Contacts of the helix formed by residues 781 - 790 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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757C VAL* 3.8 28.7 - - + -
759C VAL* 4.1 13.0 - - + -
777C ALA 3.0 9.9 + - - +
780C ILE* 1.3 88.0 - - + +
782C VAL* 1.3 70.6 + - + +
783C MET 3.5 1.6 - - - -
784C PRO* 3.5 1.8 - - - +
785C ILE* 3.2 36.7 + - + +
884C LEU* 3.6 28.0 - - + -
887C VAL* 3.9 15.5 - - + -
888C ILE* 4.9 2.7 - - + -
898C MET* 4.1 17.3 - - + -
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Residues in contact with VAL 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704C VAL* 4.5 15.9 - - + -
727C ILE* 3.7 41.2 - - + +
729C LEU* 4.4 13.0 - - + -
759C VAL* 4.9 2.0 - - + -
777C ALA 3.0 19.5 + - - +
778C PHE* 4.0 41.7 - - + -
781C VAL* 1.3 77.2 - - + +
783C MET* 1.3 60.3 + - - +
786C ALA* 2.8 31.5 + - + +
827C LEU* 4.7 5.4 - - + -
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Residues in contact with MET 783 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778C PHE* 3.2 29.5 + - + +
779C ARG* 5.0 0.7 - - - +
782C VAL* 1.3 74.1 - - - +
784C PRO* 1.3 64.5 - - + +
786C ALA* 3.6 2.1 - - - +
787C ARG* 2.8 66.9 + - - +
826C GLN* 3.1 49.6 - - + +
827C LEU* 3.8 27.4 - - - -
830C LEU* 4.0 19.1 - - + -
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Residues in contact with PRO 784 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778C PHE 3.6 1.6 - - - +
779C ARG 3.0 27.6 - - - +
780C ILE* 3.5 12.3 - - - +
781C VAL 3.5 9.9 - - - +
783C MET* 1.3 93.0 - - + +
785C ILE* 1.3 56.0 + - - +
787C ARG* 3.7 6.8 - - + +
788C GLU* 2.8 30.5 + - - +
897C CYS* 3.6 28.6 - - + +
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Residues in contact with ILE 785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725C LEU* 3.8 16.6 - - + -
727C ILE* 4.2 8.1 - - + -
757C VAL* 3.7 23.3 - - + -
781C VAL* 3.2 30.7 + - + +
782C VAL 4.0 1.8 - - - +
784C PRO* 1.3 75.7 - - - +
786C ALA* 1.3 60.0 + - - +
788C GLU* 3.7 3.8 - - - +
789C PHE* 2.8 29.3 + - - +
891C HIS* 4.8 0.9 - - + -
895C TRP* 3.7 43.4 - - + +
897C CYS* 3.8 19.3 - - - -
898C MET* 4.0 16.4 - - + -
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Residues in contact with ALA 786 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702C LEU* 3.7 14.8 - - + -
725C LEU* 4.3 10.8 - - - -
727C ILE* 4.8 1.6 - - + -
782C VAL* 2.8 22.5 + - + +
783C MET* 3.6 7.0 - - - +
785C ILE* 1.3 76.4 - - - +
787C ARG* 1.3 51.4 + - - +
789C PHE* 3.4 0.7 + - - +
790C SER 2.6 31.4 + - - -
791C PRO* 3.3 9.0 - - - +
830C LEU* 3.6 31.9 - - + -
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Residues in contact with ARG 787 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783C MET* 2.8 48.6 + - + +
784C PRO* 3.8 6.1 - - + +
786C ALA* 1.3 70.8 - - - +
788C GLU* 1.3 66.0 + - - +
790C SER* 3.4 17.8 + - - +
829C ASN* 3.5 42.0 + - - +
830C LEU* 3.7 16.4 - - + +
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Residues in contact with GLU 788 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700C LYS* 5.1 0.7 + - - -
784C PRO 2.8 16.5 + - - +
785C ILE* 3.7 4.0 - - - +
787C ARG* 1.3 74.2 - - - +
789C PHE* 1.3 66.5 + - - +
790C SER* 4.1 3.1 - - - -
894C TYR 4.6 1.4 - - - +
895C TRP* 3.7 22.4 - - + -
896C GLY* 2.9 23.9 + - - -
897C CYS* 3.1 36.7 + - + +
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Residues in contact with PHE 789 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700C LYS* 2.7 51.1 + - + +
701C ILE 3.6 34.8 - - - -
702C LEU* 4.1 0.9 - - + -
722C PRO 3.8 10.5 - - - -
723C SER 3.7 14.4 - - - -
725C LEU* 3.6 30.1 - - + -
755C PHE* 3.7 38.4 - + - -
785C ILE 2.8 17.6 + - - +
786C ALA 3.5 2.2 - - - +
788C GLU* 1.3 75.0 - - - +
790C SER* 1.3 65.1 + - - +
791C PRO* 3.7 27.8 - - + -
895C TRP* 3.9 9.5 - + + -
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Residues in contact with SER 790 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700C LYS* 3.9 11.5 - - - +
786C ALA 2.6 15.7 + - - -
787C ARG* 3.4 15.9 + - - +
788C GLU 3.3 3.3 - - - -
789C PHE* 1.3 78.7 - - - +
791C PRO* 1.3 71.2 + - - +
792C ASP* 4.6 2.9 - - - +
830C LEU* 5.8 0.2 - - - -
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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
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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