Contacts of the helix formed by residues 681 - 698 (chain B) in PDB entry 2PZ5
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 THR 681 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ILE* 3.9 6.1 - - - -
651B ILE* 4.1 11.2 - - + -
656B TYR* 3.6 18.2 - - + +
673B GLU* 5.2 0.2 + - - -
679B VAL* 5.3 7.0 - - + -
680B TYR* 1.3 88.0 - - - +
682B HIS* 1.3 61.8 + - - +
683B GLN* 3.3 22.1 + - - +
684B SER* 2.8 31.8 + - - +
685B ASP 3.4 2.6 + - - -
744B PRO* 5.1 4.2 - - - +
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Residues in contact with HIS 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ALA* 3.6 42.1 + - + +
621B LYS* 4.1 5.1 - - - +
622B CYS 3.5 34.7 + - - -
623B ILE* 3.8 6.1 - - - +
651B ILE* 3.9 27.1 - - + +
681B THR* 1.3 74.4 - - - +
683B GLN* 1.3 68.6 + - + +
685B ASP* 3.0 24.2 + - - +
686B VAL* 3.1 14.1 + - - +
750B PHE* 3.7 7.1 - - + -
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Residues in contact with GLN 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B THR* 3.1 11.6 - - - +
682B HIS* 1.3 85.5 - - + +
684B SER* 1.3 63.5 + - - +
685B ASP 3.2 0.2 - - - -
686B VAL* 3.4 15.8 + - - +
687B TRP 3.4 6.2 + - - -
744B PRO* 3.5 34.7 - - + +
745B SER* 5.0 3.5 - - - +
747B ARG* 2.9 33.3 + - - +
748B PRO 3.0 21.3 + - - +
749B THR* 3.9 27.3 - - - +
750B PHE* 4.9 1.4 - - - +
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Residues in contact with SER 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ALA* 3.7 12.4 + - - +
673B GLU* 3.0 24.1 + - - +
674B ALA* 5.3 1.2 + - - -
679B VAL* 4.6 2.8 + - - +
680B TYR* 3.4 34.1 + - - -
681B THR* 2.8 31.2 + - - +
683B GLN* 1.3 79.2 - - - +
685B ASP* 1.3 60.1 + - - +
687B TRP* 3.4 12.8 + - - +
688B SER* 3.4 13.9 + - - -
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Residues in contact with ASP 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B MET* 3.5 16.7 - - + +
622B CYS 4.4 1.2 - - - +
623B ILE* 3.5 9.8 - - - +
624B HIS* 3.0 26.0 + - - +
625B ARG* 3.0 15.5 + - - -
626B ASP 4.7 0.2 + - - -
627B LEU* 4.2 5.7 - - - +
680B TYR* 2.6 29.3 + - - -
681B THR 3.4 1.4 + - - -
682B HIS* 3.0 16.0 + - - +
684B SER* 1.3 77.4 - - - +
686B VAL* 1.3 50.5 + - - +
688B SER* 3.0 9.9 + - - -
689B PHE* 2.8 33.4 + - - +
750B PHE* 3.7 17.4 - - + -
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Residues in contact with VAL 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B HIS 3.1 13.8 + - - +
683B GLN* 3.5 21.1 - - - +
684B SER 3.3 0.2 - - - -
685B ASP* 1.3 74.5 - - - +
687B TRP* 1.3 66.8 + - - +
689B PHE* 3.1 5.2 + - - +
690B GLY 3.0 17.8 + - - -
739B CYS* 3.4 32.2 - - + +
747B ARG* 4.0 7.9 - - + -
748B PRO* 3.4 31.9 - - + +
749B THR 4.6 0.2 - - - -
750B PHE* 3.7 31.2 - - + +
753B LEU* 4.3 3.8 - - + -
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Residues in contact with TRP 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LYS 5.2 1.4 + - - -
