Contacts of the helix formed by residues 512 - 525 (chain A) in PDB entry 6O0Z
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 SER 512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508A LEU* 3.6 28.0 - - - +
509A PRO* 3.6 20.5 + - - -
510A LYS 3.4 3.8 + - - -
511A HIS* 1.3 81.5 - - - +
513A LEU* 1.3 62.6 + - - +
514A LEU* 3.2 16.7 + - - +
515A TYR* 3.4 10.6 + - - +
516A GLU* 3.0 27.5 + - - +
617A GLU* 5.3 2.6 - - - +
620A VAL* 4.2 15.9 - - - +
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Residues in contact with LEU 513 (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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511A HIS 4.9 1.1 - - - +
512A SER* 1.3 74.8 + - - +
514A LEU* 1.3 67.3 + - + +
516A GLU* 3.3 5.5 + - + +
517A TYR* 2.9 49.4 + - + +
593A THR* 4.4 22.7 - - + +
594A TYR* 4.5 26.2 - - + +
597A LEU* 6.0 9.0 - - + -
607A LEU* 5.8 4.0 - - - +
613A GLU* 4.8 11.4 - - + +
616A LEU* 4.0 31.6 - - + +
617A GLU* 5.8 3.5 - - - +
620A VAL* 4.8 7.5 - - + +
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Residues in contact with LEU 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU* 5.4 9.6 - - + -
512A SER* 3.2 8.3 + - - +
513A LEU* 1.3 81.8 - - + +
515A TYR* 1.3 56.8 + - - +
517A TYR* 3.4 10.5 + - + +
518A PHE* 2.9 29.1 + - - +
613A GLU* 5.4 6.3 - - + +
614A ASP* 6.0 0.7 - - - -
617A GLU* 4.3 23.8 - - + -
664A ARG* 5.2 17.7 - - + +
667A ILE* 4.9 17.2 - - + +
668A ASN* 4.6 28.3 - - + +
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Residues in contact with TYR 515 (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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508A LEU* 5.1 11.1 - - + +
509A PRO 4.3 9.0 - - - +
510A LYS* 3.7 40.1 - - + +
512A SER* 3.4 20.5 + - - +
513A LEU 3.3 0.4 - - - -
514A LEU* 1.3 78.8 - - - +
516A GLU* 1.3 58.4 + - + +
518A PHE* 3.3 17.7 + + + +
519A THR* 2.9 39.4 + - + +
660A GLY* 4.5 4.8 - - - -
661A ARG* 4.2 30.9 + - - +
662A LEU* 4.4 29.3 - - + +
667A ILE* 5.5 4.5 - - + -
5B C 4.8 7.0 + - - -
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Residues in contact with GLU 516 (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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510A LYS 5.1 3.1 - - - +
511A HIS* 4.8 5.8 - - - -
512A SER 3.0 21.0 + - - +
513A LEU* 3.7 9.6 - - + +
514A LEU 3.3 0.2 - - - -
515A TYR* 1.3 74.4 - - + +
517A TYR* 1.3 60.8 + - + +
519A THR* 3.2 12.0 - - + +
520A VAL* 3.0 29.5 + - - +
590A SER 4.6 9.6 - - - +
591A LEU* 3.4 24.7 - - + +
593A THR* 3.7 26.5 - - + -
594A TYR* 6.4 0.7 - - + -
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Residues in contact with TYR 517 (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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513A LEU* 2.9 36.0 + - + +
514A LEU* 3.7 10.3 - - + +
516A GLU* 1.3 77.7 - - + +
518A PHE* 1.3 57.0 + - - +
520A VAL* 3.3 13.6 - - + +
521A TYR* 3.0 48.4 + + + +
591A LEU* 4.3 18.6 - - + -
594A TYR* 5.2 11.5 - + + -
607A LEU 4.6 10.9 + - - -
608A ASP* 5.8 1.2 - - - -
613A GLU* 6.5 1.3 - - + -
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Residues in contact with PHE 518 (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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514A LEU 2.9 18.1 + - - +
515A TYR* 3.5 18.4 - + - +
516A GLU 3.2 0.2 - - - -
517A TYR* 1.3 76.6 - - - +
519A THR* 1.3 61.7 + - - +
521A TYR* 3.4 4.0 + - - +
522A ASN* 2.9 37.4 + - + +
662A LEU* 3.6 30.1 - - + -
666A LEU* 6.2 1.3 - - + -
