Contacts of the helix formed by residues 659 - 672 (chain K) in PDB entry 4P6X
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 SER 659 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610K TRP* 3.6 2.5 - - - -
657K GLN 3.5 2.1 + - - -
658K VAL* 1.3 79.2 - - - +
660K TYR* 1.3 64.7 + - - +
661K GLU* 4.0 8.4 + - - +
662K GLU* 2.9 37.8 + - - +
663K TYR* 3.0 19.9 + - - +
704K ARG* 3.4 27.2 - - - +
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Residues in contact with TYR 660 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537K GLU* 3.7 32.0 + - + -
540K GLU* 3.4 28.2 - - - +
610K TRP* 3.3 42.5 - + + -
659K SER* 1.3 72.9 - - - +
661K GLU* 1.3 70.2 + - - +
663K TYR* 3.0 19.5 + + - +
664K LEU* 3.0 51.1 + - + +
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Residues in contact with GLU 661 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533K VAL* 3.5 34.7 - - + +
537K GLU* 4.4 17.4 - - - +
659K SER* 3.4 6.9 + - - +
660K TYR* 1.3 83.2 + - - +
662K GLU* 1.3 64.3 + - - +
664K LEU* 3.4 4.6 + - + -
665K CYS* 3.3 27.7 + - - -
700K ALA* 4.1 15.3 - - + +
703K LYS* 3.6 26.8 + - + +
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Residues in contact with GLU 662 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658K VAL* 3.5 7.8 - - + +
659K SER* 2.9 40.4 + - - +
660K TYR 3.3 0.4 - - - -
661K GLU* 1.3 77.4 - - - +
663K TYR* 1.3 57.2 + - - +
665K CYS 3.4 0.3 + - - -
666K MET* 3.0 34.2 + - - +
697K LEU* 3.7 6.1 - - + +
700K ALA* 4.0 24.4 - - + +
701K ILE* 3.6 7.9 - - + +
704K ARG* 3.5 12.2 + - - +
714K ARG* 2.6 45.6 + - - -
718K LEU* 3.4 21.2 - - + +
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Residues in contact with TYR 663 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540K GLU* 3.7 8.1 + - - -
606K PHE* 3.3 42.8 - + - -
607K ALA* 3.4 20.6 + - - +
610K TRP* 3.4 55.9 - + + +
653K LEU* 5.3 0.7 - - + -
658K VAL* 3.9 7.1 - - + +
659K SER 3.0 13.4 + - - +
660K TYR* 3.0 33.0 + + - +
662K GLU* 1.3 73.9 - - - +
664K LEU* 1.3 68.3 + - + +
666K MET* 3.2 7.1 + - - +
667K LYS* 2.9 60.3 + - - +
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Residues in contact with LEU 664 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533K VAL* 4.2 8.1 - - + +
536K LEU* 3.7 27.7 - - + +
537K GLU* 3.8 25.8 - - + +
540K GLU* 3.9 22.4 - - + +
577K TRP* 5.4 0.4 - - - +
660K TYR* 3.0 57.7 + - + +
661K GLU* 3.4 13.0 + - - +
663K TYR* 1.3 85.7 - - + +
665K CYS* 1.3 60.5 + - - +
667K LYS* 3.5 7.5 + - - +
668K VAL* 3.4 26.2 + - - +
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Residues in contact with CYS 665 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533K VAL* 4.0 15.3 - - - -
536K LEU* 4.3 8.5 - - - -
661K GLU 3.3 14.7 + - - +
662K GLU 3.8 6.1 - - - +
663K TYR 3.2 0.4 - - - -
664K LEU* 1.3 76.4 - - - +
666K MET* 1.3 66.7 + - - +
668K VAL* 3.4 5.3 + - - +
669K LEU* 3.1 27.4 + - - +
693K TYR* 4.4 6.4 - - + +
696K GLU* 3.6 34.1 - - + -
697K LEU* 3.8 28.7 - - + +
700K ALA* 4.4 3.8 - - - -
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Residues in contact with MET 666 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606K PHE* 3.8 24.7 - - + -
658K VAL* 4.2 9.9 - - - -
662K GLU 3.0 27.6 + - - +
