
541A ASN* 3.1 27.0 + - - +
542A MET* 4.2 17.0 - - + +
598A ILE* 4.3 4.9 - - + -
609A LEU* 4.0 13.0 - - + -
612A ALA* 3.7 25.6 - - + -
613A CYS* 3.8 23.1 - - - -
666A TRP* 4.0 20.2 - - + -
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Residues in contact with GLY 539 (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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535A THR 3.0 17.7 + - - +
536A LYS* 3.9 8.1 - - - -
537A VAL 3.4 2.0 - - - -
538A LEU* 1.3 76.1 - - - +
540A LYS* 1.3 62.4 + - - -
541A ASN 3.2 1.0 + - - -
542A MET* 3.2 22.5 + - - +
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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