Contacts of the helix formed by residues 628 - 643 (chain B) in PDB entry 1ZY7
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 CYS 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B GLY 3.2 19.5 - - - +
388B LEU* 4.0 15.0 - - - +
389B ALA 4.4 3.1 - - - +
390B LEU* 3.9 13.7 - - + -
401B ARG* 3.7 0.4 - - - -
624B ALA* 3.9 19.5 - - - -
625B SER* 3.1 31.4 + - - +
626B ARG 3.5 0.4 - - - -
627B LEU* 1.3 80.2 - - - +
629B LYS* 1.3 67.4 + - - +
630B HIS* 3.7 5.2 - - - -
631B ALA* 3.1 18.5 + - - -
632B LEU* 2.9 19.6 + - - +
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Residues in contact with LYS 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLY* 3.4 24.6 + - - +
389B ALA 5.6 7.5 + - - +
391B ASN* 4.2 9.7 - - - +
401B ARG* 3.5 7.9 - - - +
628B CYS* 1.3 71.8 - - - +
630B HIS* 1.3 58.3 + - - +
632B LEU* 3.2 4.0 + - - +
633B TYR* 2.8 31.7 + - - +
658B TYR* 3.8 19.6 - - + +
662B LYS* 4.0 0.4 - - - +
694B GLN* 3.7 34.3 - - + +
695B ASP* 2.9 29.8 + - - +
697B PHE* 3.9 4.0 - - + -
902B IHP 2.9 56.5 + - - +
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Residues in contact with HIS 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG 4.0 13.5 - - - +
387B GLY 2.9 20.8 + - - +
388B LEU* 3.8 20.6 - - + +
628B CYS* 4.0 1.8 - - - -
629B LYS* 1.3 77.0 - - - +
631B ALA* 1.3 58.9 + - - +
633B TYR* 3.3 3.3 + - - +
634B CYS* 2.9 32.4 + - + +
697B PHE* 4.0 19.3 - + + -
698B SER 4.3 1.8 - - - -
699B LEU* 3.6 21.6 - - + +
700B THR* 3.2 42.4 + - - -
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Residues in contact with ALA 631 (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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625B SER 3.5 17.9 - - - +
626B ARG* 3.4 26.7 - - - +
628B CYS* 3.1 11.1 + - - +
630B HIS* 1.3 79.8 + - - +
632B LEU* 1.3 66.9 + - - +
634B CYS* 3.3 9.6 + - - +
635B ARG* 3.2 25.0 + - - +
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Residues in contact with LEU 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ARG* 3.6 42.6 - - + +
404B LEU* 4.0 30.1 - - + -
405B ARG* 4.1 25.8 - - + -
408B TYR* 3.9 16.4 + - + +
532B LEU* 5.6 2.2 - - + -
626B ARG 4.3 7.2 - - - +
627B LEU* 3.6 9.2 - - - +
628B CYS 2.9 13.3 + - - +
629B LYS* 3.7 7.4 - - - +
631B ALA* 1.3 74.6 - - - +
633B TYR* 1.3 58.1 + - - +
635B ARG* 3.2 8.4 + - + +
636B TRP* 2.9 27.0 + - - +
658B TYR* 5.1 5.2 - - + +
902B IHP 4.7 7.0 - - - +
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Residues in contact with TYR 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU* 4.0 9.9 - - + -
629B LYS 2.8 17.1 + - - +
630B HIS* 3.5 7.0 - - - +
631B ALA 3.2 0.2 - - - -
632B LEU* 1.3 74.9 - - - +
634B CYS* 1.3 54.0 + - - +
636B TRP* 3.2 26.5 + + - -
637B MET* 2.8 53.5 + - + +
656B ASN 2.7 31.9 + - - -
657B VAL 3.7 0.5 - - - -
658B TYR* 3.4 40.3 - + + -
661B SER* 2.8 31.4 + - - -
697B PHE* 4.1 9.2 - + - -
699B LEU* 3.5 28.0 - - + -
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Residues in contact with CYS 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B HIS* 2.9 18.3 + - - +
631B ALA* 3.3 13.7 - - - +
633B TYR* 1.3 77.2 - - - +
635B ARG* 1.3 64.8 + - + +
637B MET* 3.4 2.3 + - - +
638B ARG* 3.1 29.7 + - - +
699B LEU* 3.8 20.1 - - + +
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Residues in contact with ARG 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ARG* 3.8 37.5 + - + +
408B TYR* 3.6 29.7 - - + +
409B THR* 2.9 39.8 + - - +
412B GLU* 3.1 22.5 + - - +
626B ARG 6.0 0.9 - - - +
631B ALA 3.2 13.0 + - - +
632B LEU* 3.2 10.0 + - + +
634B CYS* 1.3 80.2 - - + +
636B TRP* 1.3 63.2 + - - +
