Contacts of the helix formed by residues 292 - 301 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B THR* 4.1 11.1 - - + -
291B GLY* 1.3 85.8 - - - +
293B CYS* 1.3 59.2 - - - +
294B GLY* 4.4 5.4 - - - +
295B THR* 2.9 39.2 + - + +
296B THR* 3.2 10.2 + - - +
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Residues in contact with CYS 293 (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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115B ASN* 6.0 0.4 - - - +
117B GLY* 4.1 5.7 - - - -
248B VAL* 3.5 30.3 - - + -
249B GLY* 4.2 6.5 - - - -
274B PHE* 3.9 31.0 - - - -
275B ASN* 4.8 2.5 - - - -
276B THR* 5.4 0.4 - - - +
291B GLY 3.3 4.3 + - - -
292B PRO* 1.3 66.3 - - - +
294B GLY* 1.3 65.8 + - - +
295B THR 2.9 3.1 + - - -
296B THR* 3.6 7.2 - - - -
297B LEU* 3.3 31.8 + - + +
298B PRO* 3.5 4.2 - - - +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLY 5.4 0.2 - - - +
295A THR 4.9 3.7 - - - +
298A PRO* 4.7 3.1 - - - +
299A GLU* 6.6 0.2 - - - -
115B ASN* 4.7 7.0 + - - -
116B ALA* 3.6 14.4 - - - +
117B GLY* 4.1 16.3 - - - -
292B PRO* 3.2 6.0 - - - +
293B CYS* 1.3 77.7 - - - +
295B THR* 1.3 58.3 + - - +
298B PRO* 3.1 22.7 - - - +
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Residues in contact with THR 295 (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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294A GLY 4.5 5.3 - - - +
295A THR* 2.8 50.0 + - + +
292B PRO* 2.9 30.3 + - + +
294B GLY* 1.3 80.0 - - - +
296B THR* 1.3 69.0 + - + +
298B PRO* 3.8 6.8 - - - +
299B GLU* 4.0 12.6 + - - +
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Residues in contact with THR 296 (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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40B MET* 4.2 6.9 - - + +
274B PHE* 3.4 29.1 - - - +
289B PHE* 4.3 19.5 + - + +
290B GLN 4.0 20.0 - - - +
291B GLY* 4.3 6.8 + - - +
292B PRO 3.2 7.8 + - - +
293B CYS* 3.6 16.6 + - - -
295B THR* 1.3 79.4 - - + +
297B LEU* 1.3 62.8 + - - +
299B GLU* 3.4 8.3 + - - +
300B ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 297 (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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117B GLY* 4.1 13.9 - - - +
120B ALA* 4.3 3.6 - - + -
121B ILE* 3.9 19.1 - - + -
246B LEU* 3.8 29.2 - - + -
248B VAL* 3.6 40.4 - - + -
274B PHE* 4.2 17.3 - - + -
293B CYS* 3.3 21.2 + - + +
296B THR* 1.3 77.4 + - - +
298B PRO* 1.4 63.3 - - + +
300B ALA* 3.1 2.6 + - - -
301B LEU* 2.7 53.6 + - + +
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Residues in contact with PRO 298 (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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116A ALA* 3.7 20.3 - - + +
294A GLY 4.5 1.3 - - - +
298A PRO* 4.4 11.7 - - + -
116B ALA* 3.8 26.2 - - + +
117B GLY* 4.8 0.2 - - - -
120B ALA* 3.7 14.1 - - + +
123B GLU* 6.0 0.4 - - - +
293B CYS 3.5 2.9 - - - +
294B GLY 3.1 29.2 - - - +
295B THR 3.8 4.9 - - - +
296B THR 3.6 3.1 - - - -
297B LEU* 1.4 93.1 - - + +
299B GLU* 1.3 61.4 + - - +
301B LEU 3.8 0.9 - - - -
302B ALA* 3.1 26.9 + - - +
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Residues in contact with GLU 299 (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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115A ASN* 6.5 0.9 - - + -
116A ALA* 3.8 13.8 - - + +
294A GLY 5.5 1.6 - - - +
40B MET* 2.8 47.9 - - + +
44B ARG* 3.4 22.8 + - - -
295B THR 4.0 10.1 + - - +
296B THR* 3.4 8.7 + - - +
297B LEU 3.2 0.4 - - - -
298B PRO* 1.3 80.1 - - - +
300B ALA* 1.3 62.2 + - - +
302B ALA* 3.6 6.4 + - - +
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Residues in contact with ALA 300 (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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40B MET* 3.8 19.9 - - - -
43B PHE* 3.7 21.6 - - + -
44B ARG* 2.8 18.3 + - - +
47B PHE* 3.8 4.7 - - - -
274B PHE* 3.6 31.2 - - + -
296B THR 3.0 17.6 + - - +
297B LEU* 3.1 4.2 + - - +
299B GLU* 1.3 77.7 - - - +
301B LEU* 1.3 62.1 + - + +
302B ALA 3.3 0.2 - - - -
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Residues in contact with LEU 301 (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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43B PHE* 5.1 0.7 - - + -
47B PHE* 3.4 32.2 - - + -
53B ILE* 5.5 1.8 - - + -
55B ILE* 4.4 5.6 - - + -
120B ALA* 4.0 21.5 - - + +
121B ILE* 3.9 30.5 - - + -
124B CYS* 3.8 16.5 - - + +
127B ARG* 2.8 28.4 + - - -
246B LEU* 3.7 25.4 - - + -
297B LEU* 2.7 34.9 + - + +
298B PRO 3.8 2.2 - - - +
300B ALA* 1.3 73.8 - - - +
302B ALA* 1.3 60.1 + - - +
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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