669B TRP 3.9 6.6 + - - -
670B MET 3.5 11.2 + - - +
671B ALA* 3.6 24.7 - - + -
672B PRO* 3.5 31.6 - - + -
683B GLN 3.4 4.2 + - - -
684B SER 3.5 9.6 - - - +
685B ASP 3.2 0.4 - - - -
686B VAL* 1.3 77.9 - - - +
688B SER* 1.3 65.6 + - - +
690B GLY* 3.0 12.0 + - - -
691B VAL* 3.3 22.0 + - + +
704B TYR* 4.3 12.7 + - - -
716B LEU* 4.0 21.7 - - + +
721B ARG* 3.9 20.9 - - - -
739B CYS 3.4 12.7 + - - +
740B TRP* 3.2 50.1 + + + -
741B HIS 3.6 6.5 - - - -
742B ALA* 4.6 0.9 - - - -
747B ARG* 3.4 24.5 - - - +
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Residues in contact with SER 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ARG 5.1 2.9 + - - -
627B LEU* 3.8 30.3 + - - +
669B TRP* 2.8 28.6 + - - +
670B MET* 4.8 1.6 - - - -
671B ALA 5.0 0.2 + - - -
680B TYR* 3.9 9.4 + - - -
684B SER 3.4 10.1 + - - -
685B ASP* 3.0 12.2 + - - -
687B TRP* 1.3 76.7 - - - +
689B PHE* 1.3 66.4 + - - +
691B VAL* 3.0 8.4 + - - +
692B LEU* 2.9 20.8 + - - +
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Residues in contact with PHE 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B THR* 3.5 32.3 - - + -
610B LEU* 3.8 15.0 - - + -
611B ALA* 3.7 28.7 - - + -
614B MET* 4.3 2.2 - - + -
627B LEU* 3.7 21.7 - - + +
685B ASP 2.8 16.1 + - - +
686B VAL* 3.1 8.9 + - - +
688B SER* 1.3 73.2 - - - +
690B GLY* 1.3 57.6 + - - +
692B LEU* 3.2 14.0 + - + +
693B MET* 2.8 54.7 + - + +
739B CYS* 4.6 0.7 - - - -
750B PHE* 3.8 20.4 - + + -
753B LEU* 3.7 24.7 - - + -
757B LEU* 4.4 5.8 - - + -
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Residues in contact with GLY 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B VAL 3.0 10.5 + - - -
687B TRP 3.0 6.6 + - - -
689B PHE* 1.3 77.2 - - - +
691B VAL* 1.3 61.0 + - - +
693B MET* 3.1 15.8 + - - +
694B TRP 3.1 16.3 + - - -
736B MET* 4.0 2.2 - - - +
739B CYS* 3.7 16.8 - - - +
740B TRP* 3.3 23.2 - - - -
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Residues in contact with VAL 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LYS 3.6 22.0 - - - +
669B TRP* 3.5 31.6 - - + +
687B TRP* 3.6 27.4 - - + +
688B SER 3.0 6.0 + - - +
690B GLY* 1.3 72.7 - - - +
692B LEU* 1.3 60.8 + - - +
694B TRP* 3.0 5.1 + - - +
695B GLU* 2.8 28.3 + - + +
703B PRO* 3.8 21.5 - - + -
704B TYR* 4.8 2.5 - - - +
722B MET* 4.0 8.7 - - + -
740B TRP* 3.6 18.6 - - + +
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Residues in contact with LEU 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B LEU* 4.5 1.6 - - + -
610B LEU* 3.9 22.0 - - + -
627B LEU* 3.9 26.9 - - + -
628B ALA* 3.6 8.7 - - - -
629B ALA* 3.3 37.0 - - + +
632B VAL* 4.4 7.2 - - + -
669B TRP* 4.6 0.8 - - - +
688B SER 2.9 11.7 + - - +
689B PHE* 3.3 28.5 - - + +
691B VAL* 1.3 77.7 - - - +
693B MET* 1.3 61.9 + - + +
695B GLU* 3.2 12.6 + - - +
696B ILE* 3.0 36.9 + - + +
