Contacts of the helix formed by residues 705 - 716 (chain A) in PDB entry 5J3V
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 CYS 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A LEU* 4.5 30.3 - - - -
701A HIS 4.8 1.3 - - - -
702A VAL* 3.1 6.1 + - - +
703A LYS 3.0 1.4 + - - -
704A PRO* 1.3 85.4 - - - +
706A ILE* 1.3 64.0 + - - +
707A ALA 3.2 2.7 - - - -
708A ASP* 3.4 8.1 + - + +
709A PHE* 3.1 50.0 + - + -
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Residues in contact with ILE 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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699A PHE* 3.9 28.0 - - + -
702A VAL* 3.6 22.2 - - + +
703A LYS* 3.2 24.5 + - - +
704A PRO 3.5 0.2 - - - -
705A CYS* 1.3 78.9 - - - +
707A ALA* 1.3 62.9 + - - +
709A PHE* 4.1 6.3 - - + -
710A MET* 3.0 45.7 + - + +
735A ILE* 4.1 22.9 - - + -
739A MET* 4.3 15.7 - - + -
743A MET* 5.7 0.7 - - - -
746A TYR* 4.3 19.3 - - + +
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Residues in contact with ALA 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 LYS 5.0 0.2 + - - -
704A PRO 5.0 5.3 + - - +
705A CYS 3.2 1.2 - - - -
706A ILE* 1.3 80.0 - - - +
708A ASP* 1.3 62.5 + - + +
711A PRO* 3.3 20.3 - - - +
746A TYR* 3.9 25.5 + - + +
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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
----------------------------------------------------------
673A TYR* 3.8 32.1 + - + -
705A CYS* 3.4 8.9 + - + +
706A ILE 3.2 0.2 - - - -
707A ALA* 1.3 83.0 - - - +
709A PHE* 1.3 65.4 + - + +
710A MET 3.6 0.2 - - - -
711A PRO* 3.7 7.9 - - - +
712A ILE* 3.6 24.1 - - - +
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Residues in contact with PHE 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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669A LEU* 3.9 23.6 - - + -
672A MET* 4.7 6.7 - - + -
673A TYR* 4.0 24.7 - + + -
676A MET* 3.6 36.7 - - + +
691A LEU* 3.8 26.9 - - + -
702A VAL* 4.2 13.0 - - + -
705A CYS* 3.1 44.0 + - + +
706A ILE* 3.1 11.4 + - + +
708A ASP* 1.3 82.0 - - - +
710A MET* 1.3 65.8 + - + +
712A ILE* 3.1 8.2 + - - +
713A LEU* 3.0 33.7 + - + +
735A ILE* 5.6 0.4 - - + -
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Residues in contact with MET 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A ILE* 3.0 34.3 + - + +
709A PHE* 1.3 76.5 - - - +
711A PRO* 1.4 63.2 - - + +
713A LEU* 3.1 20.5 + - + +
714A GLY* 2.7 28.1 + - - -
732A ILE* 4.3 13.9 - - + -
735A ILE* 4.2 13.5 - - - -
743A MET* 3.7 30.5 - - + -
746A TYR* 3.7 16.8 - - + -
749A MET* 3.6 18.3 - - + +
750A VAL* 3.6 29.9 - - + +
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Residues in contact with PRO 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 ALA 3.3 25.1 - - - +
708A ASP* 3.7 10.5 - - - +
709A PHE 3.5 3.4 - - - -
710A MET* 1.4 93.8 - - + +
712A ILE* 1.3 52.2 + - + +
714A GLY* 3.4 1.9 + - - +
715A THR* 2.7 36.0 + - - -
749A MET* 4.2 23.6 - - + -
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Residues in contact with ILE 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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673A TYR* 3.6 35.9 - - + -
676A MET* 3.7 38.4 - - + +
677A GLN* 3.9 20.6 - - + -
688A PHE* 4.0 4.5 - - + -
708A ASP 3.6 11.7 - - - +
709A PHE 3.1 6.8 + - - +
711A PRO* 1.3 74.8 - - + +
713A LEU* 1.3 63.9 + - - +
715A THR* 3.2 6.3 + - - -
716A ASN* 2.5 47.3 + - - +
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Residues in contact with LEU 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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676A MET* 5.7 0.4 - - - -
688A PHE* 3.6 33.7 - - + -
691A LEU* 3.8 25.4 - - + -
709A PHE* 3.0 19.0 + - + +
710A MET* 3.1 33.4 + - + +
712A ILE* 1.3 78.3 - - - +
714A GLY* 1.3 61.1 + - - +
715A THR 3.4 0.3 + - - -
716A ASN 3.4 8.7 + - - -
717A LEU* 3.3 21.1 + - - +
728A ALA* 4.1 23.2 - - - +
731A ALA* 4.2 3.1 - - + -
732A ILE* 4.1 19.5 - - + -
735A ILE* 3.9 11.7 - - + -
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Residues in contact with GLY 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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710A MET 2.7 18.6 + - - -
711A PRO* 3.4 3.3 + - - -
713A LEU* 1.3 73.5 - - - +
715A THR* 1.3 62.0 + - - +
717A LEU* 3.7 21.9 - - - +
749A MET* 4.0 14.6 - - - -
750A VAL* 4.5 5.1 - - - +
753A GLN* 3.2 23.1 + - - +
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Residues in contact with THR 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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711A PRO 2.7 20.2 + - - -
712A ILE* 3.5 11.2 - - - -
713A LEU 3.2 0.2 - - - -
714A GLY* 1.3 75.8 - - - +
716A ASN* 1.3 63.2 + - - +
717A LEU 3.1 9.6 + - - -
718A ASN* 3.9 12.5 + - - +
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Residues in contact with ASN 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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676A MET 4.4 3.0 + - - -
684A ARG* 2.9 38.0 + - - -
688A PHE* 3.4 35.7 - - + -
712A ILE* 2.5 38.6 + - - +
713A LEU 3.4 6.8 + - - +
715A THR* 1.3 81.1 - - - +
717A LEU* 1.3 55.6 + - - +
718A ASN* 3.1 11.0 + - - +
721A PHE* 5.8 0.8 - - - -
724A VAL* 3.9 9.1 - - + +
725A CYS* 3.4 22.3 + - - -
728A ALA* 3.8 4.7 - - + +
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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