Contacts of the helix formed by residues 675 - 693 (chain B) in PDB entry 2PZI
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 GLU 675 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B THR* 5.0 9.2 - - + -
672B PRO* 3.5 20.9 + - + +
674B THR* 1.3 80.5 + - - +
676B PRO* 1.4 79.3 - - - +
677B ARG* 3.2 33.0 + - + +
678B VAL* 3.0 32.3 + - + +
679B LEU* 3.2 12.1 + - - +
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Residues in contact with PRO 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B THR 3.4 9.4 - - - +
675B GLU* 1.4 93.2 - - - +
677B ARG* 1.3 58.9 + - + +
679B LEU* 3.1 8.8 + - + +
680B GLN* 2.9 45.1 + - - +
724B LEU* 3.9 11.5 - - + +
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Residues in contact with ARG 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ASP* 4.2 14.6 + - - +
428B VAL* 3.7 44.0 + - - +
429B ALA* 3.9 28.1 + - - +
431B THR* 4.9 0.4 - - - -
638B THR* 4.8 9.5 + - - -
641B LEU* 4.0 14.8 - - + -
675B GLU* 3.2 17.6 + - - +
676B PRO* 1.3 77.6 - - + +
678B VAL* 1.3 66.1 + - - +
680B GLN* 3.4 19.7 + - - +
681B ILE* 3.0 30.9 + - - +
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B THR* 4.3 14.8 - - + -
641B LEU* 4.0 10.5 - - + -
668B VAL* 3.7 28.0 - - + +
671B LEU* 4.0 23.1 - - + +
672B PRO* 3.3 27.1 - - + +
673B PRO* 4.6 6.1 - - + +
675B GLU* 3.0 25.1 + - + +
677B ARG* 1.3 76.2 - - - +
679B LEU* 1.3 57.5 + - + +
681B ILE* 3.3 2.1 + - - -
682B ARG* 3.1 33.5 + - - +
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Residues in contact with LEU 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PRO* 3.1 30.3 - - + +
674B THR* 4.3 13.2 - - - +
675B GLU 3.2 5.6 + - - +
676B PRO* 3.1 7.7 + - + +
678B VAL* 1.3 73.0 - - + +
680B GLN* 1.3 64.8 + - - +
682B ARG* 3.2 38.5 - - - +
683B ALA* 3.4 6.2 + - - +
720B SER* 4.8 4.9 - - - +
723B SER* 4.8 19.7 - - - +
724B LEU* 3.6 30.7 - - + +
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Residues in contact with GLN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B THR* 3.4 42.7 + - - +
676B PRO* 2.9 34.4 + - - +
677B ARG* 3.6 24.0 + - - +
679B LEU* 1.3 77.2 - - - +
681B ILE* 1.3 60.9 + - - +
683B ALA* 3.4 6.4 + - - +
684B LEU* 3.2 18.7 + - - +
724B LEU* 3.8 17.1 - - + +
726B ARG* 3.9 25.1 - - - +
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Residues in contact with ILE 681 (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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428B VAL* 4.2 14.1 - - + -
431B THR* 3.8 31.0 - - + +
641B LEU* 3.8 33.7 - - + +
644B ALA* 4.4 1.3 - - + -
645B VAL* 3.9 32.3 - - + -
668B VAL* 4.0 20.4 - - + -
677B ARG* 3.0 21.8 + - + +
678B VAL 3.9 0.4 - - - +
679B LEU 3.3 0.2 - - - -
680B GLN* 1.3 73.8 - - - +
682B ARG* 1.3 56.1 + - - +
683B ALA 3.2 0.2 - - - -
684B LEU* 3.0 6.1 + - + -
685B VAL* 2.8 41.2 + - + +
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Residues in contact with ARG 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B VAL* 3.4 20.3 - - + +
669B GLU* 4.6 12.5 - - - +
678B VAL* 3.1 25.0 + - - +
679B LEU* 3.2 33.5 - - - +
681B ILE* 1.3 75.5 - - - +
683B ALA* 1.3 60.2 + - - +
685B VAL 3.5 0.5 + - - -
686B LEU* 3.2 23.7 + - + +
704B LEU* 3.3 66.3 + - + +
706B PHE* 5.1 4.0 - - - -
720B SER* 4.7 17.2 + - - +
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Residues in contact with ALA 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU 3.4 6.0 + - - +
680B GLN* 3.6 10.3 - - - +
681B ILE 3.2 0.6 - - - -
682B ARG* 1.3 78.3 - - - +
684B LEU* 1.3 54.0 + - - +
686B LEU* 3.3 4.1 + - - +
687B GLY* 2.6 34.7 + - - -
717B VAL* 4.4 8.1 - - + +
720B SER* 3.9 25.3 - - - -
721B LEU* 4.3 25.6 - - + -
724B LEU* 5.1 1.3 - - + -
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Residues in contact with LEU 684 (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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427B LEU 5.3 1.3 - - - +
431B THR* 3.9 27.4 - - + -
645B VAL* 4.0 32.3 - - + -
648B LEU* 4.1 8.3 - - + +
680B GLN 3.2 11.1 + - - +
681B ILE* 3.0 13.5 + - + +
683B ALA* 1.3 80.5 - - - +
685B VAL* 1.3 56.2 + - + +
687B GLY* 4.4 2.5 - - - +
688B GLY* 2.9 27.7 + - - +
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Residues in contact with VAL 685 (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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644B ALA* 4.6 2.2 - - + -
