Contacts of the helix formed by residues 528 - 534 (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 ILE 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A MET* 3.7 27.4 - - - -
173A PRO* 4.4 15.3 - - + -
174A PRO* 4.5 7.4 - - + -
178A GLU* 5.8 2.0 - - - +
193A PHE* 5.5 2.9 - - + -
201A ARG* 3.3 23.3 - - - +
455A HIS* 3.7 20.6 - - - +
483A TRP* 3.8 19.1 - - + -
526A THR* 2.9 5.1 + - - +
527A GLY* 1.3 76.2 - - - +
529A ARG* 1.3 60.7 + - - +
530A SER* 3.8 8.7 - - - +
531A GLU* 2.8 56.6 + - + +
532A SER* 3.3 5.3 + - - -
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Residues in contact with ARG 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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481A MET* 4.1 2.2 - - + -
483A TRP* 3.3 36.4 - - + +
484A SER 4.9 0.2 + - - -
485A ASP* 2.1 46.6 + - - -
492A TYR 5.6 0.6 + - - -
493A GLU* 3.2 26.4 - - - +
517A PRO* 3.3 19.0 - - - +
520A ALA* 4.7 7.8 - - - +
521A THR* 4.0 13.3 + - - -
526A THR 5.0 0.6 + - - -
527A GLY* 3.1 33.1 + - - -
528A ILE* 1.3 72.7 - - - +
530A SER* 1.3 58.1 + - - +
532A SER* 3.3 16.8 - - - +
533A GLU* 2.9 38.4 + - + +
582A PHE* 3.6 24.4 - - - -
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Residues in contact with SER 530 (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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455A HIS* 3.4 27.0 - - - -
456A ASP* 3.6 37.7 - - - +
459A VAL* 5.6 1.0 - - - +
481A MET* 3.8 13.0 - - - -
483A TRP* 3.8 10.8 - - - -
528A ILE* 3.8 4.0 - - - +
529A ARG* 1.3 78.6 - - - +
531A GLU* 1.3 58.8 + - - +
534A THR* 3.1 28.9 + - - -
535A GLU* 4.0 4.3 + - - +
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Residues in contact with GLU 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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171A MET* 5.6 0.3 - - - +
201A ARG* 3.1 28.1 + - - -
205A PHE* 6.1 1.0 - - - -
455A HIS* 4.9 4.5 + - - +
526A THR* 2.9 27.2 + - + -
528A ILE* 2.8 33.1 + - + +
530A SER* 1.3 79.2 - - - +
532A SER* 1.3 63.6 + - - +
534A THR* 3.3 16.7 + - - +
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Residues in contact with SER 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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520A ALA* 4.9 4.5 + - - +
524A SER* 3.3 36.8 + - - -
526A THR* 3.8 9.8 + - - +
528A ILE 3.3 2.7 + - - -
529A ARG* 3.3 32.4 + - - -
531A GLU* 1.3 77.0 - - - +
533A GLU* 1.3 67.3 + - - +
534A THR* 3.4 6.2 + - - +
583A ASN* 3.8 17.2 - - - +
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Residues in contact with GLU 533 (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* 3.7 22.0 - - - -
493A GLU* 2.6 39.9 - - - +
529A ARG* 2.9 24.3 + - + +
530A SER 4.4 0.2 - - - +
532A SER* 1.3 76.9 + - - +
534A THR* 1.3 76.9 + - - +
582A PHE* 3.5 3.6 - - - +
583A ASN* 2.7 29.8 + - - +
584A ARG 3.1 7.4 + - - -
585A MET* 2.9 29.1 + - + -
586A PRO* 3.5 17.3 - - - +
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Residues in contact with THR 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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481A MET* 4.8 0.7 - - - +
530A SER 3.1 18.9 + - - +
531A GLU* 3.3 14.3 + - - +
532A SER 3.2 7.3 - - - +
533A GLU* 1.3 95.1 + - - +
535A GLU* 1.3 58.9 + - - +
536A SER* 2.8 26.4 + - - -
586A PRO* 4.1 1.7 - - - +
589A ARG* 2.9 19.8 + - - -
618A PHE* 5.2 1.2 - - - -
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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