Contacts of the helix formed by residues 289 - 298 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A GLN 4.0 1.0 + - - -
288A MET* 1.3 75.9 - - - +
290A ASN* 1.3 66.8 + - - +
291A TRP* 3.2 14.8 - - + -
292A GLN* 3.1 20.5 + - - +
293A LEU* 3.0 18.6 + - - +
306A ASN* 3.7 1.3 - - - +
308A ASP 3.8 8.3 + - - +
309A ASP* 3.4 14.1 - - - +
310A THR* 3.1 32.3 - - + +
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Residues in contact with ASN 290 (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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289A ALA* 1.3 72.1 - - - +
291A TRP* 1.3 61.5 + - - +
293A LEU* 3.6 7.7 - - - +
294A ILE* 3.0 26.5 + - - +
300A VAL* 4.0 8.7 - - + +
301A GLU 2.9 45.1 + - - +
303A TYR 5.5 0.6 - - - +
306A ASN* 2.7 27.2 + - - +
309A ASP* 3.1 26.8 + - - +
456A GLN* 4.1 13.9 + - - +
457A VAL* 4.0 20.6 - - + +
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR 3.6 16.6 - - - +
172A GLY* 3.8 26.0 - - - -
173A VAL* 3.6 9.1 - - + +
176A ALA* 4.5 12.8 - - + -
289A ALA* 3.2 18.6 - - + +
290A ASN* 1.3 78.0 - - - +
292A GLN* 1.3 84.3 + - + +
294A ILE* 3.5 4.3 - - - +
295A HIS* 3.3 31.4 + - + +
309A ASP* 4.7 0.8 + - - -
310A THR* 4.0 10.9 + - - -
312A ASP* 3.7 30.1 + - - -
457A VAL* 3.9 15.1 - - + +
461A GLN* 3.4 32.2 - - - +
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Residues in contact with GLN 292 (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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287A GLN 3.9 6.5 + - - +
288A MET* 3.7 27.6 - - + -
289A ALA* 3.1 32.8 + - - +
291A TRP* 1.3 108.8 + - + +
293A LEU* 1.3 59.9 + - - +
295A HIS* 4.4 5.4 - - - +
296A MET* 2.9 37.7 + - + +
310A THR* 5.0 1.4 + - - +
309P PHE* 4.8 12.9 - - + -
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Residues in contact with LEU 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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252A HIS* 4.0 10.5 - - + +
285A TYR* 4.9 0.4 - - + -
288A MET* 3.7 24.5 - - + +
289A ALA 3.0 12.7 + - - +
290A ASN* 3.2 27.3 + - - +
292A GLN* 1.3 75.3 - - - +
294A ILE* 1.3 56.3 + - - +
297A TYR* 2.6 46.8 + - + +
298A GLY 3.0 5.4 + - - -
299A PHE* 3.2 52.4 - - + +
301A GLU* 4.1 16.6 - - + +
306A ASN* 3.9 11.9 - - - +
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Residues in contact with ILE 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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154A GLU 5.4 0.4 - - - +
156A PRO* 2.9 28.4 - - + +
159A TRP* 4.1 22.2 - - + -
168A LEU* 4.8 6.7 - - + -
173A VAL* 3.9 21.1 - - + -
290A ASN 3.0 14.7 + - - +
291A TRP 3.5 11.7 - - - +
293A LEU* 1.3 76.3 - - - +
295A HIS* 1.3 65.5 + - - +
298A GLY* 3.0 18.0 + - - +
299A PHE 3.1 16.7 + - - +
300A VAL* 3.8 12.8 - - + -
453A GLN* 3.8 32.8 - - + +
454A ALA 4.5 0.7 - - - +
457A VAL* 4.1 13.9 - - + -
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Residues in contact with HIS 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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155A HIS* 3.5 15.6 - - - +
156A PRO* 4.1 9.8 - - - +
157A MET* 5.8 2.4 - - + +
173A VAL* 4.4 10.1 - - + -
176A ALA* 3.8 25.4 - - + +
177A VAL* 4.1 19.7 - - + -
180A ASP* 2.6 32.6 + - - -
221A MET* 4.4 6.2 - - + +
291A TRP* 3.3 23.8 + - + +
292A GLN* 3.8 4.7 - - - +
294A ILE* 1.3 85.3 - - - +
296A MET* 1.3 86.5 + - - +
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Residues in contact with MET 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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122A TRP* 4.6 6.5 - - + -
155A HIS* 2.9 19.0 + - - -
221A MET* 3.7 38.8 - - + +
222A ALA* 3.5 15.8 + - - +
292A GLN* 2.9 21.7 + - + +
295A HIS* 1.3 105.5 - - - +
297A TYR* 1.3 65.5 + - + +
309P PHE* 3.0 64.2 - - + -
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Residues in contact with TYR 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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154A GLU* 5.6 0.2 - - - +
155A HIS* 4.0 8.0 + - - -
221A MET 3.8 1.1 - - - -
222A ALA* 3.1 39.0 - - + -
285A TYR* 3.4 32.3 + + + +
288A MET* 3.4 17.5 - - + -
293A LEU* 2.6 26.8 + - + +
296A MET* 1.3 78.5 - - + +
298A GLY* 1.3 62.9 + - - +
299A PHE* 3.3 20.5 + + + -
484A SAM 2.6 32.8 + - - +
309P PHE* 3.1 41.9 - + - -
310P LYS* 3.1 30.3 + - - +
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Residues in contact with GLY 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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154A GLU* 3.6 41.1 - - - +
155A HIS* 4.1 4.5 - - - -
293A LEU 3.0 0.6 + - - -
294A ILE* 3.0 23.8 + - - -
296A MET 3.8 0.6 - - - -
297A TYR* 1.3 78.5 - - - +
299A PHE* 1.3 59.4 + - - +
453A GLN* 3.3 17.8 + - - -
484A SAM 5.2 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