Contacts of the helix formed by residues 633 - 654 (chain B) in PDB entry 3ZNS
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 HIS 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B VAL 5.1 1.6 - - - +
530B LYS* 3.2 64.2 + - + +
630B ASN* 2.8 32.3 + - - +
632B LEU* 1.3 101.7 + - + +
634B SER* 1.3 62.8 + - - +
635B SER 3.4 2.2 - - - -
636B ASN* 3.6 11.8 + - - +
637B ALA* 3.2 22.9 + - - +
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Residues in contact with SER 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B HIS* 2.8 33.2 + - - -
629B TRP* 3.4 27.3 - - - -
630B ASN* 2.8 38.1 + - - +
633B HIS* 1.3 76.3 - - - +
635B SER* 1.3 60.8 + - - +
637B ALA* 3.3 2.6 + - - +
638B ALA* 2.9 32.7 + - - +
666B PRO* 5.4 0.2 - - - +
681B PHE* 5.7 0.2 - - - -
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Residues in contact with SER 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B TYR 2.7 27.9 + - - +
590B GLY 3.2 21.8 + - - -
591B THR 3.5 3.4 + - - -
592B ASN* 3.8 27.8 + - - -
629B TRP* 3.5 13.2 - - - -
632B LEU 5.5 0.2 - - - -
633B HIS 3.4 0.6 - - - +
634B SER* 1.3 77.3 - - - +
636B ASN* 1.3 65.1 + - - +
638B ALA* 4.1 1.9 - - - +
639B ARG* 3.0 29.4 + - - +
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Residues in contact with ASN 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B VAL* 4.2 15.2 - - + +
571B LYS* 3.8 30.5 - - - +
592B ASN* 4.1 17.3 + - - +
632B LEU 4.0 13.9 - - - +
633B HIS* 3.6 11.6 + - - +
634B SER 3.3 0.2 - - - -
635B SER* 1.3 80.0 + - - +
637B ALA* 1.3 51.3 + - - +
639B ARG* 3.4 9.8 + - - +
640B TRP* 2.8 35.3 + - - +
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Residues in contact with ALA 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B VAL* 4.0 24.9 - - - +
528B MET* 3.9 8.4 - - - +
531B HIS* 3.8 25.4 - - + +
633B HIS 3.2 15.4 + - - +
634B SER 3.3 3.8 + - - +
636B ASN* 1.3 78.5 - - - +
638B ALA* 1.3 58.7 + - - +
640B TRP* 3.2 3.4 + - - +
641B ALA* 3.0 28.6 + - - +
665B ARG 3.8 4.3 - - - +
666B PRO* 3.9 6.5 - - + -
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Residues in contact with ALA 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B TYR 5.4 0.7 - - - +
629B TRP* 5.5 0.9 - - + -
634B SER 2.9 17.9 + - - +
635B SER* 4.1 3.4 - - - +
637B ALA* 1.3 76.5 - - - +
639B ARG* 1.3 62.1 + - - +
641B ALA* 3.3 4.8 + - - +
642B ALA* 3.2 21.5 + - - +
666B PRO* 3.8 23.9 - - + +
681B PHE* 4.1 17.5 - - + -
682B PHE* 3.9 27.0 - - + +
684B SER* 4.8 0.5 + - - -
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Residues in contact with ARG 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LYS* 4.0 32.4 - - + +
572B ALA* 2.8 52.3 + - - +
573B SER* 3.9 9.3 - - - +
574B LEU* 4.0 15.0 - - - +
577B LEU* 3.9 18.6 - - + +
590B GLY* 3.3 33.0 + - - -
597B LEU* 5.8 4.4 - - - +
635B SER* 3.0 22.8 + - - +
636B ASN* 3.8 7.9 - - - +
638B ALA* 1.3 75.5 - - - +
640B TRP* 1.3 56.7 - - - +
642B ALA* 3.5 3.1 + - - -
643B GLY 3.0 15.1 + - - -
682B PHE* 4.1 11.4 - - + -
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Residues in contact with TRP 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ASP* 3.5 13.8 - - + +
527B VAL* 4.0 31.6 - - + -
528B MET* 4.0 22.7 - - + -
568B ARG* 2.8 56.1 + - - -
569B GLY 3.5 17.5 - - - -
570B ARG* 3.2 18.2 - - + +
571B LYS* 3.6 44.6 - - + +
636B ASN 2.8 18.2 + - - +
637B ALA 3.2 5.4 + - - +
