Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 2WMH
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 ASN 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.1 49.1 + - + +
42A ASN* 3.7 6.1 - - - -
184A HIS* 4.6 9.7 + - - -
213A LYS 4.9 1.8 + - - -
215A LEU 3.8 2.2 + - - -
216A VAL* 3.4 37.9 - - + +
217A LEU 3.4 0.2 + - - -
238A TRP* 3.9 5.8 - - - +
243A CYS* 3.3 15.7 - - - -
244A ASP* 1.3 95.0 + - - +
246A TRP* 1.3 60.4 + - - +
296A THR* 2.7 26.1 + - - +
297A VAL* 4.5 0.4 - - + -
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Residues in contact with TRP 246 (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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216A VAL* 4.1 6.3 - - - -
217A LEU 3.1 14.6 - - - +
219A THR* 4.3 4.7 - - + -
231A ASP* 4.2 17.3 - - - -
234A VAL* 3.8 23.6 - - + +
235A SER* 3.5 24.9 - - - -
238A TRP* 3.5 32.8 - + + -
243A CYS* 4.7 1.6 - - - -
245A ASN* 1.3 74.6 - - - +
247A GLY* 1.3 85.5 + - - +
290A VAL* 3.6 42.4 - - + -
293A GLY* 3.1 32.5 + - - -
294A GLY 3.5 2.1 + - - -
295A GLY* 3.3 17.0 - - - +
296A THR* 2.9 27.0 + - - -
297A VAL* 3.4 4.5 + - - +
381A ILE* 4.2 14.4 - - + -
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Residues in contact with GLY 247 (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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216A VAL* 4.4 0.2 - - - +
217A LEU 3.2 6.3 + - - -
218A ALA* 3.1 10.6 - - - +
219A THR* 2.9 20.3 + - - +
246A TRP* 1.3 95.9 - - - +
248A SER* 1.3 62.8 + - - -
290A VAL* 3.9 8.3 - - - -
297A VAL* 3.1 15.7 - - - -
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Residues in contact with SER 248 (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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188A HIS* 3.4 11.9 - - - -
218A ALA* 3.7 2.4 - - - +
219A THR* 3.4 20.2 - - - -
247A GLY* 1.3 75.2 - - - -
249A SER* 1.3 55.6 + - - +
250A THR* 3.9 15.7 + - - -
287A MET* 5.4 0.3 - - - -
290A VAL* 3.3 27.4 - - - +
297A VAL 3.0 8.7 + - - +
298A TYR* 3.7 10.9 - - - -
299A ASN 2.8 31.9 + - - +
300A PHE* 6.1 0.2 - - - -
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Residues in contact with SER 249 (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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157A ILE* 6.1 0.2 - - - -
188A HIS* 3.3 27.3 + - - -
219A THR* 2.8 14.5 + - - -
220A LYS* 3.5 39.9 - - - +
221A ASN* 3.8 5.5 + - - +
248A SER* 1.3 73.0 - - - +
250A THR* 1.3 62.4 + - - +
251A ASP* 3.5 4.5 + - - +
299A ASN* 3.3 11.0 + - - +
300A PHE 4.3 12.3 + - - -
301A GLU* 4.5 6.4 + - - +
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Residues in contact with THR 250 (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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221A ASN* 4.4 1.3 - - - -
248A SER* 3.9 16.7 + - - -
249A SER* 1.3 69.8 - - - +
251A ASP* 1.3 61.2 + - - +
252A THR* 3.9 1.6 + - + +
254A LYS* 4.4 0.4 - - - +
278A GLU* 5.0 0.9 - - - +
283A ILE* 4.2 24.9 - - + +
286A GLU* 3.5 49.0 + - + +
287A MET* 4.6 5.2 + - - +
299A ASN 2.8 7.9 + - - -
300A PHE* 3.3 24.5 - - + -
301A GLU 3.1 23.5 + - - +
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Residues in contact with ASP 251 (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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220A LYS* 3.6 8.0 + - + +
221A ASN* 3.6 6.2 + - - +
222A THR* 2.6 47.8 + - - +
249A SER* 3.5 10.1 + - - +
250A THR* 1.3 72.8 - - - +
252A THR* 1.3 59.0 + - - +
253A TRP* 2.9 36.7 + - - +
254A LYS* 2.8 36.3 + - - +
301A GLU* 3.3 22.4 - - + +
1B GAL 5.2 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