Contacts of the strand formed by residues 469 - 472 (chain G) in PDB entry 4E2I
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 LEU 469 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408G PHE* 3.7 29.4 - - + -
412G MET* 4.0 8.7 - - - -
439G LEU 4.7 2.0 - - - +
440G LEU* 3.5 31.0 - - + +
443G CYS* 3.5 27.1 - - + -
444G GLY 3.4 18.3 + - - +
445G GLY* 3.8 0.7 - - - -
446G LYS 3.4 18.5 + - - +
467G GLN* 3.9 3.4 - - - +
468G PHE* 1.3 86.7 + - + +
470G VAL* 1.3 66.8 + - - +
471G VAL* 4.3 6.7 - - + -
522G PRO* 4.3 1.1 - - - -
523G PRO 3.0 11.4 - - - +
524G GLY* 3.9 8.3 - - - -
525G ILE* 6.4 1.1 - - + -
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Residues in contact with VAL 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421G TYR* 4.6 5.6 - - + +
446G LYS 3.4 4.7 - - - +
448G LEU* 3.5 38.6 - - + -
464G ALA* 3.7 28.5 - - + -
469G LEU* 1.3 78.2 - - - +
471G VAL* 1.3 67.0 + - - +
472G PHE* 4.1 19.5 - - + -
521G PHE* 4.1 7.6 - - + -
522G PRO* 3.9 13.0 - - + +
523G PRO 2.8 16.3 + - - +
524G GLY* 3.1 1.7 - - - -
525G ILE 2.8 31.1 + - - +
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Residues in contact with VAL 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436G ALA* 3.7 31.6 - - + +
440G LEU* 3.5 31.9 - - + +
446G LYS 3.3 3.6 + - - -
447G ALA* 3.4 16.8 - - + +
448G LEU 2.9 25.8 + - - +
469G LEU* 4.3 5.4 - - + -
470G VAL* 1.3 83.7 - - - +
472G PHE* 1.3 63.4 + - - +
473G GLU* 3.4 25.2 + - - +
525G ILE* 3.4 14.1 - - + +
527G THR* 5.1 0.7 - - + -
505L VAL* 4.7 2.2 - - + -
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Residues in contact with PHE 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421G TYR* 3.7 24.7 - + - -
448G LEU* 3.7 28.0 - - + -
449G ASN* 4.8 0.9 - - - +
450G VAL* 3.6 33.7 - - + -
461G LEU* 4.4 11.2 - - + -
470G VAL* 4.1 12.6 - - + -
471G VAL* 1.3 70.3 - - - +
473G GLU* 1.3 61.0 + - - +
475G VAL* 4.3 9.0 - - + -
494G LEU* 4.2 15.0 - - + -
497G LEU* 5.4 5.6 - - + -
501G LEU* 4.9 4.7 - - + -
521G PHE* 4.4 15.3 - + - -
525G ILE 2.9 10.6 + - - +
526G VAL* 3.5 35.9 - - + -
527G THR* 2.8 34.4 + - - +
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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