639B ARG* 1.3 75.6 - - - +
641B ALA* 1.3 58.0 + - - +
644B SER* 2.7 58.3 + - - -
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Residues in contact with ALA 641 (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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528B MET* 4.1 9.3 - - - -
637B ALA 3.0 13.5 + - - +
638B ALA* 3.3 9.4 + - - +
640B TRP* 1.3 77.0 - - - +
642B ALA* 1.3 63.2 + - - +
644B SER* 3.3 1.4 + - - -
645B VAL* 3.1 29.3 + - - +
664B VAL* 4.1 14.5 - - + +
665B ARG 4.0 9.2 - - - +
666B PRO 3.8 22.2 - - - +
684B SER* 3.7 10.3 - - - +
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Residues in contact with ALA 642 (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 ALA* 3.9 13.2 - - + -
577B LEU* 4.1 6.1 - - + -
638B ALA 3.2 10.2 + - - +
639B ARG 3.8 6.5 - - - +
641B ALA* 1.3 79.9 - - - +
643B GLY* 1.3 61.0 + - - +
645B VAL* 3.6 1.6 + - - +
646B THR* 3.0 29.4 + - - -
682B PHE* 4.6 3.1 - - + -
684B SER* 3.4 21.7 + - - +
687B ILE* 4.0 26.5 - - + -
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Residues in contact with GLY 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ARG* 3.3 25.7 - - - -
571B LYS 4.1 1.1 - - - -
572B ALA* 3.6 18.3 - - - +
639B ARG 3.0 11.3 + - - -
642B ALA* 1.3 76.2 - - - +
644B SER* 1.3 56.6 + - - +
646B THR* 3.5 7.1 + - - -
647B ASP* 2.8 32.7 + - - +
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Residues in contact with SER 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ILE* 3.4 32.0 - - - +
568B ARG 3.7 1.4 + - - -
569B GLY* 3.3 20.9 - - - -
570B ARG 3.5 0.8 + - - -
640B TRP* 2.7 43.0 + - - -
641B ALA 3.7 3.4 - - - -
643B GLY* 1.3 74.1 - - - +
645B VAL* 1.3 60.6 + - - +
647B ASP* 3.3 2.8 + - - +
648B LEU* 2.9 29.5 + - - +
664B VAL* 4.1 5.2 - - - -
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Residues in contact with VAL 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ALA 3.1 16.6 + - - +
642B ALA 4.1 2.9 - - - +
644B SER* 1.3 73.9 - - - +
646B THR* 1.3 64.2 + - - +
648B LEU* 3.3 7.7 + - - +
649B ALA* 2.9 22.3 + - - +
662B ALA* 3.9 22.2 - - + -
664B VAL* 4.0 11.7 - - + -
684B SER* 4.1 21.8 - - - +
685B VAL* 4.5 4.5 - - + -
688B ALA* 3.9 16.6 - - + -
795B LEU* 5.0 4.0 - - + -
836B VAL* 4.7 11.3 - - + +
838B ALA* 3.9 24.5 - - + -
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Residues in contact with THR 646 (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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570B ARG* 3.8 17.9 - - - +
576B GLU* 3.9 10.8 + - - +
642B ALA 3.0 21.4 + - - -
643B GLY* 3.5 7.1 - - - -
645B VAL* 1.3 76.6 - - - +
647B ASP* 1.3 63.7 + - - +
649B ALA* 3.2 3.1 + - - +
650B PHE* 3.0 52.9 + - + -
687B ILE* 3.8 10.9 - - - +
688B ALA* 3.5 27.0 + - - +
691B GLN* 4.2 7.6 - - + -
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Residues in contact with ASP 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ILE* 5.3 2.5 - - + -
567B LEU* 6.0 0.4 - - + -
569B GLY* 4.8 9.1 - - - -
570B ARG* 2.7 50.1 + - + +
643B GLY 2.8 16.9 + - - +
644B SER* 3.3 7.2 + - - +
646B THR* 1.3 73.2 - - - +
648B LEU* 1.3 62.5 + - - +
650B PHE* 3.4 8.6 + - - +
651B LYS* 3.3 44.7 + - - +
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Residues in contact with LEU 648 (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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521B GLY* 4.2 10.5 - - - -
