Contacts of the helix formed by residues 301 - 305 (chain A) in PDB entry 2WCO
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 MET 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A PRO 4.4 7.4 - - - +
294A LEU* 3.0 21.2 + - + +
296A HIS* 4.5 4.3 - - + -
299A LEU* 3.7 10.7 - - + +
300A VAL* 1.3 73.9 - - - +
302A ASP* 1.3 61.0 + - - +
303A THR* 3.6 15.3 - - + +
304A VAL* 3.0 27.0 + - - +
305A ASN* 3.4 4.0 + - - -
408A VAL* 3.8 31.2 - - + -
410A ARG* 4.4 3.6 - - - +
415A THR* 3.7 30.5 - - + -
416A ALA 4.0 2.7 - - - +
417A GLY* 3.8 25.1 - - - -
447A THR* 5.3 0.2 - - - +
449A TRP* 3.7 24.7 - - + -
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Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL 3.4 0.8 + - - -
301A MET* 1.3 67.8 - - - +
303A THR* 1.3 60.8 + - - +
304A VAL 3.0 6.6 + - - -
305A ASN* 3.0 30.5 + - - +
306A GLY 4.1 2.1 + - - -
309A ILE* 3.6 29.4 - - + +
324A SER* 4.6 1.2 - - - -
325A ASP* 3.5 23.7 + - - +
328A HIS* 5.0 0.5 - - - -
445A MET* 5.7 2.7 - - + -
447A THR* 5.9 4.0 + - + -
449A TRP* 5.4 3.2 - - - -
458A TYR* 3.7 20.4 - - + +
463A TRP* 2.9 40.3 + - + -
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Residues in contact with THR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 4.3 2.8 - - - +
294A LEU* 4.6 3.1 - - - +
301A MET* 3.6 19.5 - - + +
302A ASP* 1.3 75.9 - - - +
304A VAL* 1.3 65.5 + - - +
305A ASN 3.5 0.2 - - - -
306A GLY 4.9 1.7 + - - -
406A ARG* 2.8 47.5 + - - +
417A GLY* 4.0 16.2 - - - +
418A LEU 4.7 0.6 + - - -
419A ALA* 3.9 20.4 - - + +
445A MET* 4.3 17.2 - - + +
447A THR* 4.0 22.7 - - + +
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 3.9 8.7 - - + +
249A TYR* 3.3 13.9 - - - +
250A SER* 3.8 15.9 - - - +
251A GLY* 2.9 33.8 + - - +
294A LEU* 4.1 17.0 - - + -
300A VAL* 4.1 12.1 - - + -
301A MET 3.0 14.8 + - - +
302A ASP 3.0 0.4 - - - -
303A THR* 1.3 88.0 - - - +
305A ASN* 1.3 58.1 + - - +
306A GLY 3.5 2.7 - - - -
404A MET* 3.8 33.4 - - + -
406A ARG* 4.2 7.9 - - + +
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Residues in contact with ASN 305 (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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249A TYR* 3.6 8.9 - - - -
251A GLY* 3.1 30.0 - - - -
252A THR* 3.9 14.8 - - + +
300A VAL* 3.1 29.8 + - - +
301A MET 3.4 6.0 + - - +
302A ASP* 3.0 29.7 + - - +
304A VAL* 1.3 78.5 - - - +
306A GLY* 1.3 66.9 - - - +
307A ARG 3.2 0.3 + - - -
308A ALA* 3.0 23.3 + - + +
309A ILE* 3.9 10.5 - - + +
325A ASP* 4.2 1.2 - - - +
328A HIS* 3.9 13.1 - - + -
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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
------------------------------------------------------------
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