Contacts of the helix formed by residues 584 - 595 (chain A) in PDB entry 5KVI
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 ARG 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A GLN* 5.3 1.8 - - - +
533A GLU* 4.1 0.2 - - - -
562A LYS* 6.0 0.6 - - - +
578A LEU* 4.5 3.4 - - + -
581A ILE* 3.6 20.0 + - + +
582A PHE* 3.3 13.9 + - - +
583A ASN* 1.3 83.7 - - - +
585A MET* 1.3 66.8 + - - +
586A PRO* 3.3 3.4 - - - -
587A ILE* 2.8 31.3 + - + +
588A ALA 3.1 8.7 + - - -
607A LEU 2.6 36.8 + - - -
608A PHE* 3.6 38.6 + - + -
609A ASN 5.4 0.2 - - - -
610A ILE 5.0 0.4 - - - -
611A HIS 2.4 32.0 + - - -
612A GLU* 3.4 29.2 + - - +
614A LEU* 3.9 9.4 - - - +
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Residues in contact with MET 585 (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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481A MET* 3.9 26.5 - - + -
493A GLU* 3.4 39.2 + - + +
494A ALA 4.0 11.0 - - - +
495A ILE* 3.7 36.3 - - + -
533A GLU* 2.9 24.3 + - + +
576A ILE 5.7 0.2 - - - +
578A LEU* 4.4 8.2 - - + +
584A ARG* 1.3 76.1 - - - +
586A PRO* 1.3 65.5 - - + +
588A ALA* 2.9 8.6 + - - +
589A ARG* 2.9 42.8 + - - +
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Residues in contact with PRO 586 (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 GLU* 3.5 27.8 - - - +
534A THR* 4.1 2.2 - - - +
536A SER 3.4 24.2 - - - +
537A GLU* 4.2 0.2 - - - -
538A ALA* 2.9 25.7 + - + +
583A ASN 4.4 4.0 - - - +
584A ARG* 3.4 5.6 - - - +
585A MET* 1.3 93.8 - - + +
587A ILE* 1.3 60.7 + - + +
589A ARG* 3.5 3.0 + - + +
590A LYS 3.2 12.8 + - - -
618A PHE* 3.6 40.4 - - + -
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Residues in contact with ILE 587 (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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538A ALA* 4.2 11.7 - - + -
541A ILE* 3.9 26.2 - - + -
583A ASN 5.3 0.9 - - - +
584A ARG* 2.8 34.5 + - + +
586A PRO* 1.3 75.9 - - + +
588A ALA* 1.3 65.9 + - - +
590A LYS* 3.1 4.7 + - - +
591A ILE* 3.0 24.3 + - + +
607A LEU* 4.0 20.0 - - + +
608A PHE* 3.8 16.4 - - + -
614A LEU* 3.8 29.2 - - + -
616A VAL* 4.8 11.7 - - + -
618A PHE* 5.9 2.5 - - + -
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Residues in contact with ALA 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 4.0 8.7 - - + -
576A ILE* 3.8 25.3 - - + +
578A LEU* 4.8 2.0 - - + -
584A ARG 3.1 6.0 + - - +
585A MET* 2.9 25.6 + - - +
587A ILE* 1.3 77.7 - - - +
589A ARG* 1.3 62.0 + - - +
591A ILE* 3.3 2.6 + - - +
592A ILE* 3.1 28.8 + - - +
608A PHE* 3.6 19.6 - - + -
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Residues in contact with ARG 589 (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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456A ASP* 3.2 25.9 + - - -
478A HIS* 3.5 7.0 - - - -
479A GLN* 3.0 40.5 + - - +
481A MET* 3.8 17.4 - - - +
495A ILE* 3.3 20.3 - - + +
534A THR 2.9 27.1 + - - -
535A GLU* 3.2 14.3 + - - +
536A SER 3.0 25.9 + - - -
537A GLU* 3.5 24.9 - - + +
585A MET* 2.9 27.8 + - - +
586A PRO 3.6 7.2 - - - +
588A ALA* 1.3 76.2 - - - +
590A LYS* 1.3 56.0 + - - +
592A ILE* 3.3 1.3 + - - -
593A LYS* 2.9 27.4 + - - +
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Residues in contact with LYS 590 (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 GLU* 3.8 8.0 - - - +
538A ALA* 3.5 27.4 - - + +
539A SER 3.3 22.9 - - - +
540A GLU* 4.6 2.5 - - - +
541A ILE* 3.8 32.2 - - + +
586A PRO 3.2 8.0 + - - +
587A ILE 3.1 9.6 + - - +
589A ARG* 1.3 78.4 - - - +
591A ILE* 1.3 67.1 + - + +
593A LYS* 3.3 3.0 + - - +
594A ASP* 2.9 58.3 + - - +
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Residues in contact with ILE 591 (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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541A ILE* 6.1 0.9 - - + -
566A PHE* 4.8 2.2 - - + -
573A VAL* 4.3 21.1 - - + +
576A ILE* 4.3 13.9 - - + -
587A ILE* 3.0 25.7 + - + +
588A ALA 3.3 5.8 + - - +
590A LYS* 1.3 79.6 - - + +
592A ILE* 1.3 61.9 + - - +
594A ASP* 3.5 7.3 + - - +
595A GLY* 3.3 17.5 + - - -
596A GLU 4.9 0.2 + - - -
598A HIS* 4.2 25.7 + - + +
604A VAL* 3.3 32.3 - - + -
607A LEU* 4.5 4.5 - - + -
608A PHE* 3.5 26.2 - - + -
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Residues in contact with ILE 592 (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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446A LYS* 3.4 24.0 - - + -
479A GLN* 3.1 21.3 - - - +
495A ILE* 3.6 48.2 - - + +
496A GLY* 4.4 3.1 - - - -
573A VAL* 4.1 33.2 - - + +
574A VAL* 4.1 10.3 - - - +
575A GLY* 3.8 14.1 - - - +
576A ILE* 4.0 6.3 - - + +
588A ALA 3.1 14.3 + - - +
589A ARG 4.0 1.1 - - - +
591A ILE* 1.3 76.4 - - - +
593A LYS* 1.3 62.9 + - - +
595A GLY* 3.3 10.7 + - - -
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Residues in contact with LYS 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 5.0 15.7 - - + -
446A LYS* 3.2 28.4 + - + -
479A GLN* 3.8 8.7 - - + +
537A GLU* 2.8 32.8 - - - +
589A ARG 2.9 17.6 + - - +
590A LYS* 3.9 3.6 - - - +
592A ILE* 1.3 76.5 - - - +
594A ASP* 1.3 65.9 + - - +
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Residues in contact with ASP 594 (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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446A LYS* 5.0 0.7 + - - -
590A LYS* 2.9 54.4 + - - +
591A ILE* 3.8 7.5 - - - +
593A LYS* 1.3 81.5 - - - +
595A GLY* 1.3 66.3 + - - +
596A GLU* 3.2 32.5 + - + +
598A HIS* 5.5 3.5 + - - +
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Residues in contact with GLY 595 (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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446A LYS* 4.6 6.7 - - - -
572A VAL* 3.6 31.6 - - - +
573A VAL* 5.0 0.7 - - - -
591A ILE 3.3 10.4 + - - -
592A ILE 3.3 8.9 + - - -
593A LYS 3.3 3.1 - - - -
594A ASP* 1.3 79.4 - - - +
596A GLU* 1.3 61.6 + - - +
597A GLN* 4.1 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