648B LEU* 3.7 23.4 - - + +
661B ILE* 4.2 15.2 - - + +
664B ALA* 4.4 10.5 - - + -
665B ALA* 4.1 21.3 - - + +
668B VAL* 4.2 21.5 - - + -
681B ILE* 2.8 26.3 + - + +
682B ARG 3.8 4.7 - - - +
684B LEU* 1.3 74.4 - - - +
686B LEU* 1.3 61.8 + - - +
688B GLY* 3.4 0.9 + - - -
689B ALA* 2.9 28.6 + - - +
703B ILE* 4.9 3.4 - - + -
704B LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B ARG* 3.2 17.6 + - - +
683B ALA 3.8 2.9 - - - +
685B VAL* 1.3 75.4 - - - +
687B GLY* 1.3 63.0 + - - +
689B ALA* 3.3 5.1 + - - +
690B LEU* 3.0 24.4 + - - +
703B ILE* 3.5 31.4 - - + +
704B LEU* 4.1 15.3 - - + +
706B PHE* 4.3 13.0 - - + -
713B LEU* 3.6 27.6 - - + +
716B GLY* 3.5 19.1 - - - +
717B VAL* 4.0 13.9 - - + +
720B SER* 3.3 27.1 - - - +
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Residues in contact with GLY 687 (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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683B ALA 2.6 22.3 + - - -
684B LEU* 3.9 3.8 - - - -
686B LEU* 1.3 72.5 - - - +
688B GLY* 1.3 60.1 + - - +
690B LEU* 3.6 6.9 + - - +
691B ASP* 3.4 22.0 + - - +
717B VAL* 3.6 16.0 - - - +
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Residues in contact with GLY 688 (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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648B LEU* 4.9 15.0 - - - -
684B LEU* 2.9 19.9 + - - +
685B VAL 3.7 1.3 - - - -
687B GLY* 1.3 75.8 - - - +
689B ALA* 1.3 65.0 + - - +
691B ASP* 3.3 6.3 + - - +
692B TRP* 3.0 23.5 + - - +
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Residues in contact with ALA 689 (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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648B LEU* 4.8 1.8 - - - +
661B ILE* 4.0 14.4 - - + -
685B VAL 2.9 17.2 + - - +
686B LEU 3.6 4.7 - - - +
688B GLY* 1.3 74.4 - - - +
690B LEU* 1.3 64.0 + - - +
692B TRP* 3.1 11.1 + - - +
693B LEU* 3.0 24.9 + - - +
703B ILE* 3.9 20.6 - - + -
708B PHE* 4.0 7.4 - - + -
713B LEU* 3.6 17.9 - - + -
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Residues in contact with LEU 690 (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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686B LEU 3.0 16.1 + - - +
687B GLY* 3.7 7.0 - - - +
689B ALA* 1.3 75.4 - - - +
691B ASP* 1.3 63.1 + - - +
693B LEU* 3.2 18.2 + - - +
694B LYS* 3.9 5.4 + - - +
710B SER* 3.3 41.7 - - - +
713B LEU* 3.6 19.6 - - + +
714B ARG* 4.0 33.7 - - + +
717B VAL* 5.0 9.2 - - + -
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Residues in contact with ASP 691 (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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687B GLY 3.4 10.5 + - - +
688B GLY* 3.3 9.3 + - - +
689B ALA 3.3 0.6 - - - -
690B LEU* 1.3 77.7 - - - +
692B TRP* 1.3 64.6 + - - +
694B LYS* 3.1 51.6 + - - +
695B ASP* 5.3 1.9 - - - +
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Residues in contact with TRP 692 (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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648B LEU* 6.4 0.2 - - + -
655B GLU* 3.7 12.1 + - - -
656B VAL* 2.7 31.5 + - + -
657B THR* 4.5 0.2 - - - -
658B GLU* 3.5 38.6 - - + -
661B ILE* 3.5 18.6 - - + +
688B GLY 3.0 14.2 + - - +
689B ALA* 3.2 11.4 - - - +
691B ASP* 1.3 75.9 + - - +
693B LEU* 1.3 84.7 + - + +
694B LYS 3.2 1.6 + - - -
695B ASP* 3.2 3.9 + - - +
696B ASN* 3.0 67.4 + - + +
697B LYS 3.7 11.2 - - - -
698B ALA* 3.6 12.3 - - + -
708B PHE* 3.7 14.4 - + - -
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Residues in contact with LEU 693 (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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689B ALA 3.0 14.3 + - - +
690B LEU* 3.4 10.5 - - - +
691B ASP 3.1 0.8 - - - -
692B TRP* 1.3 97.9 - - + +
694B LYS* 1.3 62.8 + - - +
695B ASP 3.2 0.7 - - - -
696B ASN 3.2 23.9 - - - +
697B LYS* 4.7 0.7 - - - -
698B ALA* 4.0 13.9 - - + +
708B PHE* 3.8 13.7 - - + +
709B THR* 3.5 13.9 - - - -
710B SER* 3.4 37.2 - - - +
713B LEU* 3.8 11.2 - - + -
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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
------------------------------------------------------------
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