667A ILE* 4.0 31.6 - - + -
679A ILE* 5.9 5.2 - - + -
680A LEU* 6.0 2.9 - - + -
683A LEU* 5.2 15.0 - - + -
693A PHE* 3.8 29.6 - - + -
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Residues in contact with THR 519 (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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515A TYR* 2.9 28.5 + - + +
516A GLU* 3.2 22.9 - - + +
518A PHE* 1.3 81.7 - - - +
520A VAL* 1.3 58.8 + - + +
522A ASN* 3.8 6.5 - - - +
523A GLU* 2.9 27.7 + - - +
589A ALA* 4.5 20.1 - - - +
590A SER 5.5 3.4 - - - +
591A LEU* 5.4 2.0 - - + -
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Residues in contact with VAL 520 (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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516A GLU 3.0 22.0 + - - +
517A TYR* 3.3 22.2 - - + +
519A THR* 1.3 78.1 - - + +
521A TYR* 1.3 67.9 + - + +
523A GLU* 3.3 6.0 + - + +
524A LEU* 2.9 40.9 + - + +
549A VAL* 5.2 9.2 - - + -
553A PHE* 4.3 23.8 - - + -
589A ALA 4.7 14.6 - - - +
591A LEU* 3.9 20.2 - - + -
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Residues in contact with TYR 521 (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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517A TYR* 3.0 36.2 + + + +
518A PHE* 4.0 4.0 - - - +
520A VAL* 1.3 81.0 - - + +
522A ASN* 1.3 59.6 + - - +
524A LEU* 4.4 5.4 - - + +
525A THR* 2.3 40.1 + - - -
545A LYS* 5.0 9.6 - - + -
546A LYS* 4.9 10.0 - - - +
549A VAL* 4.5 23.5 - - + +
680A LEU* 4.6 9.9 - - + -
683A LEU* 3.7 23.1 - - + +
684A LYS* 3.6 40.2 - - + +
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Residues in contact with ASN 522 (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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518A PHE* 2.9 34.5 + - + +
519A THR* 3.9 7.2 - - - +
521A TYR* 1.3 75.5 - - - +
523A GLU* 1.3 63.0 + - - +
525A THR* 4.5 2.8 + - - -
526A LYS* 4.9 6.2 + - - +
683A LEU* 5.5 2.8 - - - +
693A PHE* 5.4 7.2 - - + -
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Residues in contact with GLU 523 (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 THR 2.9 17.4 + - - +
520A VAL* 3.5 8.7 - - + +
521A TYR 3.2 0.2 - - - -
522A ASN* 1.3 80.7 - - - +
524A LEU* 1.3 69.1 + - + +
525A THR 3.5 1.3 + - - -
526A LYS 4.6 1.0 + - - -
527A VAL* 3.5 18.7 + - - +
589A ALA* 4.4 17.3 - - + -
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Residues in contact with LEU 524 (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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520A VAL* 2.9 29.9 + - + +
521A TYR* 3.6 7.6 - - + -
523A GLU* 1.3 88.8 - - + +
525A THR* 1.3 59.7 + - - +
527A VAL* 3.9 19.1 - - + +
540A LEU* 5.1 7.4 - - - +
545A LYS* 4.9 13.0 - - + +
548A ILE* 5.8 8.5 - - + -
549A VAL* 6.0 5.4 - - + +
553A PHE* 5.5 7.4 - - + -
684A LYS 5.7 0.5 - - - +
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Residues in contact with THR 525 (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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521A TYR* 2.3 28.7 + - - +
522A ASN* 5.0 2.5 - - - -
523A GLU 3.5 0.6 - - - -
524A LEU* 1.3 76.9 + - - +
526A LYS* 1.3 59.4 + - - +
527A VAL 3.2 8.1 + - - +
540A LEU* 5.0 6.1 - - - +
682A PHE 4.8 3.6 - - - +
683A LEU* 2.4 40.3 + - - +
684A LYS 4.4 7.5 + - - +
685A SER 4.9 4.9 - - - -
690A ASN* 3.4 32.9 - - - +
691A ARG 4.2 13.5 - - - +
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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