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Residues in contact with MET 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B THR* 3.7 24.9 - - + +
689B PHE* 2.8 30.5 + - + +
690B GLY* 3.1 15.0 + - - +
692B LEU* 1.3 76.5 - - + +
694B TRP* 1.3 63.9 + - - +
696B ILE* 3.2 8.7 + - + +
697B PHE* 3.0 35.4 + - + -
732B LEU* 4.9 4.0 - - - +
735B MET* 3.7 29.6 - - + +
736B MET* 3.6 35.7 - - + -
739B CYS* 3.5 32.8 - - - -
757B LEU* 5.5 0.4 - - - -
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Residues in contact with TRP 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690B GLY 3.1 11.3 + - - +
691B VAL 3.0 10.2 + - - +
693B MET* 1.3 78.6 - - - +
695B GLU* 1.3 64.5 + - + +
697B PHE* 3.3 1.4 + - - +
698B THR* 2.9 58.5 + - + +
701B GLY* 3.9 4.7 - - - -
702B SER 3.3 36.8 - - - -
703B PRO* 3.6 7.0 - - + -
705B PRO* 4.2 12.8 - - + -
722B MET* 3.4 45.8 - - + +
723B ASP 2.9 26.4 + - - -
725B PRO* 3.5 19.7 - - + +
733B TYR* 5.4 0.2 - + - -
736B MET* 4.0 10.7 - - - -
740B TRP* 4.0 11.2 - + + -
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Residues in contact with GLU 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B ARG* 3.7 18.0 + - - +
576B LEU* 4.6 1.1 - - - -
628B ALA* 3.6 1.4 - - - -
629B ALA* 2.8 42.7 + - + +
630B ARG* 4.9 1.9 + - - +
669B TRP* 2.8 42.3 + - - +
691B VAL* 2.8 17.1 + - + +
692B LEU* 3.5 10.5 - - - +
694B TRP* 1.3 78.9 - - + +
696B ILE* 1.3 58.9 + - - +
698B THR* 3.1 11.1 + - - -
700B GLY* 2.6 33.7 + - - -
701B GLY 3.9 12.5 - - - +
703B PRO* 4.5 8.3 - - + -
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Residues in contact with ILE 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B LEU* 3.9 17.0 - - + -
576B LEU* 3.7 11.8 - - + +
603B LEU* 3.7 29.0 - - + +
606B CYS* 3.8 23.1 - - - -
607B THR* 3.9 27.4 - - + +
610B LEU* 3.9 17.7 - - + -
629B ALA* 5.7 0.2 - - + -
689B PHE* 6.3 0.4 - - + -
692B LEU* 3.0 27.9 + - + +
693B MET* 3.5 9.0 - - - +
694B TRP 3.2 0.2 - - - -
695B GLU* 1.3 76.4 - - + +
697B PHE* 1.3 65.6 + - + +
699B LEU* 3.0 27.7 + - - +
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Residues in contact with PHE 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B PHE* 3.9 13.7 - + - -
603B LEU* 3.7 37.0 - - + +
604B VAL* 4.1 10.1 - - + -
607B THR* 3.5 27.6 - - + -
693B MET* 3.0 31.1 + - + +
696B ILE* 1.3 77.5 - - + +
698B THR* 1.3 59.4 + - - +
699B LEU* 3.2 10.9 - - - +
725B PRO* 3.7 27.1 - - + +
726B ALA 4.1 10.0 - - - +
727B ASN 4.9 3.4 - - - -
728B CYS* 4.3 16.4 - - + -
732B LEU* 3.6 35.7 - - + -
736B MET* 3.9 15.7 - - + -
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Residues in contact with THR 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ARG* 3.2 15.8 + - - -
694B TRP* 2.9 55.6 + - + +
695B GLU* 3.1 5.2 + - - -
697B PHE* 1.3 76.3 - - - +
699B LEU* 1.3 68.8 - - - +
701B GLY* 3.0 26.1 + - - -
725B PRO* 3.6 19.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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