Contacts of the helix formed by residues 574 - 581 (chain D) in PDB entry 7KHI
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 VAL 574 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527D LEU* 5.6 2.2 - - + -
533D ALA* 4.0 26.5 - - + +
536D LEU* 5.5 5.6 - - + -
537D TYR* 4.5 7.0 - - + +
542D ALA* 5.1 11.0 - - + -
543D SER 4.1 16.4 - - - +
544D LEU 3.9 9.2 - - - +
546D ALA* 3.6 16.6 + - + +
548D VAL* 4.0 20.6 - - + +
550D VAL* 5.8 0.7 - - - -
573D THR* 1.3 74.9 - - + +
575D GLY* 1.3 64.2 + - - +
577D ALA* 3.0 9.3 + - - +
578D ILE* 3.0 43.4 + - + +
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Residues in contact with GLY 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D MET* 3.5 36.1 - - - +
544D LEU* 3.0 29.1 + - - -
573D THR* 3.3 2.8 - - - +
574D VAL* 1.3 74.6 - - - +
576D ARG* 1.3 57.1 + - - +
578D ILE* 3.2 4.6 + - - +
579D LEU* 2.9 25.1 + - - +
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Residues in contact with ARG 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D MET 4.3 0.2 + - - -
514D THR* 3.1 37.6 + - + +
515D ARG* 4.8 0.4 - - - +
516D ASP* 4.1 18.6 - - - +
547D ARG* 6.2 0.6 - - - +
571D ASP 5.3 0.6 + - - -
572D THR* 3.1 28.0 - - - +
573D THR* 3.3 28.5 + - - +
574D VAL 3.2 0.6 - - - -
575D GLY* 1.3 75.2 - - - +
577D ALA* 1.3 56.8 + - - +
579D LEU* 3.4 7.9 + - - +
580D TRP* 2.8 27.2 + - - +
589D TYR* 3.9 6.1 - - - +
592D VAL* 3.6 23.4 - - + +
593D ASN* 2.9 34.2 + - - -
594D GLN* 3.3 17.0 + - - +
595D ALA* 4.4 3.4 - - - +
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Residues in contact with ALA 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D PRO* 3.8 26.6 - - + +
533D ALA* 4.2 14.4 - - + -
550D VAL* 4.6 17.0 - - + -
552D ILE* 5.7 2.0 - - + -
572D THR* 5.1 0.4 - - + -
573D THR 3.2 10.2 + - - +
574D VAL* 3.0 9.5 + - - +
576D ARG* 1.3 75.6 - - - +
578D ILE* 1.3 66.3 + - - +
580D TRP* 2.8 19.7 + - - +
581D MET 3.0 9.9 + - - -
589D TYR* 4.2 7.7 + - - +
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Residues in contact with ILE 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D MET* 4.9 5.2 - - + -
530D PRO 5.2 0.2 - - - -
533D ALA* 4.6 1.3 - - + -
534D GLU* 4.1 33.0 - - + +
537D TYR* 4.0 23.8 - - + -
544D LEU* 4.3 17.0 - - + -
574D VAL* 3.0 34.6 + - + +
575D GLY* 3.6 5.4 - - - +
577D ALA* 1.3 74.4 - - - +
579D LEU* 1.3 61.7 + - - +
581D MET* 3.2 27.6 - - + +
582D ILE* 4.4 4.0 + - - +
627D THR* 5.8 1.1 + - - +
631D TYR* 3.8 27.8 - - + +
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Residues in contact with LEU 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D LEU* 4.5 11.0 - - + -
513D MET* 3.7 16.1 - - - -
514D THR* 4.1 8.7 - - + -
575D GLY 2.9 16.9 + - - +
576D ARG* 3.6 4.3 - - - +
578D ILE* 1.3 72.4 - - - +
580D TRP* 1.3 64.9 + - - +
581D MET 3.0 3.6 + - - -
582D ILE* 3.1 35.7 + - + +
583D VAL* 3.9 6.4 + - + +
592D VAL* 4.2 22.7 - - + -
596D LEU* 3.1 35.7 - - + -
604D MET* 4.5 7.4 - - + -
620D PHE* 5.9 2.0 - - + -
624D ILE* 5.5 5.6 - - + -
627D THR* 4.3 13.2 - - + -
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Residues in contact with TRP 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D PRO* 4.0 23.6 - - + +
552D ILE* 4.7 12.5 - - + +
553D THR 4.1 23.2 + - - +
554D GLU* 4.2 12.6 - - + -
555D TYR* 6.3 0.7 - + - -
576D ARG 2.8 13.6 + - - +
577D ALA* 2.8 11.0 + - - +
579D LEU* 1.3 74.1 - - - +
581D MET* 1.3 68.9 + - - +
582D ILE 3.2 0.5 + - - -
583D VAL* 3.3 46.6 + - + +
584D PRO 5.0 2.5 - - - -
585D LYS* 5.1 3.6 - - - -
587D LEU 3.2 24.0 - - - -
588D PRO 4.0 2.5 - - - -
589D TYR* 3.4 54.5 - + + -
591D ILE* 5.0 0.7 - - + -
592D VAL* 4.4 8.0 - - + +
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Residues in contact with MET 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ARG* 3.7 30.3 - - - +
530D PRO* 3.5 44.4 - - + +
531D LYS* 3.7 25.8 - - - +
534D GLU* 3.9 13.0 - - + -
577D ALA 3.0 5.3 + - - -
578D ILE* 3.2 23.6 - - + +
579D LEU 3.0 0.8 - - - -
580D TRP* 1.3 81.7 - - - +
582D ILE* 1.3 66.1 + - + +
583D VAL 4.0 3.3 - - - +
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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