Contacts of the strand formed by residues 370 - 374 (chain B) in PDB entry 4CAA
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 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 3.8 21.5 - + - -
252A PHE* 4.3 15.5 - + - -
253A ILE 3.5 13.0 - - - +
254A LEU* 3.9 4.7 - - + -
255A PRO* 3.9 3.1 - - - -
260A MET* 3.9 2.9 - - - +
288A LEU* 4.5 4.3 - - + -
289A PRO* 4.0 25.8 - - + -
291A PHE* 4.2 15.0 - + - -
366B PHE* 3.8 28.5 - + + -
368B ARG 3.2 14.4 - - - -
369B PRO* 1.3 74.5 - - - +
371B LEU* 1.3 75.8 + - - +
372B MET* 5.1 2.0 - - + -
387B LYS* 3.5 7.3 - - - +
388B VAL* 3.1 61.5 + - + -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.4 26.7 - - + +
252A PHE* 3.5 4.3 - - - -
253A ILE* 2.9 50.2 + - + +
255A PRO* 5.0 0.7 - - + -
260A MET* 4.1 14.8 - - + -
263A VAL* 4.4 17.3 - - + -
264A GLU* 4.7 2.7 - - + +
267A LEU* 4.0 35.2 - - + -
370B PHE* 1.3 84.9 - - - +
372B MET* 1.3 65.1 + - - +
373B ILE* 6.1 0.7 - - + -
385B MET* 4.8 7.6 - - + -
386B SER 3.7 4.9 - - - +
387B LYS* 3.4 23.6 - - + -
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Residues in contact with MET 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 5.1 0.7 - - + -
244A TYR* 3.6 23.8 - - - +
250A ALA* 4.1 6.1 - - + -
251A LEU 3.2 8.7 - - - +
252A PHE* 3.2 38.8 - - + -
291A PHE* 4.4 10.5 - - + -
338A LEU* 4.3 14.8 - - + -
340A VAL* 3.9 27.6 - - + -
370B PHE* 5.0 4.3 - - + -
371B LEU* 1.3 78.4 - - - +
373B ILE* 1.3 67.6 + - - +
374B ILE* 4.2 13.2 - - + -
384B PHE 4.1 0.7 - - - +
385B MET* 3.8 2.4 - - - +
386B SER* 3.0 43.3 + - - +
388B VAL* 6.0 2.2 - - + -
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.3 15.0 - - + -
250A ALA* 3.5 1.8 - - - -
251A LEU* 2.8 42.8 + - + +
253A ILE* 4.4 17.9 - - + -
267A LEU* 5.4 3.1 - - + -
272A LEU* 4.2 23.3 - - + -
275A TRP* 5.3 5.2 - - + -
371B LEU* 5.5 0.9 - - + -
372B MET* 1.3 77.7 - - - +
374B ILE* 1.3 62.0 + - - +
375B VAL* 3.6 17.8 + - + -
382B ILE* 3.5 35.9 - - + -
384B PHE 3.5 4.3 - - - +
385B MET* 3.6 22.2 - - + +
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.2 31.0 - - + -
244A TYR* 4.3 13.2 - - + +
248A ALA* 5.1 0.4 - - + -
249A SER 3.3 12.8 - - - +
250A ALA* 4.9 0.7 - - + -
338A LEU* 4.1 19.3 - - + -
347A ALA* 4.4 3.1 - - + -
372B MET* 4.2 15.7 - - + -
373B ILE* 1.3 71.9 - - - +
375B VAL* 1.3 63.8 + - - +
382B ILE* 4.2 0.9 - - - +
383B PHE* 3.2 43.0 + - + +
384B PHE* 2.9 46.5 + - + +
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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
------------------------------------------------------------
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