Contacts of the helix formed by residues 357 - 366 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355D ASP 3.1 10.1 + - - +
356D LEU* 1.3 75.1 - - - +
358D SER* 1.3 59.9 + - - +
359D THR 3.5 2.0 - - - -
360D TRP* 3.7 18.4 - - + -
361D GLN* 2.5 56.9 + - - +
364D GLU* 3.4 28.5 + - - -
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Residues in contact with SER 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D LEU* 4.8 0.4 - - - +
357D HIS* 1.3 76.4 + - - +
359D THR* 1.3 59.6 + - - +
361D GLN* 4.6 3.4 - - - -
362D TYR* 2.8 22.5 + - - +
365D ARG* 3.1 13.5 + - - +
120E GLU* 4.3 27.0 - - - +
121E GLU* 4.3 5.4 - - - +
124E GLU* 3.8 28.4 + - - +
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Residues in contact with THR 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D TRP* 3.9 14.9 + - - -
345D ARG* 4.8 10.8 - - + +
348D ALA* 3.7 25.3 - - + +
349D THR* 5.0 2.7 - - + -
357D HIS 5.0 0.2 - - - +
358D SER* 1.3 74.8 - - - +
360D TRP* 1.3 66.5 + - - +
362D TYR* 3.0 10.8 + - - +
363D TYR* 3.0 42.4 + - + +
117E LEU* 4.6 1.2 - - + +
121E GLU* 3.0 37.2 + - - +
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Residues in contact with TRP 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D ALA* 2.4 28.9 + - + -
349D THR* 3.0 35.0 - - + -
350D ASN 4.7 0.9 - - - -
353D ARG 5.6 0.2 + - - -
356D LEU* 2.9 36.6 + - + +
357D HIS* 3.3 20.2 + + + +
359D THR* 1.3 77.8 - - - +
361D GLN* 1.3 58.0 + - - +
363D TYR* 3.2 9.1 + + - +
364D GLU* 3.0 27.4 + - - +
536D LEU* 5.2 0.9 - - + -
537D LYS* 3.2 56.3 - - + -
540D ILE* 5.5 10.3 - - + +
541D ARG* 3.3 33.2 - - + -
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Residues in contact with GLN 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D HIS* 2.5 42.4 + - + +
358D SER* 3.6 2.4 - - - +
360D TRP* 1.3 69.8 - - - +
362D TYR* 1.3 59.7 + - - +
364D GLU* 3.0 30.2 + - + +
365D ARG* 2.9 70.4 + - + +
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Residues in contact with TYR 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D ARG* 4.5 5.0 + - - -
358D SER 2.8 12.9 + - - +
359D THR 3.0 6.2 + - - +
361D GLN* 1.3 76.3 - - - +
363D TYR* 1.3 82.3 + + - +
365D ARG* 3.1 15.8 - - - +
366D THR* 2.9 42.2 + - + +
116E LYS 3.9 13.8 + - - -
117E LEU* 3.5 19.5 - - + -
118E THR* 3.4 30.5 - - + -
121E GLU* 3.3 34.5 - - - +
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Residues in contact with TYR 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D ARG* 2.7 52.4 + - + +
349D THR* 4.5 11.7 - - + -
359D THR* 3.0 37.7 + - + +
360D TRP* 3.9 5.6 - + - +
361D GLN 3.1 0.2 - - - -
362D TYR* 1.3 101.4 - + - +
364D GLU* 1.3 58.4 + - - +
365D ARG 3.2 2.4 + - - -
366D THR* 3.4 15.2 + - - -
367D VAL* 3.3 17.7 - - - +
540D ILE* 3.6 43.6 - - + +
547D ARG* 3.7 10.3 + - - -
40E LEU* 3.6 24.1 - - + +
117E LEU* 4.3 2.8 - - - +
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D HIS* 3.4 16.7 + - - -
360D TRP* 3.0 11.8 + - - +
361D GLN* 3.0 51.7 + - + +
363D TYR* 1.3 76.1 - - - +
365D ARG* 1.3 58.9 + - + +
367D VAL* 3.4 22.7 - - - +
536D LEU* 5.5 14.1 - - + +
540D ILE* 5.0 2.4 - - + +
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Residues in contact with ARG 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D SER* 3.1 14.5 + - - +
361D GLN* 2.9 51.4 + - + +
362D TYR* 3.1 36.4 - - + +
364D GLU* 1.3 79.7 - - + +
366D THR* 1.3 60.5 + - + +
367D VAL* 3.1 16.4 + - - +
118E THR* 5.0 5.1 + - - +
120E GLU* 5.1 11.5 + - - +
121E GLU* 5.7 0.6 - - - +
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Residues in contact with THR 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D TYR* 2.9 45.0 + - + +
363D TYR* 3.4 19.2 + - - -
365D ARG* 1.3 74.6 - - + +
367D VAL* 1.3 59.7 + - - +
40E LEU* 2.7 26.6 + - - +
41E GLY* 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