Contacts of the strand formed by residues 249 - 254 (chain A) in PDB entry 3M0V
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TYR* 3.7 7.3 - - + -
216A LEU* 3.3 11.0 - - + +
218A SER* 6.1 0.4 - - - +
241A ILE* 5.8 0.2 - - + -
242A ALA* 3.5 12.4 - - - +
245A LEU* 3.5 37.7 - - + -
246A GLY 3.0 10.5 + - - +
248A LYS* 1.3 78.2 - - - +
250A GLN* 1.3 63.1 + - - +
276A LYS* 2.9 28.6 + - - +
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Residues in contact with GLN 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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215A LYS* 3.3 28.8 + - - +
216A LEU 2.9 7.5 + - - +
217A PHE* 3.3 16.9 - - + -
218A SER* 3.2 26.3 + - - -
242A ALA* 4.0 6.2 - - - +
247A PRO 4.5 9.2 + - - +
248A LYS 3.8 3.3 + - - +
249A ALA* 1.3 81.2 - - - +
251A CYS* 1.3 64.4 + - - +
275A GLY 3.3 27.0 + - - +
276A LYS* 3.7 5.2 - - + +
277A LEU 4.0 10.2 + - - +
278A GLY* 3.4 29.7 - - - +
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Residues in contact with CYS 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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217A PHE* 5.1 0.4 - - - -
218A SER 3.7 3.6 - - - -
238A ASN* 3.3 51.8 - - + +
239A TYR* 3.8 7.0 - - - -
242A ALA* 3.8 13.2 - - - -
250A GLN* 1.3 73.0 - - - +
252A LEU* 1.3 61.2 + - - +
253A VAL* 4.0 0.8 + - - -
271A LEU* 4.0 24.9 - - + -
276A LYS* 2.7 20.8 + - - +
277A LEU* 3.7 5.2 - - - +
278A GLY* 2.7 26.9 + - - -
279A GLY 3.4 3.5 + - - +
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Residues in contact with LEU 252 (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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177A THR* 3.8 18.6 - - + +
217A PHE* 4.1 17.7 - - + -
218A SER 2.9 14.6 + - - +
219A GLU* 3.7 38.4 - - + +
220A HIS* 3.9 5.7 + - - -
238A ASN* 3.8 6.9 + - - -
250A GLN 4.1 0.8 + - - -
251A CYS* 1.3 73.2 - - - +
253A VAL* 1.3 66.1 + - - +
254A ASP 3.9 1.2 + - - -
279A GLY 3.5 13.7 - - - +
281A HIS* 3.5 41.1 - - + +
325A MET* 3.5 32.3 - - + -
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Residues in contact with VAL 253 (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 HIS* 4.3 9.2 - - + -
252A LEU* 1.3 75.6 - - - +
254A ASP* 1.3 63.2 + - - +
255A LEU* 3.8 2.5 + - + -
258A HIS* 3.7 24.7 - - + +
264A ILE* 4.3 14.8 - - + -
267A ILE* 4.6 6.3 - - + -
268A VAL* 4.6 4.9 - - + -
271A LEU* 3.7 31.2 - - + -
277A LEU* 4.0 12.6 - - + -
279A GLY 3.0 6.9 + - - -
280A PHE* 3.3 26.8 - - + -
281A HIS 2.9 23.5 + - - +
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Residues in contact with ASP 254 (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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219A GLU* 3.1 18.5 - - + +
220A HIS* 5.3 2.0 + - - -
252A LEU 3.9 3.0 + - - -
253A VAL* 1.3 72.8 - - - +
255A LEU* 1.3 63.7 + - - +
256A GLY* 3.1 9.4 + - - -
257A HIS* 3.0 39.7 + - - +
258A HIS* 3.2 12.3 + - - -
281A HIS* 3.3 11.7 - - + +
283A ASN* 2.8 27.7 + - - -
289A ASP* 4.0 0.3 - - - +
327A ASP* 3.2 4.0 - - - +
501A MN 2.2 31.9 + - - -
502A MN 3.8 0.9 + - - -
2001A RNS 3.2 3.3 + - - -
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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