Contacts of the helix formed by residues 701 - 714 (chain C) in PDB entry 4P3N
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 ILE 701 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633C TYR* 3.6 25.1 - - + +
636C LYS* 5.6 2.2 - - + -
637C VAL* 4.2 17.0 - - + -
640C GLN* 3.3 31.9 - - + +
641C PHE* 3.9 22.0 - - + -
684C GLY* 3.4 18.2 + - - +
685C THR* 4.6 4.3 - - - +
686C VAL* 4.9 5.8 - - + -
699C ARG 3.8 1.4 + - - -
700C THR* 1.3 72.9 - - - +
702C SER* 1.3 57.3 + - - +
704C THR* 3.4 7.4 + - - +
705C ILE* 2.9 39.5 + - + +
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Residues in contact with SER 702 (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 THR* 3.6 10.8 + - - -
701C ILE* 1.3 82.0 - - - +
703C GLU* 1.3 60.0 + - - +
705C ILE* 3.5 8.8 + - - +
706C GLU* 2.9 28.6 + - - +
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Residues in contact with GLU 703 (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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699C ARG* 3.6 34.0 + - + +
700C THR* 3.1 46.3 + - - +
702C SER* 1.3 79.4 + - - +
704C THR* 1.3 60.4 - - - +
706C GLU* 3.6 13.2 - - - +
707C ARG* 2.9 29.1 + - - +
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Residues in contact with THR 704 (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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641C PHE* 3.2 19.9 - - - -
674C LEU* 4.9 2.8 - - - +
686C VAL* 3.9 11.5 - - + +
688C ILE* 4.0 21.4 - - - +
699C ARG* 3.8 15.0 - - + -
700C THR 2.3 38.4 - - - +
701C ILE* 3.4 8.5 - - - +
703C GLU* 1.3 71.9 - - - +
705C ILE* 1.3 57.3 + - - +
706C GLU 3.3 0.2 - - - -
707C ARG* 4.4 4.3 - - - -
708C LEU* 3.0 36.9 + - - +
723C PHE* 4.2 6.7 - - - -
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Residues in contact with ILE 705 (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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640C GLN* 4.2 22.7 - - + +
641C PHE* 3.5 35.0 - - + -
644C ALA* 4.0 20.2 - - + -
646C PHE* 3.6 7.1 - - + -
701C ILE* 2.9 36.0 + - + +
702C SER* 3.7 9.4 - - - +
704C THR* 1.3 74.3 - - - +
706C GLU* 1.3 60.6 + - - +
709C GLN* 2.9 33.0 + - - +
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Residues in contact with GLU 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C SER 2.9 17.8 + - - +
703C GLU* 3.6 12.7 - - - +
704C THR 3.3 0.2 - - - -
705C ILE* 1.3 78.9 - - - +
707C ARG* 1.3 58.5 + - - +
709C GLN* 3.2 9.2 + - + +
710C GLN* 2.9 46.5 + - + +
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Residues in contact with ARG 707 (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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699C ARG* 5.8 3.1 - - - +
703C GLU 2.9 19.4 + - - +
704C THR 4.0 0.2 - - - +
706C GLU* 1.3 72.7 - - - +
708C LEU* 1.3 65.2 + - - +
710C GLN* 3.2 35.7 + - - +
711C LEU* 3.1 53.3 + - + +
714C PHE* 6.3 0.2 - - - -
722C GLU* 2.7 29.5 + - - +
723C PHE* 3.0 48.1 + - + +
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Residues in contact with LEU 708 (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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614C PHE* 3.2 28.3 - - + -
621C VAL* 4.2 17.7 - - + -
641C PHE* 3.5 31.2 - - + -
646C PHE* 3.5 16.8 - - + -
672C PHE* 3.9 28.3 - - + -
674C LEU* 5.7 2.9 - - + -
704C THR* 3.0 15.7 + - - +
707C ARG* 1.3 72.9 - - - +
709C GLN* 1.3 59.6 - - - +
711C LEU* 3.2 4.6 + - + -
712C LYS* 2.9 25.6 + - - +
723C PHE* 3.4 32.3 - - + -
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Residues in contact with GLN 709 (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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644C ALA* 3.4 33.2 + - - +
645C LYS* 5.1 0.8 - - - +
646C PHE* 3.5 20.9 - - - -
705C ILE* 2.9 22.2 + - + +
706C GLU* 3.2 10.3 + - + +
708C LEU* 1.3 77.8 - - - +
710C GLN* 1.3 51.3 + - - +
712C LYS* 3.3 19.1 + - - +
713C GLU* 2.6 52.3 + - + +
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Residues in contact with GLN 710 (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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706C GLU* 2.9 35.9 + - + +
707C ARG* 3.4 39.3 - - - +
709C GLN* 1.3 75.7 - - + +
711C LEU* 1.3 61.8 + - - +
713C GLU* 3.2 18.3 + - - +
714C PHE* 3.1 44.3 + - + +
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Residues in contact with LEU 711 (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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614C PHE* 4.2 13.2 - - + +
615C TRP* 4.7 2.4 + - - +
672C PHE* 4.4 0.4 - - + -
707C ARG* 3.1 44.1 + - + +
708C LEU* 3.2 14.1 + - + +
710C GLN* 1.3 75.7 - - - +
712C LYS* 1.3 59.7 + - - +
714C PHE* 4.2 0.9 - - - -
715C ARG* 3.3 2.1 + - - -
716C SER* 3.2 46.0 + - - +
719C ALA* 3.5 35.7 - - + +
722C GLU* 4.3 10.8 - - + +
723C PHE* 4.0 24.7 - - + -
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Residues in contact with LYS 712 (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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351C TYR* 4.3 16.6 + - - -
614C PHE* 3.8 12.2 - - + -
615C TRP* 3.8 24.9 - - + +
620C GLN* 4.3 7.4 - - - +
645C LYS* 3.8 34.4 + - - +
646C PHE* 4.2 16.6 - - + -
708C LEU 2.9 17.0 + - - +
709C GLN* 3.6 16.4 - - - +
711C LEU* 1.3 75.9 - - - +
713C GLU* 1.3 65.7 + - - +
715C ARG* 3.4 17.0 + - - +
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Residues in contact with GLU 713 (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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709C GLN* 2.6 53.8 + - + +
710C GLN* 3.2 20.9 + - - +
712C LYS* 1.3 75.0 - - - +
714C PHE* 1.3 84.6 - - + +
715C ARG* 3.2 16.7 + - - +
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Residues in contact with PHE 714 (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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489C VAL* 5.3 3.1 - - - +
707C ARG* 6.3 0.4 - - - -
710C GLN* 3.1 29.7 + - + +
711C LEU* 4.8 1.6 - - - +
713C GLU* 1.3 95.3 - - + +
715C ARG* 1.3 71.8 + - - +
716C SER* 3.2 8.9 + - - +
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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