Contacts of the strand formed by residues 754 - 759 (chain C) in PDB entry 1JZ3
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 LYS 754 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750C GLU* 3.4 7.0 - - - +
751C LEU* 2.7 41.3 + - - +
752C GLY 3.1 0.7 - - - +
753C ASN* 1.3 114.8 + - - +
755C ARG* 1.3 64.4 + - - +
756C TRP* 3.6 30.7 - - + -
769C TRP 3.5 8.1 - - - +
770C ILE* 4.7 5.6 - - + -
861C SER 5.4 1.1 - - - -
862C GLY* 4.5 21.1 - - - +
1022C GLN* 2.7 42.2 + - + +
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Residues in contact with ARG 755 (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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748C CYS* 3.6 34.1 - - - +
749C ILE 3.2 10.8 - - - +
750C GLU* 3.5 29.7 + - - +
754C LYS* 1.3 80.4 - - - +
756C TRP* 1.3 69.1 + - - +
757C GLN* 3.6 9.3 + - - -
768C MET* 3.3 7.6 - - - +
769C TRP* 2.9 80.5 + - + +
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Residues in contact with TRP 756 (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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748C CYS* 3.4 4.3 - - - +
749C ILE* 2.9 53.9 + - + +
751C LEU* 4.1 15.3 - - + -
754C LYS* 3.6 41.3 - - + -
755C ARG* 1.3 79.0 - - - +
757C GLN* 1.3 58.8 + - - +
758C PHE* 4.0 9.2 - - + -
765C LEU* 4.1 2.9 - - + -
767C GLN 3.9 3.1 - - - -
768C MET* 3.6 26.8 - - + -
858C ILE* 3.5 39.9 - - + -
862C GLY* 3.7 28.7 - - - -
864C MET* 3.5 39.9 - - + +
1020C TRP 5.8 0.2 - - - -
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Residues in contact with GLN 757 (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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746C ASP* 3.4 27.4 + - - +
747C PHE 3.9 2.5 - - - -
748C CYS* 3.9 12.6 - - - -
755C ARG* 3.6 15.4 + - - -
756C TRP* 1.3 72.6 - - - +
758C PHE* 1.3 60.6 + - - +
765C LEU* 3.5 4.6 - - - +
766C SER* 2.8 41.0 + - - +
767C GLN* 2.8 35.0 + - - +
769C TRP* 3.4 25.7 - - + -
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Residues in contact with PHE 758 (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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746C ASP* 3.4 5.4 - - - -
747C PHE* 3.0 42.2 + - + +
749C ILE* 3.9 20.0 - - + -
756C TRP* 4.0 13.7 - - + -
757C GLN* 1.3 74.7 - - - +
759C ASN* 1.3 65.9 + - - +
760C ARG* 3.4 1.9 + - - +
763C GLY 5.2 3.1 - - - -
764C PHE* 3.5 5.8 - - - +
765C LEU* 3.9 37.2 - - + -
825C CYS* 5.6 2.9 - - - -
836C ILE* 4.0 30.5 - - + -
838C THR* 5.7 0.2 - - + -
856C TYR* 3.6 56.8 - + + -
858C ILE* 4.2 4.9 - - + -
864C MET* 4.2 7.9 - - - -
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Residues in contact with ASN 759 (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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745C MET* 4.0 11.5 - - - +
746C ASP* 3.4 12.6 + - - +
758C PHE* 1.3 72.4 - - - +
760C ARG* 1.3 57.4 + - - +
761C GLN* 2.4 40.1 + - - +
762C SER* 2.9 26.2 + - - +
763C GLY* 2.8 30.5 + - - -
764C PHE 2.9 10.6 + - - +
766C SER* 3.9 19.2 + - - +
825C CYS* 4.5 1.4 - - - -
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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