Contacts of the helix formed by residues 289 - 298 (chain B) in PDB entry 3RC0
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 ALA 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLN 4.1 1.0 + - - -
288B MET* 1.3 76.0 - - - +
290B ASN* 1.3 66.8 + - - +
291B TRP* 3.7 17.7 - - + -
292B GLN* 3.0 17.1 + - - +
293B LEU* 3.0 19.1 + - - +
308B ASP 3.8 8.7 + - - +
309B ASP* 3.4 13.9 - - - +
310B THR* 3.1 33.2 - - + +
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Residues in contact with ASN 290 (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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289B ALA* 1.3 71.6 - - - +
291B TRP* 1.3 57.1 - - - +
293B LEU* 3.5 8.4 - - - +
294B ILE* 3.0 30.8 + - - +
300B VAL* 4.1 9.7 - - + +
301B GLU 2.9 43.2 + - - +
303B TYR* 5.5 0.6 - - - +
306B ASN* 2.8 26.6 + - - +
309B ASP* 2.9 24.3 + - - +
456B GLN* 4.0 16.6 + - - +
457B VAL* 4.5 20.2 - - + +
460B GLY* 5.8 0.2 - - - -
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Residues in contact with TRP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR 3.8 15.3 - - - +
172B GLY* 4.1 22.4 - - - -
173B VAL* 3.7 12.3 - - + +
176B ALA* 4.4 14.8 - - + -
289B ALA* 3.2 19.0 - - + +
290B ASN* 1.3 78.4 - - - +
292B GLN* 1.3 83.9 + - + +
294B ILE* 3.5 6.2 - - - +
295B HIS* 3.2 35.4 + - + +
309B ASP* 4.7 0.4 + - - -
310B THR* 4.1 15.2 + - - -
311B ALA* 6.1 0.4 - - - +
312B ASP* 4.3 24.2 + - - -
457B VAL* 4.0 11.7 - - + +
461B GLN* 3.6 30.2 - - - +
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Residues in contact with GLN 292 (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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287B GLN 4.2 5.4 + - - +
288B MET* 3.5 30.0 - - + +
289B ALA* 3.0 31.5 + - - +
291B TRP* 1.3 109.4 + - + +
293B LEU* 1.3 59.2 + - - +
295B HIS* 4.4 5.2 - - - +
296B MET* 2.9 40.3 + - + +
310B THR* 5.0 0.9 + - - +
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Residues in contact with LEU 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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252B HIS* 4.1 9.2 - - + +
285B TYR* 5.1 0.7 - - + -
288B MET* 3.4 32.5 - - + +
289B ALA 3.0 14.9 + - - +
290B ASN* 3.3 28.5 + - - +
292B GLN* 1.3 75.9 - - - +
294B ILE* 1.3 56.2 + - - +
297B TYR* 2.8 37.3 + - + +
298B GLY 3.0 5.7 + - - -
299B PHE* 3.0 50.8 - - + +
301B GLU* 4.0 16.4 - - + +
306B ASN* 3.8 11.0 - - - +
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Residues in contact with ILE 294 (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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154B GLU 5.4 0.4 - - - +
156B PRO* 2.9 29.9 - - + +
159B TRP* 4.0 24.0 - - + -
168B LEU* 4.4 8.1 - - + -
173B VAL* 3.9 21.3 - - + -
290B ASN 3.0 16.2 + - - +
291B TRP 3.5 10.8 - - - +
293B LEU* 1.3 75.1 - - - +
295B HIS* 1.3 67.3 + - - +
298B GLY* 3.0 15.5 + - - -
299B PHE 3.0 14.2 + - - +
300B VAL* 3.8 14.1 - - + -
453B GLN* 3.9 30.7 - - + +
457B VAL* 4.1 13.9 - - + -
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Residues in contact with HIS 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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155B HIS* 3.4 14.7 - - - +
156B PRO* 3.9 11.0 - - - +
157B MET* 5.7 3.5 - - + +
173B VAL* 4.4 9.0 - - + -
176B ALA* 3.8 24.5 + - + +
177B VAL* 4.1 20.2 - - + -
180B ASP* 2.5 34.7 + - - -
221B MET* 4.4 5.7 - - - +
291B TRP* 3.2 24.1 + - + +
292B GLN* 3.9 5.3 - - - +
293B LEU 3.4 0.2 - - - -
294B ILE* 1.3 86.0 - - - +
296B MET* 1.3 85.3 + - - +
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Residues in contact with MET 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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122B TRP* 4.2 13.0 - - + -
155B HIS* 2.8 20.2 + - - -
221B MET* 3.5 53.0 - - + +
222B ALA* 3.5 6.4 + - - +
288B MET* 4.8 6.1 - - + -
292B GLN* 2.9 25.2 + - + +
295B HIS* 1.3 103.5 - - - +
297B TYR* 1.3 78.5 + - + +
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Residues in contact with TYR 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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154B GLU* 5.6 0.3 - - - +
155B HIS* 3.9 8.8 - - - -
221B MET 3.7 6.2 + - - -
222B ALA* 3.1 39.0 - - + -
285B TYR* 3.5 34.5 + + + +
288B MET* 3.6 28.8 - - + +
292B GLN 4.2 0.2 - - - -
293B LEU* 2.8 27.5 + - + +
296B MET* 1.3 87.8 - - + +
298B GLY* 1.3 61.6 + - - +
299B PHE* 3.4 20.5 + + + -
480B SAM 2.7 30.5 + + - +
310Q LYS* 2.7 40.6 + - - +
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Residues in contact with GLY 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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154B GLU* 3.7 41.7 - - - +
155B HIS* 4.1 3.6 - - - -
293B LEU 3.0 0.2 + - - -
294B ILE* 3.0 24.5 + - - -
296B MET 3.8 0.4 - - - -
297B TYR* 1.3 79.1 - - - +
299B PHE* 1.3 59.3 + - - +
453B GLN* 3.2 17.4 + - - -
480B SAM 5.1 1.8 + - - -
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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