638B ARG* 3.2 35.1 + - - +
639B VAL* 3.1 25.3 + - - +
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Residues in contact with TRP 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TYR* 3.4 26.6 - + - +
532B LEU* 3.0 50.0 + - + -
535B ILE* 3.8 25.1 - - + +
536B PHE* 3.2 34.6 - + - -
632B LEU 2.9 8.7 + - - +
633B TYR* 3.2 32.1 + + + +
635B ARG* 1.3 75.1 - - - +
637B MET* 1.3 61.6 + - - +
639B VAL* 3.1 4.6 + - - +
640B HIS* 2.8 57.5 + + + -
652B ILE* 4.1 10.3 - - + -
655B PRO* 3.6 33.2 - - + -
661B SER* 4.4 2.0 - - - -
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Residues in contact with MET 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B TYR* 2.8 57.0 + - + +
634B CYS 3.7 3.8 - - - +
635B ARG 3.3 0.2 - - - -
636B TRP* 1.3 78.7 - - + +
638B ARG* 1.3 62.5 + - - +
640B HIS* 3.3 6.0 + - - +
641B GLY* 3.1 19.4 + - - -
655B PRO* 3.7 39.9 - - + +
656B ASN* 4.7 2.2 - - - +
699B LEU* 3.6 24.2 - - + -
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Residues in contact with ARG 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLU* 2.6 39.3 + - - +
634B CYS* 3.1 19.6 + - - +
635B ARG* 3.4 36.4 - - - +
636B TRP 3.2 0.2 - - - -
637B MET* 1.3 75.8 - - - +
639B VAL* 1.3 63.2 + - - +
641B GLY* 3.3 10.3 + - - -
642B LYS* 3.4 29.2 + - - +
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Residues in contact with VAL 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TYR* 4.0 21.5 - - + +
411B LEU* 4.2 11.7 - - + -
412B GLU* 3.7 28.7 - - + -
415B LEU* 4.2 8.3 - - + -
536B PHE* 3.5 27.1 - - + -
635B ARG 3.1 12.4 + - - +
636B TRP 3.1 7.4 + - - +
638B ARG* 1.3 73.7 - - - +
640B HIS* 1.3 65.8 + - - +
642B LYS* 2.9 18.6 + - - +
643B VAL* 3.0 28.5 + - + +
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Residues in contact with HIS 640 (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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536B PHE* 3.6 11.7 - + + -
636B TRP* 2.8 52.4 + + + +
637B MET* 3.3 11.4 + - - +
639B VAL* 1.3 71.7 - - - +
641B GLY* 1.3 63.4 + - - +
642B LYS 3.3 0.9 + - - -
643B VAL* 3.4 16.5 + - - +
648B LEU* 4.3 18.4 - - + +
652B ILE* 2.8 32.0 + - + +
653B THR 4.0 6.7 - - - -
655B PRO* 3.4 28.9 - - + +
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Residues in contact with GLY 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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637B MET 3.1 13.8 + - - -
638B ARG* 3.3 4.9 + - - -
639B VAL 3.2 0.4 - - - -
640B HIS* 1.3 80.6 + - - +
642B LYS* 1.3 60.9 + - - +
643B VAL 4.9 0.9 - - - +
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Residues in contact with LYS 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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412B GLU* 2.8 48.8 + - + +
415B LEU* 4.0 30.2 - - + +
638B ARG* 3.4 29.3 - - - +
639B VAL* 2.9 7.4 + - - +
641B GLY* 1.3 79.1 - - - +
643B VAL* 1.3 63.9 + - - +
644B PRO* 3.4 9.2 - - - +
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Residues in contact with VAL 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 6.0 0.4 - - + -
415B LEU* 3.8 14.6 - - + -
434B PHE* 4.2 17.9 - - + -
536B PHE* 4.0 12.3 - - + -
639B VAL* 3.0 37.1 + - + +
640B HIS 3.4 11.9 + - - +
641B GLY 4.9 1.1 - - - +
642B LYS* 1.3 77.6 - - - +
644B PRO* 1.3 82.7 - - + +
645B SER* 3.4 2.3 + - - -
647B LEU* 3.9 16.8 - - + +
648B LEU* 3.9 25.3 - - + +
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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
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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