Contacts of the strand formed by residues 353 - 356 (chain A) in PDB entry 2P2M
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 ILE 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A PHE* 5.4 0.2 - - + -
293A PHE* 3.6 56.3 - - + +
295A TYR* 4.6 9.4 - - + -
299A ASP* 3.9 29.4 - - + +
300A ILE 3.0 5.2 + - - +
301A TYR* 3.6 28.9 - - + -
302A TRP 2.8 28.8 + - - +
351A VAL* 3.1 6.4 - - - +
352A ASN* 1.3 87.3 - - + +
354A LEU* 1.3 63.4 + - - +
381A ARG* 5.9 0.4 - - + -
382A ILE* 3.5 20.2 - - + +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 3.5 44.6 - - + +
304A THR* 4.0 13.7 - - + -
342A MET* 3.7 31.9 - - + -
346A VAL* 4.4 10.1 - - + -
351A VAL* 4.6 1.3 - - + -
353A ILE* 1.3 76.5 - - - +
355A TYR* 1.3 56.5 + - - +
356A THR* 4.1 1.6 - - + -
380A LEU* 3.8 16.3 - - + +
382A ILE 3.1 7.1 + - - -
383A LEU* 3.3 12.8 - - + -
384A GLY 2.7 31.4 + - - -
398A TYR* 3.5 10.5 + - + +
402A ILE* 4.0 18.6 - - + -
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Residues in contact with TYR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.4 28.0 - + + -
301A TYR* 3.4 23.6 - - + +
302A TRP 2.9 13.7 + - - +
303A CYS* 3.4 15.2 - - - -
304A THR* 3.0 26.7 + - - +
311A THR* 3.7 20.0 - - + -
315A TYR* 3.9 10.5 - - + -
354A LEU* 1.3 73.9 - - - +
356A THR* 1.3 60.0 + - - +
384A GLY* 3.6 18.4 - - - -
385A SER 3.9 7.6 - - - -
386A VAL* 3.2 30.0 - - + +
412A THR* 2.6 33.4 + - + -
414A TRP* 3.4 1.7 + - - -
421A PHE* 3.0 19.6 - + - -
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Residues in contact with THR 356 (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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304A THR* 2.8 32.2 + - - +
334A PRO* 5.9 0.3 - - - +
342A MET* 4.5 17.7 - - - -
354A LEU* 4.7 2.9 - - + -
355A TYR* 1.3 74.6 - - - +
357A ALA* 1.3 65.0 + - - +
360A ALA* 3.8 16.2 - - + +
361A ILE* 3.9 16.6 - - + -
384A GLY 3.1 8.4 + - - -
385A SER* 3.2 6.5 - - - -
386A VAL* 3.0 30.2 + - - +
398A TYR* 3.5 29.6 - - + +
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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