Contacts of the helix formed by residues 290 - 301 (chain B) in PDB entry 2CRX
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 SER 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 4.3 0.6 - - - +
135B LEU 2.6 27.5 + - - -
137B PHE* 2.9 27.4 + - - -
265B PHE* 4.1 2.5 - - - -
286B TRP* 3.3 11.1 - - - -
287B SER* 2.8 38.1 + - - -
289B HIS* 1.3 77.0 - - - +
291B ALA* 1.3 56.4 + - - -
293B VAL* 3.5 4.1 - - - +
294B GLY 2.8 24.9 + - - -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 3.8 19.4 - - + +
167B ALA* 3.5 43.5 - - + +
168B TYR* 3.6 9.5 - - - +
265B PHE* 3.9 12.1 - - + -
288B GLY 4.5 1.5 + - - +
289B HIS 3.0 2.4 + - - -
290B SER* 1.3 72.9 - - - +
292B ARG* 1.3 60.6 + - + +
295B ALA* 2.8 33.1 + - - +
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Residues in contact with ARG 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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171B LEU* 2.5 68.7 + - + +
172B LEU* 4.5 1.5 - - - +
173B ARG* 3.2 54.9 - - - +
176B GLU* 4.9 0.6 + - - -
288B GLY 4.5 10.1 + - - +
289B HIS* 2.7 31.2 + - + +
291B ALA* 1.3 75.2 - - + +
293B VAL* 1.3 62.1 + - - +
295B ALA* 3.7 1.7 - - - +
296B ALA* 3.1 23.0 + - - +
313B GLY* 2.9 24.5 + - - -
315B TRP* 2.9 44.9 - - + +
324B TYR* 5.4 1.9 + - + -
15C G 4.2 3.8 + - - -
16C C 4.1 1.0 - - - -
25D T 6.5 0.4 - - - -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 6.2 2.0 - - + -
134B ALA* 4.2 16.8 - - + +
135B LEU 4.6 0.4 - - - +
136B ALA* 3.6 24.0 - - + +
289B HIS* 2.9 36.6 - - + +
290B SER* 3.5 9.4 - - - +
292B ARG* 1.3 74.9 - - - +
294B GLY* 1.3 62.6 + - - +
296B ALA* 3.5 7.1 + - - +
297B ARG* 3.3 30.2 + - - +
324B TYR* 4.0 40.2 - - + +
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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
----------------------------------------------------------
136B ALA* 3.7 17.0 - - - -
137B PHE 3.6 16.4 - - - -
138B GLU* 4.1 4.0 - - - +
168B TYR* 4.4 2.0 - - - -
290B SER 2.8 22.3 + - - -
293B VAL* 1.3 75.0 - - - +
295B ALA* 1.3 61.2 + - - +
297B ARG* 3.2 13.7 + - - +
298B ASP* 3.3 17.0 + - - +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 3.8 31.9 - - + +
171B LEU* 3.5 30.3 - - + -
291B ALA 2.8 22.4 + - - +
294B GLY* 1.3 69.8 - - - +
296B ALA* 1.3 65.4 + - - +
298B ASP* 3.3 2.3 + - - +
299B MET* 3.0 31.1 + - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.4 1.9 - - - +
292B ARG 3.1 12.7 + - - +
293B VAL 3.6 10.5 - - - +
294B GLY 3.3 0.2 - - - -
295B ALA* 1.3 76.8 - - - +
297B ARG* 1.3 62.1 + - - +
299B MET* 3.7 3.3 + - - -
300B ALA* 3.2 20.3 + - - +
309B ILE* 3.7 32.4 - - + +
315B TRP* 4.5 6.5 - - + -
321B VAL* 4.8 4.3 - - + -
324B TYR* 4.3 23.3 - - + -
325B ILE* 3.7 3.8 - - + +
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 4.9 11.7 - - - +
134B ALA 5.2 4.6 + - - -
136B ALA* 4.4 13.1 - - - +
138B GLU* 3.9 24.5 + - - +
293B VAL* 3.3 24.8 + - - +
294B GLY* 3.5 7.4 - - - +
295B ALA 3.1 0.8 - - - -
296B ALA* 1.3 76.3 - - - +
298B ASP* 1.3 68.0 + - - +
300B ALA* 2.9 7.7 + - - +
301B ARG* 2.9 24.7 + - - +
323B ASN 5.5 0.2 + - - -
324B TYR* 2.6 31.0 + - - +
325B ILE* 4.4 11.0 - - + +
326B ARG 5.4 3.8 - - - +
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.6 18.9 - - - +
139B ARG* 2.7 29.8 + - + +
168B TYR* 2.2 36.2 + - - +
294B GLY 3.3 6.4 + - - +
295B ALA 3.3 5.5 + - - +
297B ARG* 1.3 75.8 - - - +
299B MET* 1.3 57.8 + - + +
301B ARG* 3.4 6.3 + - - +
302B ALA* 2.9 31.8 + - - +
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Residues in contact with MET 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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171B LEU* 4.7 17.5 - - + -
295B ALA* 3.0 24.9 + - - +
296B ALA* 3.9 5.6 - - - +
298B ASP* 1.3 76.0 - - + +
300B ALA* 1.3 61.4 + - - +
302B ALA* 3.5 2.2 + - - -
303B GLY 3.4 1.9 + - - -
304B VAL* 2.8 61.0 + - + +
308B GLU* 4.3 17.0 - - - +
309B ILE* 4.0 20.2 - - + -
312B ALA* 3.9 23.8 - - + -
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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
----------------------------------------------------------
296B ALA 3.2 12.9 + - - +
297B ARG 2.9 10.1 + - - +
299B MET* 1.3 75.0 - - - +
301B ARG* 1.3 55.0 + - - +
302B ALA 2.6 3.6 + - - -
303B GLY* 2.5 33.1 + - - -
304B VAL 4.7 3.4 - - - +
309B ILE* 4.3 6.7 - - + -
325B ILE* 3.5 32.8 - - + -
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG 2.9 16.7 + - - +
298B ASP* 3.9 6.5 - - - +
300B ALA* 1.3 72.7 - - - +
302B ALA* 1.3 58.4 + - - +
303B GLY 3.4 0.5 + - - -
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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