522B LEU 4.7 0.2 - - - +
523B ILE* 4.1 10.7 - - + +
567B LEU* 4.3 10.8 - - + -
644B SER 2.9 17.4 + - - +
645B VAL* 3.7 4.9 - - - +
647B ASP* 1.3 76.9 - - - +
649B ALA* 1.3 63.5 + - - +
651B LYS* 3.5 3.9 + - - +
652B VAL* 3.2 29.7 + - + +
657B LEU* 3.8 23.8 - - + -
660B GLY* 3.7 14.1 - - - -
661B PHE 3.6 40.2 - - - +
662B ALA* 3.7 9.4 - - + +
836B VAL* 3.7 22.2 - - + -
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Residues in contact with ALA 649 (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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645B VAL 2.9 17.3 + - - +
646B THR 3.2 5.6 + - - +
648B LEU* 1.3 74.9 - - - +
650B PHE* 1.3 53.3 + - - +
652B VAL* 3.3 2.4 + - - +
653B ALA* 2.7 35.9 + - - +
688B ALA* 4.3 4.7 - - + -
692B LEU* 3.6 29.2 - - + -
793B LEU* 3.9 2.1 - - - +
795B LEU* 4.2 18.2 - - + -
836B VAL* 3.9 12.7 - - + +
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Residues in contact with PHE 650 (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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570B ARG* 5.8 0.9 - - - -
576B GLU* 5.6 1.6 - - - -
646B THR* 3.0 46.3 + - + +
647B ASP* 3.8 11.4 - - - +
648B LEU 3.4 0.2 - - - -
649B ALA* 1.3 74.8 - - - +
651B LYS* 1.3 58.5 - - + +
653B ALA* 3.2 6.8 + - + +
654B SER* 2.8 33.0 + - - -
691B GLN* 3.6 21.8 - - + -
692B LEU* 3.3 22.7 - - + -
695B GLN* 3.4 46.7 - - + -
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Residues in contact with LYS 651 (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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565B GLU* 6.3 0.2 - - + -
567B LEU* 3.6 39.7 - - + -
647B ASP* 3.3 28.5 + - - +
648B LEU 3.8 3.6 - - - +
649B ALA 3.4 0.2 - - - -
650B PHE* 1.3 77.3 - - + +
652B VAL* 1.3 58.3 + - - +
654B SER* 3.2 9.5 + - - -
656B GLU* 2.9 42.5 + - + +
657B LEU* 3.0 25.6 + - + +
593C PRO* 4.9 16.0 - - - +
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Residues in contact with VAL 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.2 22.2 + - + +
649B ALA 3.7 3.8 - - - +
651B LYS* 1.3 75.3 - - - +
653B ALA* 1.3 60.3 + - - +
655B ARG* 3.0 18.9 + - - -
657B LEU* 3.6 24.9 - - + +
658B LYS 3.6 19.3 - - - +
659B ASN 4.0 16.6 - - - -
660B GLY 4.3 0.4 - - - +
793B LEU* 4.1 3.1 - - + -
834B ALA* 3.8 27.9 - - + +
835B VAL 4.1 5.8 - - - +
836B VAL* 3.8 19.7 - - + -
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Residues in contact with ALA 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B ALA 2.7 23.0 + - - +
650B PHE* 3.6 8.5 - - - +
652B VAL* 1.3 72.7 - - - +
654B SER* 1.3 57.8 + - - +
655B ARG* 3.2 1.5 + - - +
692B LEU* 4.3 12.6 - - + -
696B SER* 5.7 4.7 - - - +
793B LEU* 4.0 17.2 - - + +
834B ALA* 5.8 0.9 - - - -
571C LYS* 5.8 0.9 + - - -
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Residues in contact with SER 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B PHE 2.8 20.9 + - - -
651B LYS* 3.2 9.9 + - - -
652B VAL 3.2 0.2 - - - -
653B ALA* 1.3 72.9 - - - +
655B ARG* 1.3 67.4 + - - +
656B GLU* 3.1 28.9 + - - +
571C LYS* 4.9 13.1 - - - +
639C ARG* 3.9 11.3 + - - -
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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
------------------------------------------------------------
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