Contacts of the helix formed by residues 781 - 790 (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 VAL 781 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B ILE* 5.2 2.2 - - + -
757B VAL* 4.1 5.8 - - + -
759B VAL* 4.0 24.5 - - + -
777B ALA 3.0 12.0 + - - +
780B ILE* 1.3 91.2 - - + +
782B VAL* 1.3 70.2 + - + +
783B MET 3.5 1.6 - - - -
784B PRO* 3.5 0.8 - - - +
785B ILE* 3.2 42.1 + - + +
884B LEU* 3.8 25.4 - - + -
887B VAL* 4.0 24.7 - - + -
888B ILE* 4.7 4.7 - - + -
898B MET* 4.5 10.3 - - - -
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Residues in contact with VAL 782 (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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704B VAL* 4.6 10.1 - - + -
727B ILE* 3.9 30.8 - - + +
729B LEU* 4.2 20.0 - - + -
759B VAL* 5.1 0.9 - - + -
777B ALA* 2.9 23.1 + - + +
778B PHE* 3.7 45.8 - - + -
781B VAL* 1.3 76.4 - - + +
783B MET* 1.3 60.7 + - - +
786B ALA* 2.9 32.3 + - + +
827B LEU* 4.5 13.0 - - + -
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Residues in contact with MET 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B PHE* 3.1 23.9 + - + +
779B ARG* 5.1 1.6 - - - +
782B VAL* 1.3 74.9 - - - +
784B PRO* 1.3 64.1 - - + +
786B ALA* 3.1 1.7 + - - +
787B ARG* 2.8 73.4 + - - +
826B GLN* 3.2 56.5 - - + +
827B LEU* 4.2 18.8 - - - -
829B ASN* 5.1 0.2 - - - +
830B LEU* 4.0 19.3 - - + -
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Residues in contact with PRO 784 (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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778B PHE 3.6 2.0 - - - +
779B ARG 3.3 25.4 - - - +
780B ILE* 3.5 15.0 - - - +
781B VAL 3.5 10.1 - - - +
783B MET* 1.3 95.3 - - + +
785B ILE* 1.3 58.8 + - - +
787B ARG* 3.7 7.1 + - + +
788B GLU* 3.2 23.2 + - - +
897B CYS* 3.5 29.5 - - + +
898B MET* 4.5 1.3 - - + -
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Residues in contact with ILE 785 (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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725B LEU* 3.9 15.0 - - + -
727B ILE* 4.4 6.7 - - + -
757B VAL* 4.1 17.9 - - + -
781B VAL* 3.2 31.6 + - + +
782B VAL 4.1 1.6 - - - +
784B PRO* 1.3 74.7 - - - +
786B ALA* 1.3 61.9 + - - +
788B GLU* 3.3 3.6 + - - +
789B PHE* 2.9 28.8 + - - +
887B VAL* 5.7 0.2 - - + -
891B HIS* 4.7 3.6 - - + -
895B TRP* 3.6 49.3 - - + +
897B CYS* 3.9 18.8 - - - -
898B MET* 4.1 16.2 - - + -
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Residues in contact with ALA 786 (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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702B LEU* 3.7 19.7 - - + -
725B LEU* 4.5 4.2 - - - +
727B ILE* 4.7 0.6 - - + +
782B VAL* 2.9 21.5 + - + +
783B MET* 3.5 7.0 - - - +
785B ILE* 1.3 77.3 - - - +
787B ARG* 1.3 55.8 + - - +
789B PHE* 3.4 4.8 + - - +
790B SER 2.9 23.6 + - - -
791B PRO* 3.2 11.6 - - - +
830B LEU* 3.5 31.9 - - + -
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Residues in contact with ARG 787 (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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783B MET* 2.8 56.0 + - - +
784B PRO* 4.0 6.3 - - + +
786B ALA* 1.3 71.6 - - - +
788B GLU* 1.3 63.4 + - - +
790B SER* 3.4 16.7 + - - +
829B ASN* 4.0 32.1 + - - +
830B LEU* 4.0 15.9 - - + +
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Residues in contact with GLU 788 (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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700B LYS* 5.2 0.3 + - - -
784B PRO 3.2 16.5 + - - +
785B ILE 3.3 4.5 + - - +
787B ARG* 1.3 74.6 - - - +
789B PHE* 1.3 65.6 + - - +
790B SER* 4.2 3.1 - - - -
894B TYR 4.5 1.6 - - - +
895B TRP* 3.6 26.3 - - + -
896B GLY* 3.0 22.2 + - - -
897B CYS* 3.1 35.0 + - - +
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Residues in contact with PHE 789 (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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700B LYS* 2.7 59.7 + - + +
701B ILE 3.6 20.0 - - - -
702B LEU* 4.2 1.8 - - + -
722B PRO 3.7 15.9 - - - -
723B SER 3.6 22.9 - - - -
725B LEU* 3.5 40.4 - - + -
755B PHE* 3.8 26.2 - + - -
785B ILE 2.9 17.0 + - - +
786B ALA 3.7 3.1 - - - +
788B GLU* 1.3 75.3 - - - +
790B SER* 1.3 63.5 + - - +
791B PRO* 4.0 17.3 - - + -
895B TRP* 3.9 10.7 - + + -
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Residues in contact with SER 790 (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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700B LYS* 3.7 13.0 - - - -
786B ALA 2.9 12.0 + - - -
787B ARG* 3.7 13.9 + - - +
788B GLU 3.4 3.7 - - - -
789B PHE* 1.3 82.0 - - - +
791B PRO* 1.3 68.4 - - - +
792B ASP* 3.9 5.0 + - - +
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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
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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