Contacts of the strand formed by residues 469 - 472 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408I PHE* 3.7 29.2 - - + -
412I MET* 4.0 9.0 - - - -
439I LEU 4.7 2.0 - - - +
440I LEU* 3.5 31.0 - - + -
443I CYS* 3.5 26.9 - - + -
444I GLY 3.4 17.8 + - - +
445I GLY* 3.8 1.2 - - - -
446I LYS 3.4 18.0 + - - +
467I GLN* 4.5 3.4 - - - +
468I PHE* 1.3 86.7 + - + +
470I VAL* 1.3 65.6 + - - +
471I VAL* 4.3 6.5 - - + -
522I PRO* 4.1 1.3 - - - +
523I PRO 3.0 11.9 - - - +
524I GLY* 3.9 9.2 - - - -
525I ILE* 6.4 1.3 - - + -
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Residues in contact with VAL 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I TYR* 4.6 6.2 - - + +
446I LYS 3.4 5.8 - - - +
448I LEU* 3.5 38.8 - - + +
464I ALA* 3.7 28.3 - - + -
467I GLN* 5.7 0.2 - - + -
469I LEU* 1.3 77.1 - - - +
471I VAL* 1.3 70.9 + - - +
472I PHE* 4.1 18.6 - - + -
521I PHE* 4.1 7.4 - - + -
522I PRO* 3.9 13.0 - - + +
523I PRO 2.8 16.5 + - - +
524I GLY* 3.1 1.6 - - - -
525I ILE 2.8 27.3 + - - +
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Residues in contact with VAL 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505H VAL* 4.8 2.2 - - + -
436I ALA* 3.7 31.6 - - + +
440I LEU* 3.5 31.6 - - + -
446I LYS 3.3 3.8 + - - -
447I ALA* 3.4 17.3 - - + +
448I LEU 2.9 27.0 + - - +
469I LEU* 4.3 5.4 - - + -
470I VAL* 1.3 82.7 - - - +
472I PHE* 1.3 62.8 + - - +
473I GLU* 3.4 25.6 + - - +
525I ILE* 3.4 14.1 - - + +
527I THR* 5.1 0.9 - - + -
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Residues in contact with PHE 472 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I TYR* 3.7 24.9 - + - -
448I LEU* 3.7 27.1 - - + -
449I ASN* 4.5 0.9 - - - +
450I VAL* 3.6 33.0 - - + -
461I LEU* 4.4 11.4 - - + -
470I VAL* 4.1 13.7 - - + -
471I VAL* 1.3 69.4 - - - +
473I GLU* 1.3 62.8 + - - +
475I VAL* 4.3 9.2 - - + -
494I LEU* 4.2 15.3 - - + -
497I LEU* 5.3 5.4 - - + -
501I LEU* 4.9 4.3 - - + -
521I PHE* 4.4 14.4 - + - -
525I ILE 2.9 11.2 + - - -
526I VAL* 3.5 37.7 - - + -
527I THR* 2.8 33.7 + - - +
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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
------------------------------------------------------------
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