Contacts of the helix formed by residues 701 - 714 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A TYR* 3.7 27.1 - - + +
637A VAL* 4.1 18.2 - - + -
640A GLN* 3.2 38.8 - - + +
641A PHE* 4.2 15.0 - - + -
684A GLY* 3.5 15.1 + - - +
686A VAL* 4.6 8.5 - - + -
699A ARG 3.8 0.6 + - - -
700A THR* 1.3 72.4 - - - +
702A SER* 1.3 58.3 + - - +
704A THR* 3.4 5.7 + - - -
705A ILE* 2.9 53.7 + - + +
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Residues in contact with SER 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A THR* 2.9 13.9 + - - -
701A ILE* 1.3 78.5 - - - +
703A GLU* 1.3 68.4 + - - +
705A ILE* 3.4 9.4 + - - +
706A GLU* 2.9 35.2 + - - +
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Residues in contact with GLU 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A ARG* 3.8 22.8 - - + +
700A THR* 3.0 45.4 + - + +
702A SER* 1.3 84.1 + - - +
704A THR* 1.3 58.6 + - - +
706A GLU* 3.1 13.5 + - - +
707A ARG* 2.9 31.1 + - - +
723A PHE* 5.6 0.2 - - - -
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Residues in contact with THR 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A PHE* 3.5 22.0 - - + -
672A PHE* 6.3 0.4 - - + -
674A LEU* 4.6 10.1 - - + -
686A VAL* 3.6 11.5 - - + +
688A ILE* 3.7 19.8 - - + +
699A ARG* 3.4 16.7 - - - +
700A THR 2.9 16.6 + - - -
701A ILE 3.7 3.8 - - - -
703A GLU* 1.3 76.5 - - - +
705A ILE* 1.3 57.7 + - - +
707A ARG* 4.0 0.7 - - - +
708A LEU* 2.9 43.9 + - + +
723A PHE* 4.1 15.0 - - + -
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Residues in contact with ILE 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A GLN* 4.4 20.9 - - + +
641A PHE* 3.7 27.6 - - + +
644A ALA* 3.7 30.7 - - + -
646A PHE* 3.7 4.6 - - + -
701A ILE* 2.9 37.6 + - + +
702A SER* 3.6 7.2 - - - +
704A THR* 1.3 74.3 - - - +
706A GLU* 1.3 59.1 + - - +
709A GLN* 2.9 38.7 + - - +
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Residues in contact with GLU 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A SER* 2.9 17.7 + - - +
703A GLU* 3.3 17.0 - - - +
705A ILE* 1.3 77.6 - - - +
707A ARG* 1.3 57.4 + - - +
709A GLN* 3.2 6.8 + - - +
710A GLN* 2.9 46.6 + - + +
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Residues in contact with ARG 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A GLU 2.9 15.6 + - - +
706A GLU* 1.3 76.0 - - - +
708A LEU* 1.3 57.9 + - - +
710A GLN* 3.2 35.1 + - - +
711A LEU* 2.9 58.9 + - + +
722A GLU* 2.6 32.4 + - - +
723A PHE* 3.0 51.3 + - + +
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Residues in contact with LEU 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A PHE* 3.2 30.1 - - + -
621A VAL* 3.9 14.8 - - + -
641A PHE* 3.4 29.2 - - + -
646A PHE* 3.6 15.9 - - + -
672A PHE* 3.5 39.0 - - + -
674A LEU* 5.8 0.4 - - + -
704A THR* 2.9 23.7 + - + +
707A ARG* 1.3 76.9 - - - +
709A GLN* 1.3 57.5 + - - +
711A LEU* 3.3 4.6 + - + +
712A LYS* 2.9 23.2 + - - +
723A PHE* 3.5 22.7 - - + -
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Residues in contact with GLN 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ALA* 2.9 30.4 + - - +
645A LYS* 4.8 3.2 - - - +
646A PHE* 3.5 20.8 - - - -
705A ILE* 2.9 31.3 + - - +
706A GLU* 3.5 7.1 - - - +
708A LEU* 1.3 74.0 - - - +
710A GLN* 1.3 60.3 + - + +
712A LYS* 3.6 7.3 - - + +
713A GLU* 2.9 54.7 + - + +
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Residues in contact with GLN 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A GLU* 2.9 33.3 + - + +
707A ARG* 3.2 38.4 + - - +
709A GLN* 1.3 78.0 - - + +
711A LEU* 1.3 62.5 + - - +
713A GLU* 3.4 9.8 + - - +
714A PHE* 3.1 41.0 + - + +
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Residues in contact with LEU 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A PHE* 4.3 8.2 - - + +
615A TRP* 4.7 1.6 + - - +
672A PHE* 4.4 0.2 - - + -
707A ARG* 2.9 46.7 + - + +
708A LEU* 3.6 11.9 - - + +
710A GLN* 1.3 76.1 - - - +
712A LYS* 1.3 61.0 + - - +
714A PHE* 4.9 1.3 - - + -
715A ARG* 3.4 1.9 + - - -
716A SER* 3.3 45.7 + - - +
719A ALA* 3.6 40.9 - - + +
722A GLU* 4.5 8.7 - - + +
723A PHE* 3.8 30.7 - - + -
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Residues in contact with LYS 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A TYR* 5.3 2.7 - - - +
614A PHE* 3.9 12.6 - - + -
615A TRP* 3.6 25.3 - - + +
620A GLN* 4.8 6.5 - - - +
646A PHE* 4.3 8.5 - - + -
708A LEU 2.9 16.9 + - - +
709A GLN* 3.6 13.7 - - + +
710A GLN 3.2 0.4 - - - -
711A LEU* 1.3 76.5 - - - +
713A GLU* 1.3 66.0 + - + +
715A ARG* 3.2 20.3 + - - +
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Residues in contact with GLU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A GLN* 2.9 37.3 + - + +
710A GLN* 4.0 11.8 - - - +
712A LYS* 1.3 80.5 - - + +
714A PHE* 1.3 77.7 + - + +
715A ARG* 3.2 17.7 + - - -
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Residues in contact with PHE 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A VAL* 5.5 2.9 - - - +
710A GLN* 3.1 26.1 + - + +
711A LEU* 4.7 2.0 - - + +
713A GLU* 1.3 93.4 - - + +
715A ARG* 1.3 71.0 + - - +
716A SER* 3.2 8.1 + - - +
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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