Contacts of the helix formed by residues 673 - 689 (chain A) in PDB entry 3ZRH
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 673 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A GLU* 3.6 30.1 + - + +
377A ASP* 5.2 4.9 + - + -
379A VAL* 4.6 20.4 - - + +
453A TRP* 3.4 37.8 - + + -
671A ARG 3.5 3.1 + - - -
672A ASN* 1.3 71.7 - - - +
674A PRO* 1.4 74.3 - - + +
675A LEU* 3.3 29.6 + - + +
676A VAL* 3.1 22.2 + - + +
677A THR* 2.9 26.7 + - - -
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Residues in contact with PRO 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ASN 3.4 7.6 - - - +
673A HIS* 1.4 99.2 - - + +
675A LEU* 1.3 60.7 + - + +
677A THR* 3.6 8.8 - - - +
678A GLN* 3.0 27.4 + - - +
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Residues in contact with LEU 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.8 15.8 - - + +
354A GLN* 3.6 52.7 - - + +
355A ILE* 3.7 20.6 - - + +
358A GLU* 3.5 24.5 - - + +
673A HIS* 3.3 16.8 + - + +
674A PRO* 1.3 79.4 - - + +
676A VAL* 1.3 60.3 + - - +
678A GLN* 3.3 11.2 + - - +
679A MET* 3.0 29.1 + - - +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 4.2 10.5 - - + -
379A VAL* 4.8 5.4 - - + -
381A PHE* 4.6 11.7 - - + -
452A THR 5.4 1.8 - - - +
453A TRP* 3.5 47.8 - - + +
672A ASN* 6.2 3.4 - - + -
673A HIS* 3.1 27.7 + - + +
675A LEU* 1.3 74.3 - - - +
677A THR* 1.3 60.2 + - - +
679A MET* 3.2 6.3 + - + +
680A VAL* 2.9 42.3 + - + +
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Residues in contact with THR 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A ASN* 3.7 22.7 + - - +
673A HIS 2.9 14.3 + - - -
674A PRO* 3.6 12.2 - - - +
676A VAL* 1.3 77.6 - - - +
678A GLN* 1.3 57.8 + - - +
680A VAL* 3.3 5.7 + - - +
681A GLU* 2.9 40.4 + - + +
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Residues in contact with GLN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.2 31.6 - - + +
354A GLN* 5.1 3.0 - - - +
674A PRO 3.0 16.6 + - - +
675A LEU* 3.6 13.3 - - - +
676A VAL 3.3 0.4 - - - -
677A THR* 1.3 76.9 - - - +
679A MET* 1.3 57.0 + - - +
681A GLU* 3.3 7.1 + - - +
682A LYS* 3.0 60.3 + - + +
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Residues in contact with MET 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO* 3.4 42.3 - - + +
345A ALA* 3.9 3.1 - - - -
347A VAL* 5.3 1.1 - - + +
348A CYS* 6.0 2.5 - - + +
351A LEU* 3.4 18.6 - - + +
352A THR* 4.6 8.1 - - + -
355A ILE* 3.9 12.3 - - + -
453A TRP 3.7 17.9 - - - +
454A GLY* 3.6 22.7 - - - +
455A ILE* 3.8 20.2 - - + -
675A LEU 3.0 15.8 + - - +
676A VAL* 3.6 12.6 - - + +
678A GLN* 1.3 78.3 - - - +
680A VAL* 1.3 58.9 - - + +
682A LYS* 3.3 5.1 + - - +
683A TRP* 2.9 27.4 + - - +
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Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO* 4.7 5.2 - - + -
381A PHE* 3.8 32.5 - - + -
382A THR 5.6 2.0 - - - +
384A PRO* 3.9 36.3 - - + -
676A VAL* 2.9 25.8 + - + +
677A THR* 3.9 5.2 - - - +
679A MET* 1.3 82.4 - - + +
681A GLU* 1.3 59.1 + - - +
683A TRP* 3.6 11.4 - - + +
684A LEU* 2.9 30.0 + - + +
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Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP* 4.4 2.8 - - - +
677A THR* 2.9 32.3 + - + +
678A GLN* 3.6 8.1 - - - +
679A MET 3.3 0.4 - - - -
680A VAL* 1.3 76.6 - - - +
682A LYS* 1.3 58.4 + - + +
684A LEU* 3.3 8.1 + - - +
685A ASP* 2.9 35.9 + - - +
