Contacts of the strand formed by residues 469 - 472 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E PHE* 3.7 30.3 - - + -
412E MET* 4.0 8.5 - - - -
439E LEU 4.7 1.8 - - - +
440E LEU* 3.5 30.7 - - + -
443E CYS* 3.5 27.1 - - + -
444E GLY 3.4 18.8 + - - +
445E GLY* 3.8 1.4 - - - -
446E LYS 3.5 18.4 + - - +
467E GLN* 4.5 3.0 - - - +
468E PHE* 1.3 85.6 + - + +
470E VAL* 1.3 66.0 + - - +
471E VAL* 4.4 7.0 - - + -
522E PRO* 4.1 1.5 - - - +
523E PRO 3.0 12.1 - - - +
524E GLY* 3.9 9.0 - - - -
525E ILE* 6.5 1.1 - - + -
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Residues in contact with VAL 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421E TYR* 4.6 5.7 - - + +
446E LYS 3.4 5.4 - - - +
448E LEU* 3.5 38.6 - - + +
464E ALA* 3.7 28.7 - - + -
467E GLN* 5.7 0.2 - - + -
469E LEU* 1.3 77.3 - - - +
471E VAL* 1.3 67.7 + - - +
472E PHE* 4.1 20.0 - - + -
521E PHE* 4.1 7.4 - - + -
522E PRO* 3.9 12.6 - - + +
523E PRO 2.7 16.5 + - - +
524E GLY* 3.1 1.9 - - - -
525E ILE 2.8 31.3 + - - +
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Residues in contact with VAL 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D VAL* 4.8 2.0 - - + -
436E ALA* 3.7 29.6 - - + +
440E LEU* 3.5 31.9 - - + -
446E LYS 3.3 3.8 + - - -
447E ALA* 3.4 17.6 - - + +
448E LEU 2.9 26.9 + - - +
469E LEU* 4.4 5.4 - - + -
470E VAL* 1.3 82.7 - - - +
472E PHE* 1.3 61.8 + - - +
473E GLU* 3.4 25.6 + - - +
525E ILE* 3.4 14.1 - - + +
527E THR* 5.0 0.9 - - + -
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Residues in contact with PHE 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421E TYR* 3.7 25.8 - + - -
448E LEU* 3.7 28.7 - - + -
449E ASN* 4.6 1.1 - - - +
450E VAL* 3.6 34.3 - - + -
461E LEU* 4.4 11.2 - - + -
470E VAL* 4.1 12.6 - - + -
471E VAL* 1.3 70.5 - - - +
473E GLU* 1.3 61.9 + - - +
475E VAL* 4.3 9.0 - - + -
494E LEU* 4.2 14.8 - - + -
497E LEU* 5.3 5.6 - - + -
501E LEU* 4.9 4.5 - - + -
521E PHE* 4.4 14.1 - + - -
525E ILE 2.9 11.2 + - - +
526E VAL* 3.5 35.7 - - + -
527E 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
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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