Contacts of the helix formed by residues 505 - 513 (chain A) in PDB entry 1V9P
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 GLY 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A HIS 3.2 4.1 + - - -
504A ARG* 1.3 75.6 - - - +
506A LEU* 1.3 65.9 + - - -
507A GLU* 2.8 7.6 + - - -
508A ARG* 3.0 9.8 + - - +
509A LEU* 2.9 18.2 + - - -
580A SER* 4.9 2.9 - - - -
582A GLU 3.5 6.1 - - - -
584A LYS* 3.5 31.7 - - - +
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Residues in contact with LEU 506 (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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505A GLY* 1.3 69.4 - - - -
507A GLU* 1.3 67.1 + - - +
509A LEU* 3.8 18.4 - - + -
510A LEU* 2.8 46.0 + - + +
526A LEU 4.9 0.7 - - - +
527A ALA* 3.4 37.9 - - + +
530A PHE* 5.1 2.7 - - + -
531A GLY 4.0 14.4 - - - +
532A THR* 4.0 8.7 - - - +
533A MET* 4.1 13.2 - - + +
536A LEU* 5.3 2.2 - - + -
580A SER 4.6 1.8 + - - -
581A MET 3.6 17.0 - - - +
582A GLU* 2.6 29.1 + - - +
583A SER 3.8 1.8 - - - +
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Residues in contact with GLU 507 (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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505A GLY* 2.8 5.0 + - - -
506A LEU* 1.3 79.1 + - - +
508A ARG* 1.3 65.2 + - + +
510A LEU* 2.9 11.1 + - - +
511A TYR* 3.2 7.8 + - - -
523A ALA* 3.9 7.9 - - - +
524A ARG* 3.9 49.2 + - + +
527A ALA* 3.3 22.4 - - + +
528A ARG* 5.0 6.3 - - + +
583A SER* 3.3 13.7 - - - -
584A LYS* 3.0 40.5 + - - +
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Residues in contact with ARG 508 (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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444A ARG 3.1 17.0 + - - -
445A LYS 4.2 8.6 + - - +
446A ALA* 2.9 34.1 + - - +
447A MET* 3.8 4.3 - - - +
448A ASP* 3.2 23.2 + - - +
504A ARG* 3.8 43.2 - - + +
505A GLY 3.0 11.9 + - - +
507A GLU* 1.3 79.0 - - + +
509A LEU* 1.3 56.0 + - - +
511A TYR* 3.5 10.2 + - - +
512A ALA* 3.1 25.5 + - - +
524A ARG* 4.4 17.7 - - - +
584A LYS* 4.8 15.7 - - - +
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Residues in contact with LEU 509 (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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441A TYR* 4.0 7.4 - - + +
447A MET* 3.4 32.9 - - + -
504A ARG 4.9 0.2 - - - +
505A GLY 2.9 13.3 + - - +
506A LEU* 3.5 22.7 - - + +
508A ARG* 1.3 75.3 - - - +
510A LEU* 1.3 66.8 + - - +
512A ALA 3.3 3.8 + - - -
513A LEU* 3.0 56.5 - - + +
533A MET* 5.0 7.0 - - - -
571A VAL* 6.1 0.4 - - + -
574A LEU* 5.3 2.5 - - + -
579A VAL* 4.0 13.0 - - + -
580A SER 4.4 3.8 - - - +
581A MET* 3.8 28.0 - - + -
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Residues in contact with LEU 510 (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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506A LEU* 2.8 52.9 + - + +
507A GLU 3.4 3.8 - - - +
509A LEU* 1.3 78.4 - - + +
511A TYR* 1.3 63.6 + - - +
513A LEU* 3.6 8.9 + - + -
514A GLY 4.0 1.6 + - - -
515A LEU* 3.7 35.2 - - + +
518A VAL* 3.9 9.1 - - + +
523A ALA* 3.9 28.3 - - + +
526A LEU* 4.1 5.4 - - + -
527A ALA* 3.9 8.1 - - + +
533A MET* 4.2 13.5 - - + -
536A LEU* 3.8 28.3 - - + -
567A PHE* 5.6 1.1 - - + -
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Residues in contact with TYR 511 (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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440A HIS* 2.9 54.5 + + - -
443A SER* 4.6 1.4 + - - -
445A LYS* 3.1 68.9 + - + +
446A ALA* 3.8 7.0 - - + -
507A GLU 3.2 4.7 + - - +
508A ARG* 3.7 9.6 - - - +
509A LEU 3.2 0.4 - - - -
510A LEU* 1.3 80.6 - - - +
512A ALA* 1.3 58.0 + - - +
514A GLY* 3.4 5.7 + - - -
518A VAL 4.2 8.4 - - - +
519A GLY* 4.1 6.1 - - - -
520A GLU* 3.7 38.1 - - + +
523A ALA* 3.9 15.4 - - + +
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Residues in contact with ALA 512 (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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437A ALA* 4.8 1.7 - - - +
440A HIS* 3.4 14.3 - - - +
441A TYR* 3.3 37.6 + - + +
446A ALA* 3.6 20.0 - - + -
447A MET* 3.6 19.5 - - + -
469A VAL* 5.7 0.3 - - - +
508A ARG 3.1 10.5 + - - +
509A LEU 3.3 8.0 + - - +
511A TYR* 1.3 73.6 - - - +
513A LEU* 1.3 58.0 + - - +
514A GLY 3.0 10.5 + - - -
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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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428A PRO* 6.1 0.9 - - - +
441A TYR* 3.7 29.4 - - + -
469A VAL* 5.9 3.1 - - + -
509A LEU* 3.0 40.4 + - + +
510A LEU* 3.6 6.5 + - + +
511A TYR 3.4 0.8 - - - -
512A ALA* 1.3 72.1 - - - +
514A GLY* 1.3 67.3 + - - +
515A LEU* 3.3 8.9 + - + +
533A MET* 5.5 1.3 - - - -
567A PHE* 3.8 36.5 - - + -
570A LEU* 4.7 16.2 - - + -
571A VAL* 4.1 13.9 - - + -
574A LEU* 4.6 12.1 - - + -
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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