Contacts of the helix formed by residues 706 - 713 (chain A) in PDB entry 3ZFM
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 SER 706 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A ASN 3.8 0.4 + - - +
705A GLY* 1.4 71.4 - - - -
707A LEU* 1.3 59.9 + - - +
708A ASP* 3.4 17.9 - - - -
709A SER* 3.2 11.5 + - - -
710A PHE* 3.1 29.5 + - - +
750A ARG* 3.1 23.0 + - - +
752A ILE 3.4 6.5 - - - -
753A LEU* 4.0 9.3 - - - +
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLY 3.7 0.6 + - - -
706A SER* 1.3 69.6 - - - +
708A ASP* 1.3 59.2 + - - +
710A PHE* 4.2 4.7 - - + -
711A LEU* 3.0 57.2 + - + +
726A MET* 4.1 12.8 - - + -
730A ILE* 3.7 29.6 - - + -
749A ALA* 3.2 19.7 + - + +
752A ILE* 2.8 29.2 + - + +
754A VAL* 3.6 25.1 - - + -
760A CYS* 3.8 11.2 - - - -
815A VAL* 4.9 0.9 - - + -
819A VAL* 3.9 15.3 - - + -
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Residues in contact with ASP 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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706A SER* 3.4 19.9 - - - -
707A LEU* 1.3 77.9 - - - +
709A SER* 1.3 69.1 + - - -
711A LEU* 5.1 0.2 - - - -
712A ARG* 3.1 60.1 + - - +
749A ALA* 3.4 24.9 + - + +
750A ARG* 3.5 25.7 - - - +
818A GLU* 4.5 8.0 - - - +
823A GLY* 3.7 13.6 - - - +
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Residues in contact with SER 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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704A ASN 5.5 0.3 + - - -
706A SER* 3.2 19.4 + - - -
708A ASP* 1.3 80.6 + - - +
710A PHE* 1.4 65.3 + - - +
712A ARG* 3.3 25.2 + - - +
713A GLN* 3.0 40.3 + - - +
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Residues in contact with PHE 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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704A ASN* 3.6 47.1 - - + +
706A SER 3.1 21.3 + - - +
707A LEU* 3.8 11.0 - - + +
709A SER* 1.4 77.8 + - - +
711A LEU* 1.4 62.0 + - + +
713A GLN* 3.6 10.9 + - - +
714A ASN* 2.9 46.3 + - - +
718A PHE* 3.3 35.2 - + - -
726A MET* 4.5 5.4 - - + -
754A VAL* 4.2 20.4 - - + -
758A LEU* 3.6 24.5 - - + -
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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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707A LEU* 3.0 41.8 + - + +
708A ASP* 4.0 1.6 - - - +
710A PHE* 1.4 74.8 - - + +
712A ARG* 1.4 60.6 + - - +
714A ASN* 3.0 19.3 + - - +
715A ASP 3.1 11.3 + - - -
718A PHE* 4.0 26.7 - - + -
723A LEU* 4.1 9.6 - - + -
726A MET* 4.0 19.5 - - - -
749A ALA* 5.7 1.1 - - + -
818A GLU 4.2 0.7 - - - +
819A VAL* 3.6 35.2 - - + +
822A TYR* 3.4 27.0 - - + +
823A GLY* 3.9 9.0 - - - +
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Residues in contact with ARG 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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708A ASP* 3.1 56.2 + - - +
709A SER* 3.3 26.1 + - - +
711A LEU* 1.4 75.3 - - - +
713A GLN* 1.4 60.4 + - + +
714A ASN 3.2 1.1 + - - -
715A ASP* 3.6 15.1 + - - +
822A TYR* 3.2 12.1 + - - +
823A GLY 3.0 29.8 + - - +
824A GLU* 4.6 2.9 - - - +
825A ARG 5.7 0.6 - - - +
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Residues in contact with GLN 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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704A ASN 5.7 0.3 - - - +
709A SER* 3.0 32.3 + - - +
710A PHE* 3.8 11.3 - - - +
711A LEU 3.2 0.2 - - - -
712A ARG* 1.4 76.6 - - + +
714A ASN* 1.3 64.5 + - - +
715A ASP 3.7 1.1 + - - -
717A GLN* 5.4 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