688A ARG* 2.9 38.2 + - - +
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Residues in contact with LYS 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A VAL* 3.7 21.0 - - + +
348A CYS* 3.9 27.8 - - + -
351A LEU* 4.2 8.7 - - + -
678A GLN* 3.0 53.6 + - + +
679A MET* 3.8 4.5 - - - +
681A GLU* 1.3 72.6 - - + +
683A TRP* 1.3 66.6 + - - +
685A ASP* 3.4 23.5 + - - +
686A ARG* 3.5 8.1 + - - +
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Residues in contact with TRP 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A CYS* 2.9 25.0 + - - -
344A PRO* 3.7 42.8 - - + +
347A VAL* 3.7 23.5 - - + +
381A PHE* 5.8 1.3 - + - -
383A LEU* 4.5 12.8 - - + -
384A PRO* 4.1 22.9 - - + -
387A ILE* 4.4 6.1 - - + -
398A LEU* 3.7 36.6 - - + -
402A VAL* 3.9 21.1 - - + -
679A MET 2.9 16.8 + - - +
680A VAL* 3.6 14.8 - - + +
682A LYS* 1.3 77.1 - - - +
684A LEU* 1.3 85.2 + - + +
686A ARG* 3.1 14.9 + - - +
687A TYR* 3.4 27.8 - + - -
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Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PRO* 3.7 23.6 - - + -
386A ASP* 3.9 19.5 - - + +
387A ILE* 4.2 20.2 - - + +
390A LEU* 4.7 10.1 - - + -
398A LEU* 4.3 10.3 - - + -
680A VAL* 2.9 16.9 + - + +
681A GLU* 3.3 15.2 + - - +
683A TRP* 1.3 94.9 - - + +
685A ASP* 1.3 61.1 + - - +
687A TYR* 2.9 7.1 + - + +
688A ARG* 2.9 54.9 + - + +
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Residues in contact with ASP 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A GLU* 2.9 21.6 + - - +
682A LYS* 3.6 22.6 - - - +
683A TRP 3.2 0.6 - - - -
684A LEU* 1.3 71.8 - - - +
686A ARG* 1.3 64.6 + - - +
688A ARG* 2.7 35.6 + - - +
689A GLN* 3.2 47.3 + - - +
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Residues in contact with ARG 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A GLN 5.7 2.6 + - - -
342A CYS* 3.0 33.6 - - - +
347A VAL* 5.2 5.8 - - + -
397A LYS* 3.6 23.0 - - - +
401A GLU* 2.7 31.8 + - - -
682A LYS 3.5 6.1 + - - +
683A TRP* 3.1 10.4 + - - +
684A LEU 3.0 1.4 - - - -
685A ASP* 1.3 81.2 - - - +
687A TYR* 1.3 75.3 + - + +
689A GLN* 3.9 5.6 + - - +
690A ILE* 3.5 20.7 + - - +
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Residues in contact with TYR 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A CYS* 3.7 12.6 + - - +
390A LEU* 4.1 15.6 - - + +
391A PRO* 5.8 0.5 - - - +
394A VAL* 3.7 23.6 - - + +
397A LYS* 4.2 9.6 - - + -
398A LEU* 3.6 44.0 + - + -
401A GLU* 2.6 42.3 + - - +
683A TRP* 3.4 41.5 - + - -
684A LEU* 2.9 7.4 + - - +
686A ARG* 1.3 88.9 - - + +
688A ARG* 1.3 62.8 + - - +
689A GLN 3.1 2.0 - - - -
690A ILE* 3.2 35.3 + - + +
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Residues in contact with ARG 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ASP* 3.4 23.0 + - - +
390A LEU* 4.2 16.8 - - + +
681A GLU* 2.9 48.4 + - - -
684A LEU* 2.9 32.8 + - + +
685A ASP* 2.7 37.8 + - - +
687A TYR* 1.3 76.6 - - - +
689A GLN* 1.3 60.7 + - + +
690A ILE 3.2 1.5 - - - +
691A ARG* 3.2 28.6 + - - -
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Residues in contact with GLN 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A ASP* 3.2 38.1 + - - +
686A ARG* 3.9 4.0 + - - +
687A TYR 3.1 1.2 - - - -
688A ARG* 1.3 81.2 - - + +
690A ILE* 1.3 62.7 + - - +
691A ARG* 3.5 17.7 + - - +
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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