663K TYR 3.2 5.1 + - - +
665K CYS* 1.3 76.8 - - - +
667K LYS* 1.3 56.7 + - - +
669K LEU* 3.1 9.1 + - - +
670K LEU* 2.9 30.3 + - - +
697K LEU* 3.9 17.9 - - + -
718K LEU* 3.4 47.1 - - + +
721K LEU* 4.0 22.2 - - + -
722K LEU* 3.7 24.2 - - + +
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Residues in contact with LYS 667 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540K GLU* 2.7 35.3 + - - -
541K PRO* 5.4 0.6 - - - +
577K TRP* 3.3 27.5 - - + +
603K LEU* 3.5 39.6 - - + +
606K PHE* 4.0 15.5 - - + -
607K ALA* 4.7 4.5 - - + -
663K TYR* 2.9 52.2 + - + +
664K LEU* 3.8 8.5 + - - +
665K CYS 3.2 0.4 - - - -
666K MET* 1.3 74.3 - - - +
668K VAL* 1.3 66.2 + - - +
670K LEU* 3.1 11.7 + - - +
671K LEU 3.2 8.7 + - - -
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Residues in contact with VAL 668 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536K LEU* 3.6 32.1 - - + -
577K TRP* 4.1 20.9 - - + -
581K ILE* 4.2 13.5 - - + -
664K LEU 3.4 14.3 + - - +
665K CYS 3.7 7.0 - - - +
666K MET 3.3 0.2 - - - -
667K LYS* 1.3 75.3 - - - +
669K LEU* 1.3 63.9 + - - +
671K LEU* 3.0 16.8 + - + +
672K LEU* 3.2 19.4 + - + +
693K TYR* 3.6 40.2 - - + -
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Residues in contact with LEU 669 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665K CYS 3.1 18.8 + - - +
666K MET* 3.1 10.0 + - - +
668K VAL* 1.3 76.6 - - - +
670K LEU* 1.3 56.8 + - - +
672K LEU* 3.0 29.4 + - + +
673K SER* 3.2 6.6 + - - -
690K ARG* 3.8 25.1 + - + +
693K TYR* 3.9 24.0 - - + +
694K ILE* 3.8 24.2 - - + -
697K LEU* 4.0 18.6 - - + -
722K LEU* 3.7 28.0 - - + -
774K PHE* 4.0 14.8 - - + -
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Residues in contact with LEU 670 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599K SER* 3.3 15.7 - - - -
602K ALA* 3.9 22.0 - - + +
603K LEU* 4.5 6.1 - - + -
606K PHE* 3.4 50.9 - - + -
666K MET 2.9 14.9 + - - +
667K LYS* 3.1 8.9 + - - +
669K LEU* 1.3 71.6 - - - +
671K LEU* 1.3 62.0 + - - +
672K LEU 3.0 5.2 - - - -
673K SER* 2.8 29.8 + - - +
722K LEU* 3.8 23.1 - - + +
725K MET* 3.8 28.3 - - + -
726K HIS* 6.5 0.2 - - + -
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Residues in contact with LEU 671 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577K TRP* 4.0 7.9 - - + -
578K ALA* 4.1 4.5 - - + -
581K ILE* 3.7 29.8 - - + -
584K PHE* 3.7 26.9 - - + -
595K LEU* 3.7 33.6 - - + +
596K LEU* 3.9 26.9 - - + +
599K SER* 3.5 20.9 + - - +
603K LEU* 4.0 13.4 - - + +
667K LYS 3.2 9.7 + - - +
668K VAL* 3.0 13.3 + - + +
670K LEU* 1.3 76.2 - - - +
672K LEU* 1.3 61.9 + - + +
673K SER 3.5 1.0 + - - -
674K THR 5.1 0.5 + - - +
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Residues in contact with LEU 672 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584K PHE* 4.9 6.7 - - + -
587K LEU* 5.2 2.0 - - + -
595K LEU* 4.0 13.7 - - + -
668K VAL* 3.2 32.5 + - + +
669K LEU* 3.0 15.6 + - + +
671K LEU* 1.3 91.7 - - + +
673K SER* 1.3 56.1 + - - +
674K THR 3.7 1.1 - - - -
686K PHE* 3.5 33.4 - - + -
689K ILE* 4.0 18.4 - - + -
690K ARG* 3.1 52.7 + - + +
693K TYR* 4.2 2.7 - - + -
772K LEU* 3.2 7.4 - - - +
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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