Contacts of the helix formed by residues 486 - 489 (chain A) in PDB entry 5W5G
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 PRO 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A PRO* 3.9 18.4 - - + -
484A VAL* 3.7 9.9 - - + +
485A GLU* 1.3 85.3 - - - +
487A GLY* 1.3 54.0 + - - -
488A LEU 3.1 0.4 - - - -
489A PHE* 3.0 27.9 + - - +
522A PRO* 3.7 15.0 - - + -
524A ILE 3.1 22.7 - - - +
525A PRO* 4.1 6.3 - - + -
526A ILE* 3.9 26.7 - - + +
529A LEU* 3.6 27.3 - - + +
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Residues in contact with GLY 487 (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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485A GLU* 3.1 16.5 + - - -
486A PRO* 1.3 77.1 - - - +
488A LEU* 1.3 58.2 + - - +
489A PHE 3.2 1.1 - - - +
524A ILE* 3.7 14.5 + - - -
529A LEU* 4.9 0.2 - - - -
538A TYR* 5.6 0.2 - - - -
541A ARG* 2.7 29.6 + - - +
542A SER* 4.7 5.7 + - - -
545A VAL* 3.9 26.3 - - - +
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Residues in contact with LEU 488 (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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456A TYR* 3.7 30.1 - - + -
457A CYS 4.0 8.5 - - - -
458A SER* 3.6 13.2 - - - +
485A GLU* 2.9 28.5 + - + +
487A GLY* 1.3 74.6 - - - +
489A PHE* 1.3 65.8 + - - +
538A TYR* 6.0 0.7 - - - -
542A SER* 6.3 0.2 - - - -
545A VAL* 4.2 14.4 - - + -
546A THR* 5.1 1.6 - - - +
549A ILE* 4.0 11.0 - - + -
562A ILE* 3.7 30.3 - - + -
564A ALA* 3.7 5.0 - - + +
565A HIS* 3.4 14.4 - - - -
568A SER* 3.6 11.7 + - - -
572A CYS* 4.1 22.9 - - - -
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Residues in contact with PHE 489 (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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458A SER* 3.8 5.6 - - - -
459A PRO* 3.9 9.4 - - + -
460A SER* 3.2 28.0 - - - -
462A ARG* 4.8 3.1 - - - -
485A GLU 4.2 0.2 + - - -
486A PRO 3.0 18.8 + - - +
488A LEU* 1.3 81.6 - - - +
490A GLU* 1.3 100.7 + - + +
492A THR* 4.0 16.4 - - + -
495A VAL* 3.6 32.8 - - + -
500A LEU* 5.0 1.1 - - + -
501A PRO* 4.5 5.6 - - + -
503A TRP* 3.5 37.2 - + + -
529A LEU* 4.6 1.8 - - + -
538A TYR* 3.6 5.5 - - - -
541A ARG* 2.9 24.2 + - - +
565A HIS* 3.6 12.6 - + - -
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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
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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