Contacts of the helix formed by residues 357 - 366 (chain B) in PDB entry 7CR3
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 HIS 357 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASP 3.1 9.3 + - - +
356B LEU* 1.3 75.6 - - - +
358B SER* 1.3 59.1 + - - +
359B THR 3.5 2.0 - - - -
360B TRP* 3.7 19.1 - - + -
361B GLN* 2.5 57.5 + - - +
364B GLU* 3.4 28.8 + - - -
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Residues in contact with SER 358 (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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357B HIS* 1.3 75.6 + - - +
359B THR* 1.3 59.0 + - - +
361B GLN* 4.6 3.4 - - - -
362B TYR* 2.8 23.4 + - - +
365B ARG* 3.1 13.0 + - - +
120C GLU* 4.3 27.4 - - - +
121C GLU* 4.3 6.6 - - - +
124C GLU* 3.9 28.4 + - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TRP* 3.9 14.9 + - - -
345B ARG* 4.8 11.0 - - + +
348B ALA* 3.7 26.0 - - + +
349B THR* 5.0 2.2 - - + -
357B HIS 5.0 0.2 - - - +
358B SER* 1.3 73.9 - - - +
360B TRP* 1.3 68.1 + - - +
362B TYR* 3.0 10.6 + - - +
363B TYR* 3.0 42.0 + - + +
117C LEU* 4.6 1.1 - - + +
121C GLU* 2.9 37.7 + - - +
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Residues in contact with TRP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA* 2.4 28.9 + - + -
349B THR* 3.0 34.3 - - + -
350B ASN 4.7 0.7 - - - -
353B ARG 5.6 0.6 + - - -
356B LEU* 2.9 34.7 + - + +
357B HIS* 3.3 20.4 + - + +
359B THR* 1.3 77.8 - - - +
361B GLN* 1.3 57.7 + - - +
363B TYR* 3.2 9.7 + + - +
364B GLU* 3.0 27.3 + - - +
536B LEU* 5.2 0.9 - - + -
537B LYS* 3.2 56.3 - - + -
540B ILE* 5.5 11.0 - - + +
541B ARG* 3.3 33.4 - - + -
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Residues in contact with GLN 361 (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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357B HIS* 2.5 42.9 + - + +
358B SER* 3.6 2.8 - - - +
360B TRP* 1.3 69.1 - - - +
362B TYR* 1.3 61.1 + - - +
364B GLU* 3.0 30.1 + - + +
365B ARG* 2.9 69.9 + - + +
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Residues in contact with TYR 362 (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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345B ARG* 4.5 5.3 + - - -
358B SER 2.8 13.1 + - - +
359B THR 3.0 9.3 + - - +
361B GLN* 1.3 75.8 - - - +
363B TYR* 1.3 80.9 + + - +
365B ARG* 3.1 16.2 - - + +
366B THR* 2.9 42.3 + - + +
116C LYS 3.9 12.5 + - - -
117C LEU* 3.5 19.7 - - + -
118C THR* 3.5 29.6 - - + -
121C GLU* 3.3 31.9 - - - +
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Residues in contact with TYR 363 (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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345B ARG* 2.7 52.3 + - + +
349B THR* 4.5 11.0 - - + -
359B THR* 3.0 38.4 + - + +
360B TRP* 3.9 6.5 - + - +
361B GLN 3.1 0.2 - - - -
362B TYR* 1.3 102.5 - + - +
364B GLU* 1.3 60.5 + - - +
365B ARG 3.2 2.2 + - - -
366B THR* 3.4 15.3 + - - -
367B VAL* 3.3 17.3 - - - +
540B ILE* 3.6 42.0 - - + +
547B ARG* 3.7 10.7 + - - -
40C LEU* 3.5 25.1 - - + +
117C LEU* 4.3 1.7 - - - +
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Residues in contact with GLU 364 (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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357B HIS* 3.4 17.2 + - - -
360B TRP* 3.0 11.2 + - - +
361B GLN* 3.0 52.4 + - + +
363B TYR* 1.3 76.1 - - - +
365B ARG* 1.3 59.2 + - + +
367B VAL* 3.4 22.1 - - - +
536B LEU* 5.5 13.1 - - + +
540B ILE* 5.0 2.6 - - + +
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Residues in contact with ARG 365 (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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358B SER* 3.1 15.2 + - - +
361B GLN* 2.9 50.1 + - + +
362B TYR* 3.1 35.0 - - - +
364B GLU* 1.3 81.5 - - + +
366B THR* 1.3 59.1 + - + +
367B VAL* 3.1 17.3 + - - +
118C THR* 5.0 5.2 + - - +
120C GLU* 5.2 11.5 + - - +
121C GLU* 5.7 0.2 - - - +
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Residues in contact with THR 366 (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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362B TYR* 2.9 45.1 + - + +
363B TYR* 3.4 18.9 + - - -
364B GLU 3.7 0.2 - - - -
365B ARG* 1.3 74.5 - - + +
367B VAL* 1.3 59.3 + - - +
40C LEU* 2.7 26.4 + - - +
41C GLY* 4.2 4.5 - - - -
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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
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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