Contacts of the strand formed by residues 732 - 739 (chain C) in PDB entry 4YOC
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 LEU 732 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717C LEU* 4.2 19.0 - - + +
720C MET* 3.9 25.4 - - + -
721C CYS* 3.6 22.7 - - - +
726C PHE* 3.8 29.8 - - + -
730C THR* 3.4 15.0 + - + +
731C SER* 1.3 80.8 - - - +
733C ILE* 1.3 58.4 + - - +
734C LEU* 3.8 13.2 - - + -
749C TYR* 2.5 34.2 + - - -
768C PHE* 3.9 12.1 - - + -
769C GLN 3.3 17.3 - - - +
770C LYS* 4.1 1.3 - - - -
771C ASP* 4.8 1.1 - - - -
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Residues in contact with ILE 733 (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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732C LEU* 1.3 73.0 - - - +
734C LEU* 1.3 62.8 + - - +
735C TYR* 3.5 24.3 - - + +
745C ARG* 3.4 45.1 - - - +
749C TYR* 3.5 2.9 - - - +
767C VAL 3.9 0.3 - - - +
768C PHE* 3.2 5.9 - - - -
769C GLN* 2.9 48.3 + - + +
770C LYS 4.1 12.3 - - - +
771C ASP* 3.4 34.5 - - + +
775C ASN* 5.1 2.7 - - - +
782C THR* 5.3 4.9 - - + -
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Residues in contact with LEU 734 (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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713C ILE* 3.7 29.6 - - + -
717C LEU* 3.7 25.1 - - + -
720C MET* 3.7 30.3 - - + -
732C LEU* 3.8 13.2 - - + -
733C ILE* 1.3 81.6 - - - +
735C TYR* 1.3 57.1 + - - +
745C ARG* 3.4 9.0 - - - +
746C ILE* 2.8 42.6 + - + -
749C TYR* 3.2 23.9 + - + +
766C ILE* 4.1 12.8 - - + -
767C VAL 3.6 1.8 - - - -
768C PHE* 3.9 9.0 - - + -
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Residues in contact with TYR 735 (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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733C ILE* 3.5 30.9 - - + +
734C LEU* 1.3 75.3 - - - +
736C GLU* 1.3 60.8 + - - +
743C THR* 3.5 31.2 - - + -
744C GLU 3.3 7.4 - - - +
745C ARG* 3.5 40.5 + - + -
746C ILE* 4.4 5.4 - - - +
766C ILE* 3.3 10.7 - - - +
767C VAL* 2.8 40.0 + - + +
769C GLN* 3.6 17.3 - - + -
782C THR* 3.3 30.9 + - - +
783C ALA* 4.2 11.7 - - + -
784C LYS* 3.8 22.5 - - + +
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Residues in contact with GLU 736 (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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1109A LYS* 4.4 8.7 + - - -
1111A LYS* 2.5 34.4 + - - -
634C ARG* 5.9 0.5 + - - -
735C TYR* 1.3 74.1 - - - +
737C GLU* 1.3 65.6 + - - +
738C VAL* 3.1 30.2 + - + +
743C THR* 3.4 4.0 - - - -
744C GLU* 2.9 38.4 + - + +
746C ILE* 4.7 2.2 - - + +
757C LEU* 3.8 37.7 - - + +
758C ASP 5.1 0.9 + - - +
764C ASP* 4.0 7.4 - - - +
765C ILE 3.4 15.8 + - - +
766C ILE* 4.5 2.2 - - + +
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Residues in contact with GLU 737 (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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581C ASN* 3.2 23.9 - - - +
582C ASP* 2.6 35.1 + - - +
634C ARG* 2.7 34.4 + - - +
690C LYS* 2.8 29.0 + - - +
735C TYR 4.1 1.4 + - - -
736C GLU* 1.3 71.8 - - - +
738C VAL* 1.3 52.4 + - - +
739C LYS 4.6 7.8 - - - +
742C LEU 4.1 3.1 - - - +
743C THR* 4.5 4.9 - - - +
765C ILE* 2.9 26.7 + - + +
767C VAL* 3.9 17.0 - - + +
787C PHE* 3.6 20.6 - - + -
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Residues in contact with VAL 738 (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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1109A LYS* 4.2 18.4 - - + +
1111A LYS* 4.0 28.4 - - + +
628C ARG* 5.2 1.9 + - - -
630C ASN* 3.8 10.4 + - - +
632C THR* 3.8 1.9 + - - +
634C ARG* 3.2 14.6 + - - -
736C GLU* 3.1 36.8 + - - +
737C GLU* 1.3 72.3 - - - +
739C LYS* 1.3 63.2 + - + +
742C LEU* 2.9 37.1 + - + +
744C GLU* 3.9 19.7 - - + +
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Residues in contact with LYS 739 (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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1067A ASP* 3.4 41.0 + - - +
1104A ARG* 3.9 6.5 - - - +
1108A ASN* 4.6 8.7 + - - +
1109A LYS 4.3 11.8 + - - +
581C ASN* 4.1 7.8 - - - +
630C ASN* 3.6 31.1 + - + +
632C THR* 3.5 13.9 - - + -
634C ARG* 4.6 2.5 - - - +
737C GLU* 3.4 4.9 - - - +
738C VAL* 1.3 80.3 + - - +
740C PRO* 1.3 86.9 - - + +
741C ASN 3.3 0.3 + - - -
742C LEU* 2.9 44.8 + - + +
743C THR* 4.9 1.0 + - - -
787C PHE* 5.9 0.5 - - - +
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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