Contacts of the strand formed by residues 375 - 379 (chain A) in PDB entry 2R8P
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 PHE 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN* 5.3 0.7 + - - -
365A ILE* 4.2 17.0 - - + -
368A PHE* 4.0 24.0 - + + -
369A GLY* 4.0 18.8 - - - -
372A LEU* 3.0 43.7 + - + +
373A PRO 3.2 4.3 - - - +
374A GLU* 1.3 78.9 - - - +
376A LEU* 1.3 60.1 + - - +
377A GLY 3.9 1.3 - - - +
390A TRP* 4.9 8.3 - + + +
403A ASN* 3.4 27.7 - - + +
427A PHE* 4.7 2.4 - - - -
428A LEU* 3.4 21.8 - - + -
430A TYR* 4.0 24.5 - + + -
503A TRP* 3.9 32.5 - + - -
507A VAL* 4.0 7.2 - - + -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 4.3 15.0 - - + -
129A ALA* 5.0 0.9 - - - -
132A THR* 4.4 6.3 - - + +
374A GLU 3.2 0.6 + - - -
375A PHE* 1.3 72.5 - - - +
377A GLY* 1.3 59.6 + - - +
396A ILE* 4.2 11.2 - - + -
402A GLY 4.4 3.1 - - - +
403A ASN* 3.6 26.7 - - - -
404A TYR 4.0 0.7 - - - +
405A ILE* 3.9 25.1 - - + -
407A TYR* 5.0 4.9 + - - -
421A ILE* 3.9 30.0 - - + +
427A PHE* 3.8 38.6 - - + -
428A LEU 3.1 9.4 + - - +
429A PRO* 3.2 21.3 - - - +
430A TYR 3.4 3.8 + - - +
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Residues in contact with GLY 377 (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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375A PHE 3.9 0.8 - - - -
376A LEU* 1.3 75.9 - - - +
378A GLY* 1.3 51.6 + - - -
403A ASN 3.0 11.2 + - - -
404A TYR* 3.2 8.8 - - - -
405A ILE* 2.7 34.1 + - - +
407A TYR* 4.7 3.6 - - - -
430A TYR* 3.2 35.9 - - - -
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Residues in contact with GLY 378 (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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377A GLY* 1.3 74.8 - - - -
379A SER* 1.3 60.9 + - - -
388A THR* 3.9 4.8 - - - +
404A TYR* 3.7 12.8 - - - -
405A ILE 3.2 14.8 - - - -
407A TYR* 3.9 12.1 - - - -
430A TYR* 3.0 11.8 + - - +
431A THR* 3.5 5.7 - - - -
432A SER* 3.3 22.9 + - - -
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Residues in contact with SER 379 (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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378A GLY* 1.3 74.8 - - - -
380A ALA* 1.3 59.8 + - - +
381A ASP* 3.0 8.2 + - - -
382A LEU 3.0 16.3 + - - -
383A ALA* 3.9 7.9 - - - -
386A ASN* 2.7 27.0 + - - -
388A THR* 3.4 20.9 - - - -
404A TYR* 3.4 9.0 + - - -
405A ILE 3.6 2.3 + - - +
406A HIS* 4.2 0.5 - - - -
407A TYR* 3.2 19.5 + - - -
414A MET* 4.1 4.9 - - - -
432A SER* 3.5 9.0 - - - +
190B ASP* 4.3 4.0 - - - +
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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