Contacts of the helix formed by residues 683 - 687 (chain A) in PDB entry 5IJ7
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 LYS 683 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TRP* 4.3 6.5 - - + -
613A HIS* 4.1 0.6 - - - -
614A LEU* 2.8 42.8 + - + +
615A LEU* 4.7 0.9 - - - +
616A LEU 5.1 0.9 - - - +
626A ILE* 3.5 24.4 - - + +
682A ASN* 1.3 73.6 - - - +
684A ILE* 1.3 54.5 + - - +
685A ARG 3.0 6.1 + - - -
686A PHE* 3.0 31.6 + - + +
568S SER* 3.8 24.5 - - - +
582S ASP* 2.8 46.2 + - - +
585S ASP* 3.2 28.3 - - + -
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Residues in contact with ILE 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU* 3.9 21.2 - - + +
626A ILE* 4.3 6.3 - - + -
638A ILE* 4.1 11.4 - - + -
639A SER* 3.9 12.3 + - - +
640A GLU 3.2 17.7 - - - +
641A TYR* 3.7 25.4 - - + -
682A ASN* 3.1 22.5 + - - +
683A LYS* 1.3 71.5 - - - +
685A ARG* 1.4 60.4 + - - +
686A PHE 3.0 5.6 - - - -
687A ALA* 3.1 24.5 + - + +
710A ILE* 3.9 30.5 - - + -
722A LEU* 3.9 22.4 - - + -
724A PHE* 5.6 0.4 - - + -
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Residues in contact with ARG 685 (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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110A MET* 4.3 0.6 - - - -
111A TYR 3.9 3.2 + - - -
113A TRP* 3.1 58.4 - - - +
641A TYR* 3.8 16.6 + - + +
642A CYS 5.5 0.4 - - - +
665A PHE* 4.6 1.6 - - - -
677A ALA* 2.6 53.7 + - + -
678A THR 3.0 18.4 + - - -
681A GLY* 4.4 4.5 - - - -
682A ASN* 2.9 23.9 + - - +
683A LYS 3.0 0.6 + - - -
684A ILE* 1.4 77.5 - - - +
686A PHE* 1.4 78.7 + - + +
687A ALA 3.4 4.8 + - - +
726A TYR* 4.2 4.5 + - - -
9001A 6BN 3.4 67.2 + - + +
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Residues in contact with PHE 686 (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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110A MET* 3.6 42.0 - - + -
113A TRP* 3.6 27.8 - + - -
616A LEU* 3.8 17.0 - - + -
624A TRP* 3.7 19.7 - - + -
625A GLY* 3.3 17.9 - - - +
626A ILE* 3.3 16.8 + - + -
683A LYS* 3.2 25.1 - - + +
684A ILE 3.0 1.0 - - - -
685A ARG* 1.4 94.3 - - + +
687A ALA* 1.3 60.8 + - - +
688A ASN* 3.2 17.7 + - - -
9001A 6BN 3.5 33.7 - + + +
568S SER* 5.1 2.2 - - - -
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Residues in contact with ALA 687 (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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626A ILE* 3.6 17.7 - - + +
684A ILE* 3.1 24.2 + - + +
685A ARG 4.0 1.6 - - - +
686A PHE* 1.3 74.3 - - - +
688A ASN* 1.3 56.3 + - - +
695A CYS* 6.5 0.2 - - + -
710A ILE* 5.9 0.7 - - + -
722A LEU* 3.5 20.4 - - + +
723A PHE 5.1 0.2 - - - -
724A PHE* 4.0 21.4 - - + -
726A TYR* 2.6 30.7 + - - -
9001A 6BN 4.0 0.6 - - - +
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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
------------------------------------------------------------
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