Contacts of the strand formed by residues 314 - 317 (chain P) in PDB entry 1E33
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 ALA 314 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39P TYR* 2.9 8.4 + - - -
59P PHE* 2.8 36.6 + - + -
62P PHE* 3.4 40.8 - - + -
277P ILE* 5.9 2.5 - - + -
278P PHE 3.2 7.0 - - - +
279P THR* 3.5 10.3 - - + -
312P GLU 3.6 1.0 + - - -
313P PRO* 1.3 79.1 - - - +
315P LEU* 1.3 68.4 + - - +
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Residues in contact with LEU 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 4.3 15.0 - - + -
38P CYS* 4.8 0.9 - - - -
39P TYR* 4.4 7.2 - - + +
49P LEU* 3.8 45.1 - - + +
52P LEU* 4.0 21.8 - - + +
53P ALA* 4.0 13.2 - - + -
57P LEU 3.2 4.0 - - - +
58P ARG* 3.9 28.3 - - + -
59P PHE* 4.7 1.6 - - - -
276P VAL 3.6 0.7 - - - +
277P ILE* 3.2 8.9 - - - +
278P PHE* 3.0 40.7 + - + -
314P ALA* 1.3 85.1 - - - +
316P ALA* 1.3 61.3 + - - +
317P PHE 4.2 0.7 - - - -
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Residues in contact with ALA 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P LEU 4.9 0.7 - - - +
56P GLY* 3.5 2.3 - - - -
57P LEU* 2.8 39.1 + - + +
59P PHE* 4.1 19.5 - - + -
275P LEU* 4.8 2.2 - - + -
276P VAL 3.4 4.5 - - - +
277P ILE* 4.7 12.1 - - + -
315P LEU* 1.3 73.8 - - - +
317P PHE* 1.3 61.8 + - - +
322P ILE* 3.9 18.4 - - + +
362P LEU* 4.7 13.9 - - + -
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Residues in contact with PHE 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P GLN 5.0 1.6 - - - -
52P LEU* 3.5 47.6 - - + +
55P GLY* 3.3 32.5 - - - -
56P GLY* 4.6 1.6 - - - -
262P MET* 3.4 34.5 - - + -
271P LEU* 4.9 7.2 - - + -
274P THR 3.6 1.9 - - - +
275P LEU* 4.2 0.4 - - - +
276P VAL* 2.7 42.5 + - + +
316P ALA* 1.3 76.3 - - - +
318P TRP* 1.3 63.7 + - - +
319P PRO* 3.3 34.1 - - + -
322P ILE* 4.2 1.2 - - - +
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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