Contacts of the helix formed by residues 555 - 562 (chain A) in PDB entry 4OG6
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 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A ASP* 2.7 23.6 + - - +
421A CYS* 3.3 30.0 - - - +
422A LYS* 3.5 14.6 - - - -
425A GLU* 3.4 10.1 - - - -
553A PHE* 4.2 0.2 - - - +
554A GLN* 1.3 79.1 - - - +
556A GLU* 1.3 64.4 + - - +
557A LYS 4.0 1.3 - - - -
558A MET* 3.0 17.2 + - - +
559A LYS* 3.1 24.4 + - - +
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Residues in contact with GLU 556 (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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425A GLU* 2.9 22.3 + - - +
554A GLN 4.0 2.7 + - - +
555A SER* 1.3 69.9 - - - +
557A LYS* 1.3 67.3 + - - +
559A LYS* 2.9 39.7 + - - +
560A GLY* 3.1 18.4 + - - -
578A GLN* 3.8 4.0 + - - -
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Residues in contact with LYS 557 (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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421A CYS* 3.8 28.3 - - + +
424A GLU* 2.7 34.9 + - - +
425A GLU* 4.5 1.4 + - - +
432A LEU* 4.2 3.8 + - + +
555A SER* 3.3 1.6 - - - -
556A GLU* 1.3 78.1 - - + +
558A MET* 1.3 64.1 + - - +
561A MET* 3.3 8.9 + - - +
578A GLN* 3.0 41.7 + - - +
579A LEU* 2.8 35.3 + - + +
580A THR* 4.1 8.7 + - - +
581A ALA* 4.1 18.5 - - + +
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Residues in contact with MET 558 (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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414A LEU* 4.1 28.9 - - + +
417A TYR* 4.1 18.4 - - + -
418A ASP* 3.6 27.4 - - + +
421A CYS* 4.1 11.9 - - - -
440A LEU* 5.5 3.4 - - + -
553A PHE* 3.4 37.4 - - + -
555A SER* 3.0 20.3 + - - +
557A LYS* 1.3 73.8 - - - +
559A LYS* 1.3 67.3 + - - +
561A MET* 3.0 44.6 + - - +
562A LYS 3.2 9.4 + - - -
565A LEU* 4.4 2.9 - - + -
579A LEU* 5.0 1.3 - - - -
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Residues in contact with LYS 559 (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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457A ILE* 6.1 0.2 - - - -
460A VAL* 5.3 7.9 + - - +
553A PHE* 3.4 39.7 - - + -
554A GLN 4.2 8.7 + - - -
555A SER 3.1 16.4 + - - +
556A GLU* 2.9 41.8 + - - +
558A MET* 1.3 76.0 - - - +
560A GLY* 1.3 61.2 + - - +
561A MET 3.4 0.2 + - - -
562A LYS* 3.4 21.0 - - - +
563A GLU* 5.2 0.7 - - - +
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Residues in contact with GLY 560 (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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556A GLU 3.1 12.4 + - - -
557A LYS 3.3 0.2 + - - -
558A MET 3.2 0.2 - - - -
559A LYS* 1.3 76.6 - - - +
561A MET* 1.3 57.9 + - - +
562A LYS 3.3 0.4 - - - -
563A GLU* 3.1 33.5 - - - +
564A LEU* 5.0 0.9 - - - +
578A GLN* 3.5 24.7 - - - +
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Residues in contact with MET 561 (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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440A LEU* 4.0 15.7 - - + -
557A LYS 3.3 8.5 + - - +
558A MET* 3.0 37.3 + - - +
560A GLY* 1.3 75.0 - - - +
562A LYS* 1.3 55.0 + - - +
563A GLU 3.0 3.4 - - - -
564A LEU* 2.8 35.2 + - + -
565A LEU* 3.3 26.6 + - + +
575A ILE* 3.6 34.8 - - + +
578A GLN* 4.0 20.2 - - + +
579A LEU* 4.0 30.5 - - + +
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Residues in contact with LYS 562 (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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457A ILE* 3.5 56.7 + - + +
459A SER* 5.9 2.0 - - - -
553A PHE* 4.9 1.8 - - + -
558A MET 3.2 7.7 + - - +
559A LYS* 3.4 18.4 - - - +
560A GLY 3.3 0.2 - - - -
561A MET* 1.3 74.6 - - - +
563A GLU* 1.3 65.3 + - - +
564A LEU 2.9 1.9 + - - -
565A LEU* 3.2 24.9 + - - +
566A VAL* 4.5 8.0 + - - +
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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