Contacts of the helix formed by residues 292 - 301 (chain A) in PDB entry 3RIG
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 PRO 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A THR* 3.6 17.2 - - + -
291A GLY* 1.4 83.9 - - - +
293A CYS* 1.3 58.0 + - - +
294A GLY* 3.2 7.0 - - - +
295A THR* 3.0 38.6 + - + +
296A THR* 3.4 5.2 + - - -
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Residues in contact with CYS 293 (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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60A GLY* 5.1 11.0 - - - -
117A GLY* 4.0 7.8 - - - -
248A VAL* 3.5 26.2 - - + -
249A GLY* 4.6 12.8 - - - -
274A PHE* 4.2 11.9 - - + +
275A ASN* 6.0 1.1 - - - -
291A GLY 3.5 2.1 + - - +
292A PRO* 1.3 70.0 - - - +
294A GLY* 1.3 55.6 + - - +
295A THR 3.0 4.9 - - - -
296A THR* 3.4 15.5 - - - +
297A LEU* 3.0 39.0 - - + +
298A PRO* 3.1 5.5 - - - +
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Residues in contact with GLY 294 (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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115A ASN* 5.1 4.2 + - - -
116A ALA* 3.6 24.4 - - - +
117A GLY 4.1 6.5 - - - -
292A PRO* 3.2 5.3 - - - +
293A CYS* 1.3 78.8 - - - +
295A THR* 1.3 59.3 + - - +
298A PRO* 3.4 15.5 - - - +
294B GLY 5.4 0.2 - - - +
295B THR* 4.5 10.9 - - - +
298B PRO* 4.5 1.6 - - - +
299B GLU* 5.2 1.7 + - - +
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Residues in contact with THR 295 (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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291A GLY* 6.2 0.2 - - - -
292A PRO* 3.0 28.1 + - + +
293A CYS 3.0 0.4 - - - -
294A GLY* 1.3 81.5 - - - +
296A THR* 1.3 73.0 + - + +
297A LEU 3.5 0.2 - - - -
298A PRO* 3.7 5.0 - - - +
299A GLU* 3.7 17.9 + - - +
294B GLY 4.9 3.6 - - - +
295B THR* 2.8 45.7 + - + +
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Residues in contact with THR 296 (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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40A MET* 4.2 5.1 - - + +
274A PHE* 3.5 25.4 - - - +
289A PHE* 4.5 11.2 + - + -
290A GLN 3.4 27.6 - - - +
291A GLY* 4.4 4.7 + - - -
292A PRO 3.5 5.3 + - - +
293A CYS* 3.4 17.0 - - - +
295A THR* 1.3 84.0 - - + +
297A LEU* 1.3 64.1 + - - +
299A GLU* 3.0 16.1 + - - +
300A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 297 (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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117A GLY* 4.1 12.8 - - - -
120A ALA* 4.5 2.2 - - + -
121A ILE* 3.8 26.2 - - + -
246A LEU* 4.1 17.0 - - + -
248A VAL* 3.7 30.3 - - + -
274A PHE* 4.2 19.3 - - + -
293A CYS* 3.0 27.9 + - + +
296A THR* 1.3 78.3 + - - +
298A PRO* 1.4 67.7 - - + +
301A LEU* 2.9 55.0 + - + +
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Residues in contact with PRO 298 (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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116A ALA* 3.8 26.5 - - + +
120A ALA* 3.8 13.1 - - + +
293A CYS 3.1 15.5 - - - +
294A GLY 3.4 19.5 - - - +
295A THR 3.7 9.9 - - - +
296A THR 3.7 2.5 - - - -
297A LEU* 1.4 89.4 - - + +
299A GLU* 1.3 59.9 + - - +
301A LEU* 4.0 0.9 - - - +
302A ALA* 3.3 24.8 + - - +
116B ALA* 3.5 21.1 - - + +
119B ARG* 6.0 0.2 - - - +
294B GLY 4.7 0.9 - - - +
298B PRO* 4.4 11.7 - - + -
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Residues in contact with GLU 299 (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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40A MET* 3.9 33.4 - - + +
44A ARG* 3.7 11.6 + - - -
295A THR* 3.7 11.2 + - - +
296A THR* 3.0 15.6 + - - +
298A PRO* 1.3 75.2 - - - +
300A ALA* 1.3 66.0 + - - +
301A LEU 3.4 0.5 + - - -
302A ALA* 3.5 14.8 + - - +
116B ALA* 3.8 11.8 - - + +
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Residues in contact with ALA 300 (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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40A MET* 3.6 25.1 - - + -
43A PHE* 3.8 9.4 - - + -
44A ARG* 2.9 21.2 + - - +
47A PHE* 3.5 12.0 - - - -
274A PHE* 3.5 39.5 - - + -
296A THR 2.9 6.8 + - - +
297A LEU* 3.9 3.1 - - - +
299A GLU* 1.3 76.2 - - - +
301A LEU* 1.3 62.3 + - + +
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Residues in contact with LEU 301 (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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43A PHE* 5.2 0.7 - - + -
47A PHE* 3.5 32.9 - - + -
53A ILE* 5.9 0.7 - - + -
55A ILE* 4.7 4.0 - - + -
120A ALA* 4.0 10.3 - - + +
121A ILE* 3.8 37.7 - - + +
124A CYS* 3.9 17.3 - - + +
127A ARG* 2.5 33.6 + - - -
246A LEU* 3.7 23.8 - - + -
297A LEU* 2.9 40.4 + - + +
298A PRO 4.0 1.8 - - - +
300A ALA* 1.3 81.2 - - + +
302A ALA* 1.3 53.6 + - - +
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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