Contacts of the helix formed by residues 525 - 537 (chain A) in PDB entry 5W6V
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 PRO 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A ALA* 4.0 12.9 - - + +
524A THR* 1.3 87.3 - - - +
526A VAL* 1.3 62.0 + - + +
527A TYR 3.4 0.7 - - - -
528A ALA* 3.9 8.7 + - + +
529A GLU* 3.6 18.4 + - - +
816A VAL* 6.1 5.3 - - + +
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Residues in contact with VAL 526 (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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454A PHE* 3.9 27.4 - - + -
495A GLY* 4.0 7.4 - - - +
496A ALA* 3.7 31.6 - - + +
499A VAL* 4.1 4.9 - - + -
520A LEU* 3.7 19.7 - - + -
521A PRO* 6.2 0.7 - - + -
524A THR* 3.0 24.1 + - + +
525A PRO* 1.3 79.2 - - + +
527A TYR* 1.3 54.0 + - - +
529A GLU* 3.1 1.6 + - - +
530A VAL* 2.7 47.4 + - + +
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Residues in contact with TYR 527 (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 LEU* 3.9 8.3 - - + -
524A THR* 3.6 4.4 + - - +
525A PRO 3.4 0.4 - - - -
526A VAL* 1.3 79.4 - - - +
528A ALA* 1.3 62.1 + - - +
530A VAL* 3.2 6.2 + - - +
531A LYS* 2.9 45.8 + - + +
544A CYS* 3.7 23.1 - - - -
810A ARG* 3.8 9.6 + - - -
813A TYR* 3.6 30.7 - + - -
1R A 3.0 110.4 + + + +
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Residues in contact with ALA 528 (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 THR 4.7 0.6 + - - -
525A PRO* 3.9 10.7 + - + +
526A VAL 3.3 0.4 - - - -
527A TYR* 1.3 79.2 - - - +
529A GLU* 1.3 52.8 + - - +
531A LYS* 3.2 2.1 + - - +
532A ARG* 2.7 36.8 + - - +
813A TYR* 3.5 47.5 - - + +
816A VAL* 4.2 20.2 - - + -
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Residues in contact with GLU 529 (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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496A ALA* 3.4 23.5 - - + +
499A VAL* 3.4 20.5 - - + +
500A GLU* 4.6 3.3 - - - +
525A PRO 3.6 12.1 + - - +
526A VAL* 3.1 7.2 + - - +
528A ALA* 1.3 76.3 - - - +
530A VAL* 1.3 64.8 + - - +
532A ARG* 2.6 50.1 + - - -
533A VAL* 3.0 37.2 + - - +
816A VAL 5.2 1.6 - - - +
817A ASP 4.8 9.0 - - - +
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A PHE* 4.9 0.7 - - + -
499A VAL* 4.1 12.8 - - + -
503A PHE* 4.2 24.9 - - + -
518A VAL* 4.1 23.6 - - + -
526A VAL* 2.7 40.6 + - + +
527A TYR* 3.5 8.1 - - - +
529A GLU* 1.3 74.1 - - - +
531A LYS* 1.3 59.7 + - + +
533A VAL* 4.1 0.5 - - - +
534A GLY* 2.8 27.9 + - - -
542A THR* 4.3 13.2 + - - +
544A CYS* 3.8 23.3 - - - -
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Residues in contact with LYS 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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527A TYR* 2.9 44.7 + - + +
528A ALA* 3.7 5.2 - - - +
530A VAL* 1.3 73.9 - - - +
532A ARG* 1.3 61.0 + - - +
534A GLY* 5.0 0.2 - - - -
535A ASP* 2.8 45.7 + - - +
542A THR* 3.1 35.6 + - - +
544A CYS* 4.4 5.3 - - - -
568A LYS* 4.6 4.0 - - - +
810A ARG* 3.3 48.4 - - - +
813A TYR* 4.8 2.7 - - + -
814A HIS* 3.4 6.4 + - + +
855A TYR 5.0 0.4 + - - -
1R A 2.9 28.1 + - - -
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Residues in contact with ARG 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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500A GLU* 3.5 21.6 + - - -
528A ALA 2.7 21.6 + - - +
529A GLU* 2.6 44.8 + - - +
531A LYS* 1.3 72.4 - - - +
533A VAL* 1.3 72.6 + - - +
536A THR* 2.4 39.2 + - + +
537A LEU* 3.2 21.8 + - - +
813A TYR 4.6 7.0 - - - +
814A HIS* 3.9 25.4 - - + +
816A VAL 4.5 14.8 - - - -
817A ASP 6.2 0.2 - - - -
843A ALA 5.7 0.7 - - - +
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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
----------------------------------------------------------
499A VAL* 3.8 10.3 - - + -
500A GLU* 3.8 15.7 - - + -
503A PHE* 3.6 26.5 - - + -
529A GLU* 3.0 40.4 + - - +
530A VAL 4.1 1.6 - - - +
532A ARG* 1.3 85.6 - - - +
534A GLY* 1.3 59.4 + - - +
537A LEU* 3.2 14.4 + - + +
538A LEU* 2.8 51.6 + - + +
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Residues in contact with GLY 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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503A PHE* 4.6 5.8 - - - -
530A VAL 2.8 21.6 + - - -
533A VAL* 1.3 76.8 - - - +
535A ASP* 1.3 60.0 + - - +
538A LEU* 5.1 0.7 - - - -
539A GLY* 2.9 27.6 + - - -
540A MET* 3.0 31.8 + - - -
542A THR* 4.9 4.7 - - - -
850A THR* 4.1 0.2 + - - -
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Residues in contact with ASP 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 LYS* 2.8 30.5 + - - +
534A GLY* 1.3 74.4 - - - +
536A THR* 1.3 58.4 + - - +
540A MET 4.7 2.9 - - - +
542A THR* 4.7 5.4 + - - -
810A ARG* 2.6 32.6 + - - -
814A HIS* 3.1 28.2 + - + +
846A VAL* 3.3 14.3 - - + +
847A HIS* 2.9 27.5 + - - +
850A THR* 3.6 9.9 + - + +
855A TYR* 3.8 19.9 - - + +
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Residues in contact with THR 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 ARG* 2.4 36.9 + - + +
535A ASP* 1.3 78.9 - - - +
537A LEU* 1.3 63.5 + - - +
814A HIS* 3.7 31.6 - - + +
842A LYS 5.5 0.7 - - - -
843A ALA* 3.5 20.2 + - - +
845A GLN 3.3 29.2 - - - +
846A VAL* 4.6 0.8 - - - -
847A HIS* 3.8 15.9 + - - +
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Residues in contact with LEU 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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500A GLU* 3.5 41.3 - - + +
504A ARG* 3.8 21.6 + - - +
532A ARG* 3.8 25.6 - - - +
533A VAL* 3.2 23.7 + - + +
536A THR* 1.3 82.2 + - - +
538A LEU* 1.3 68.1 + - + +
847A HIS* 3.5 13.4 + - - -
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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