Contacts of the helix formed by residues 360 - 366 (chain A) in PDB entry 1RRM
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 ASP 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 6.0 0.2 - - - -
161A ARG* 5.7 2.9 - - - +
162A LYS 4.2 10.4 - - - +
164A VAL* 4.3 4.5 + - - +
264A GLY* 3.6 17.4 - - - +
267A HIS* 2.9 39.9 + - - +
268A PRO* 5.0 1.5 - - + +
356A ALA 3.0 11.0 + - - +
357A ALA 3.2 14.5 + - - +
358A LEU 4.5 0.9 - - - +
359A ASP* 1.3 80.0 - - - +
361A VAL* 1.3 67.4 + - - +
362A CYS* 3.0 31.5 + - - +
363A THR* 3.2 19.7 + - - +
364A GLY 4.2 1.6 + - - -
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Residues in contact with VAL 361 (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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123A GLU* 4.3 20.4 - - + +
124A GLY* 4.5 10.3 - - - +
164A VAL* 3.8 39.0 - - + +
166A VAL* 4.4 23.1 - - + -
359A ASP 3.6 3.0 + - - +
360A ASP* 1.3 76.2 + - - +
362A CYS* 1.3 64.1 + - - +
363A THR 3.4 0.3 + - - -
364A GLY* 3.7 8.3 + - - -
365A GLY 4.9 0.9 + - - -
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Residues in contact with CYS 362 (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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164A VAL* 4.2 12.3 - - - -
259A LEU* 4.0 9.5 + - + +
260A GLY* 3.5 26.7 + - - +
263A HIS* 4.1 14.8 - - + -
264A GLY 4.3 0.4 - - - +
267A HIS* 3.9 20.4 - - - -
360A ASP* 3.0 15.3 + - - +
361A VAL* 1.3 75.0 - - - +
363A THR* 1.3 64.6 + - - +
365A GLY* 3.1 12.8 + - - -
388A FE2 2.4 32.3 - - - -
390A PGO 5.1 3.4 - - - -
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Residues in contact with THR 363 (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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260A GLY 3.9 8.9 + - - -
261A LEU* 3.9 21.5 - - + +
264A GLY* 3.3 17.0 - - - -
357A ALA 2.6 28.9 + - - +
358A LEU* 4.4 15.9 - - + +
360A ASP 3.2 10.2 + - - -
362A CYS* 1.3 79.2 - - - +
364A GLY* 1.3 62.8 + - - +
365A GLY 3.1 1.7 + - - -
366A ASN* 3.1 19.3 + - + +
370A ALA* 4.9 9.9 - - + +
375A ILE* 4.9 2.9 - - + -
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Residues in contact with GLY 364 (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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208A ARG* 3.6 19.2 + - - -
360A ASP 4.2 1.6 + - - -
361A VAL 3.7 8.3 + - - -
362A CYS 3.2 1.6 + - - -
363A THR* 1.3 78.6 - - - +
365A GLY* 1.3 58.4 + - - +
366A ASN 3.3 1.3 + - - +
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Residues in contact with GLY 365 (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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207A THR* 3.0 15.5 + - - -
208A ARG* 2.9 30.3 + - - -
257A VAL 5.8 1.8 - - - -
258A GLY* 5.7 1.1 - - - -
259A LEU 3.4 13.5 - - - +
361A VAL 4.9 0.8 + - - -
362A CYS 3.1 7.3 + - - -
363A THR 3.1 1.8 + - - -
364A GLY* 1.3 75.9 - - - +
366A ASN* 1.3 66.0 + - - +
367A PRO 3.4 0.3 - - - -
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Residues in contact with ASN 366 (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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203A GLU* 4.5 0.7 - - - +
208A ARG* 2.9 22.7 + - - -
260A GLY* 3.8 8.1 - - - -
261A LEU* 3.0 38.1 + - + +
291A TYR* 3.8 9.5 - - - -
292A ASN* 2.7 42.3 + - - -
363A THR* 3.1 17.9 + - + +
364A GLY 4.2 0.7 - - - +
365A GLY* 1.3 75.6 - - - +
367A PRO* 1.3 65.9 - - - +
368A ARG* 2.9 31.9 + - - +
369A GLU* 5.1 0.2 - - - -
370A ALA* 4.9 1.1 - - + +
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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