Contacts of the helix formed by residues 564 - 576 (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 ASP 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A HIS* 2.5 38.8 + - - -
426A PRO* 5.0 3.3 - - - +
427A ASN* 4.5 1.4 + - - -
428A PRO* 3.9 10.8 - - + +
560A GLU 3.1 12.2 + - - +
561A THR* 2.7 27.1 + - - +
563A LYS* 1.3 71.1 - - - +
565A PRO* 1.3 90.2 - - - +
566A ALA* 3.1 18.6 + - - +
567A PHE* 3.0 7.8 + - + +
568A ARG* 3.0 20.3 + - - +
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Residues in contact with PRO 565 (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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563A LYS 3.2 8.0 - - - +
564A ASP* 1.3 92.4 - - - +
566A ALA* 1.3 56.0 + - - +
568A ARG* 3.2 9.5 + - + +
569A ASP* 2.8 32.4 + - - +
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Residues in contact with ALA 566 (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 HIS* 5.5 0.4 - - + -
427A ASN* 3.9 15.7 - - - +
428A PRO* 3.6 23.3 - - + -
429A LEU* 4.0 17.9 - - + +
564A ASP* 3.1 9.9 + - - +
565A PRO* 1.3 79.7 - - - +
567A PHE* 1.3 57.0 + - - +
569A ASP* 3.2 7.3 + - - +
570A LEU* 2.8 30.6 + - - +
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Residues in contact with PHE 567 (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* 3.7 27.1 - - + +
510A LEU* 5.6 0.4 - - + -
513A LEU* 3.8 29.8 - - + -
515A LEU* 3.5 31.2 - - + -
533A MET* 3.6 24.0 - - + -
537A LEU* 4.2 3.6 - - + -
561A THR* 3.4 32.5 - - + +
562A LEU* 3.8 24.0 - - + -
564A ASP* 3.0 3.5 + - + +
566A ALA* 1.3 76.0 - - - +
568A ARG* 1.3 67.0 + - - +
570A LEU* 3.1 9.1 + - + +
571A VAL* 2.9 46.5 + - + +
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Residues in contact with ARG 568 (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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537A LEU* 2.8 66.2 + - - +
538A GLU* 5.5 3.6 + - - -
562A LEU 3.0 20.0 + - - +
563A LYS* 4.1 17.1 + - - +
564A ASP 3.0 14.1 + - - +
565A PRO* 3.4 12.8 - - + +
567A PHE* 1.3 79.0 - - - +
569A ASP* 1.3 65.9 + - - +
571A VAL* 3.0 4.2 + - - +
572A ARG* 2.9 42.1 + - - +
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Residues in contact with ASP 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.3 5.6 - - + +
565A PRO 2.8 17.1 + - - +
566A ALA* 3.2 11.9 - - - +
568A ARG* 1.3 75.3 - - - +
570A LEU* 1.3 62.9 + - - +
572A ARG* 3.2 9.9 + - - +
573A ARG* 2.7 65.5 + - - +
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Residues in contact with LEU 570 (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* 4.7 16.2 - - + +
429A LEU* 4.1 15.7 - - + -
468A ASP* 3.9 21.3 - - + +
469A VAL* 4.3 11.7 - - + +
470A ALA 4.0 8.5 - - - +
513A LEU* 4.7 18.8 - - + -
566A ALA 2.8 15.2 + - - +
567A PHE* 3.5 12.1 - - + +
569A ASP* 1.3 74.4 + - - +
571A VAL* 1.3 62.4 + - + +
573A ARG* 3.7 26.4 + - - +
574A LEU* 3.0 44.9 + - + +
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Residues in contact with VAL 571 (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* 4.1 13.0 - - + -
533A MET* 3.6 31.4 - - + -
537A LEU* 4.6 11.2 - - + -
567A PHE* 2.9 50.6 + - + +
568A ARG* 3.4 9.2 - - - +
570A LEU* 1.3 73.1 - - + +
572A ARG* 1.3 70.1 - - - +
574A LEU* 2.8 20.5 + - - +
575A LYS* 2.9 13.1 + - + +
581A MET* 4.0 12.2 - - + +
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Residues in contact with ARG 572 (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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568A ARG* 2.9 31.7 + - - +
569A ASP* 3.6 11.4 - - - +
571A VAL* 1.3 77.6 - - - +
573A ARG* 1.3 58.9 + - + +
575A LYS* 2.8 28.9 + - + +
576A GLU* 2.8 40.9 + - + +
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Residues in contact with ARG 573 (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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429A LEU* 4.0 11.7 - - - +
468A ASP* 2.9 25.5 + - - -
470A ALA* 3.0 42.9 - - + +
471A ASP* 5.3 2.9 + - - -
474A HIS* 4.7 11.4 + - - +
569A ASP* 2.7 39.2 + - - +
570A LEU* 3.7 18.3 - - - +
572A ARG* 1.3 79.5 - - + +
574A LEU* 1.3 59.8 + - - +
576A GLU* 4.1 14.1 - - - +
577A ALA* 3.7 18.0 + - - +
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Residues in contact with LEU 574 (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* 3.4 27.1 - - + +
469A VAL* 3.5 19.3 - - + -
470A ALA* 4.2 12.8 - - + -
473A TYR* 4.1 7.9 - - + -
509A LEU* 5.3 2.0 - - + -
513A LEU* 4.6 15.7 - - + -
570A LEU* 3.0 44.8 + - + +
571A VAL* 2.8 11.8 + - - +
573A ARG* 1.3 74.6 - - - +
575A LYS* 1.3 67.1 + - - +
577A ALA* 3.1 11.3 + - - +
579A VAL* 3.2 40.8 + - + +
581A MET* 4.8 7.9 - - + -
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Residues in contact with LYS 575 (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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534A ASP* 3.3 33.7 + - - +
571A VAL* 2.9 12.2 + - + +
572A ARG* 2.8 14.2 + - + +
574A LEU* 1.3 71.4 - - - +
576A GLU* 1.3 57.1 + - + +
577A ALA 2.6 5.2 + - - -
578A GLY* 2.6 29.6 + - - -
579A VAL 3.7 12.5 + - - +
581A MET* 4.1 27.2 - - + +
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Residues in contact with GLU 576 (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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474A HIS* 5.4 3.6 - - - -
476A ARG* 5.5 1.2 + - - -
572A ARG* 2.8 41.1 + - + +
573A ARG* 4.1 15.0 - - - +
574A LEU 3.3 0.2 - - - -
575A LYS* 1.3 78.4 - - + +
577A ALA* 1.3 56.2 - - - +
578A GLY 3.5 0.7 - - - -
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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