Contacts of the helix formed by residues 710 - 717 (chain A) in PDB entry 3J0A
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 ALA 710 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706A TRP* 2.9 38.8 + - + +
709A ASN* 1.3 79.2 - - + +
711A LEU* 1.3 66.9 + - - +
712A LEU 3.6 0.2 - - - -
714A HIS* 2.7 45.4 + - + +
818A TRP* 5.1 7.6 - - + -
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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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697A LEU* 3.7 29.6 - - + -
706A TRP* 3.2 20.1 + - + +
707A VAL* 3.6 37.9 - - + -
710A ALA* 1.3 80.6 - - - +
712A LEU* 1.3 65.0 + - - +
714A HIS* 5.0 0.7 - - - -
715A LEU* 3.0 52.8 + - + +
755A VAL* 5.6 0.7 - - + -
757A LEU* 3.7 32.1 - - + -
832A LEU* 4.1 16.2 - - + -
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Residues in contact with LEU 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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697A LEU* 4.9 3.1 - - + -
707A VAL 3.2 16.5 + - - +
708A GLN* 3.1 28.7 - - - +
710A ALA 3.6 0.4 - - - +
711A LEU* 1.3 81.3 - - - +
713A LYS* 1.3 57.1 + - + +
715A LEU* 3.0 5.1 + - - -
716A ASP* 2.8 53.2 + - + +
727A LEU* 4.5 14.1 - - + -
729A PHE* 3.6 38.8 - - + -
732A ARG* 5.2 11.9 - - - +
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Residues in contact with LYS 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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708A GLN* 3.6 19.9 + - - +
709A ASN* 3.1 44.0 + - - +
710A ALA 3.6 1.2 + - - -
711A LEU 3.4 0.6 - - - -
712A LEU* 1.3 82.3 - - + +
714A HIS* 1.3 61.6 + - + +
716A ASP* 4.6 4.0 - - - +
717A THR* 3.2 29.5 + - - +
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Residues in contact with HIS 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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709A ASN 4.1 5.5 + - - -
710A ALA* 2.7 46.1 + - + +
711A LEU* 3.9 2.7 - - - +
713A LYS* 1.3 81.8 - - + +
715A LEU* 1.3 62.3 + - + +
716A ASP 3.5 0.2 - - - -
717A THR* 3.4 17.5 - - - +
718A GLN* 3.7 13.3 - - - +
825A VAL* 5.7 5.3 - - + +
829A LEU* 3.9 38.7 - - + +
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Residues in contact with LEU 715 (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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697A LEU* 4.7 4.3 - - + -
711A LEU* 3.0 43.1 + - + +
712A LEU 3.0 4.3 + - - +
714A HIS* 1.3 87.1 - - + +
716A ASP* 1.3 60.0 + - - +
717A THR 3.6 0.2 - - - -
718A GLN* 4.3 7.4 - - - +
725A PHE* 3.0 64.2 - - + +
727A LEU* 4.1 20.4 - - + -
755A VAL* 6.2 0.4 - - + -
829A LEU* 4.9 2.0 - - + -
832A LEU* 3.6 36.3 - - + +
833A SER* 6.4 1.3 - - - -
836A ILE* 4.6 7.4 - - + -
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Residues in contact with ASP 716 (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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712A LEU* 2.8 33.0 + - + +
713A LYS* 4.6 3.6 - - - +
715A LEU* 1.3 79.1 - - - +
717A THR* 1.3 64.4 + - - +
718A GLN 3.1 5.5 + - - +
720A SER* 3.1 39.3 + - - -
725A PHE 4.3 11.6 - - - +
726A ASN* 5.8 0.3 - - - -
727A LEU* 5.1 1.8 - - + +
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Residues in contact with THR 717 (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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713A LYS 3.2 22.1 + - - +
714A HIS* 3.4 21.8 - - - +
716A ASP* 1.3 78.1 - - - +
718A GLN* 1.3 70.5 + - + +
719A TYR 3.8 1.7 + - - -
720A SER* 4.0 10.5 + - - -
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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