Contacts of the strand formed by residues 249 - 254 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR* 3.6 7.4 - - + -
216B LEU* 3.3 11.0 - - + +
218B SER* 6.1 0.4 - - - +
242B ALA* 3.5 10.8 - - - +
245B LEU* 3.5 42.0 - - + -
246B GLY 3.0 6.1 + - - +
247B PRO 4.3 0.2 - - - +
248B LYS* 1.3 77.2 - - - +
250B GLN* 1.3 66.1 + - - +
276B LYS* 2.8 30.1 + - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LYS* 3.4 38.0 + - - +
216B LEU 2.9 5.9 + - - +
217B PHE* 3.3 10.8 - - + -
218B SER* 3.1 26.0 + - - -
242B ALA* 4.0 7.2 - - - -
247B PRO 4.6 10.4 + - - +
248B LYS 4.0 2.6 + - - +
249B ALA* 1.3 81.4 - - - +
251B CYS* 1.3 62.5 + - - +
275B GLY 3.3 21.6 + - - -
276B LYS* 3.8 10.8 - - + +
277B LEU 4.2 7.6 + - - +
278B GLY* 3.4 27.9 - - - +
319B GLY 4.0 15.2 + - - -
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Residues in contact with CYS 251 (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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217B PHE* 5.2 0.2 - - - -
218B SER 3.6 4.3 - - - -
238B ASN* 3.3 51.8 - - + +
239B TYR* 3.8 7.2 - - - -
242B ALA* 3.8 12.1 - - - -
250B GLN* 1.3 72.8 - - - +
252B LEU* 1.3 62.2 + - - +
253B VAL 4.0 0.7 + - - -
271B LEU* 3.9 24.5 - - + -
276B LYS* 2.9 19.9 + - - +
277B LEU* 3.8 4.2 - - - +
278B GLY* 2.8 28.1 + - - -
279B GLY 3.4 2.6 + - - +
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Residues in contact with LEU 252 (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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177B THR* 3.6 26.7 - - + +
217B PHE* 4.1 17.9 - - + -
218B SER 2.9 13.8 + - - +
219B GLU* 3.8 29.3 - - + +
220B HIS* 3.8 14.6 + - - +
250B GLN 4.0 0.4 + - - -
251B CYS* 1.3 73.5 - - - +
253B VAL* 1.3 86.3 + - - +
254B ASP 4.0 1.4 + - - -
279B GLY* 3.0 23.6 - - - +
280B PHE 3.3 18.6 - - - -
281B HIS* 3.6 17.5 - - + +
325B MET* 3.7 22.4 - - + -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B HIS* 4.2 9.9 - - + -
252B LEU* 1.3 82.1 - - - +
254B ASP* 1.3 63.1 + - - +
255B LEU* 3.8 2.1 + - + +
258B HIS* 3.7 24.9 - - + +
264B ILE* 4.3 15.7 - - + -
267B ILE* 4.7 5.6 - - + -
268B VAL* 4.7 4.7 - - + -
271B LEU* 3.6 31.9 - - + -
277B LEU* 3.9 13.5 - - + -
279B GLY 2.9 7.5 + - - +
280B PHE* 3.3 23.6 - - + -
281B HIS 2.8 21.8 + - - +
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Residues in contact with ASP 254 (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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219B GLU* 3.2 19.2 - - + +
220B HIS* 5.2 1.8 + - - -
252B LEU 4.0 3.2 + - - -
253B VAL* 1.3 71.6 - - - +
255B LEU* 1.3 65.9 + - - +
256B GLY* 3.2 9.5 + - - -
257B HIS* 2.9 42.4 + - - +
258B HIS* 3.3 10.4 + - - -
281B HIS* 3.2 15.5 - - + +
283B ASN* 2.9 23.9 + - - -
289B ASP* 4.0 1.0 - - - +
327B ASP* 3.1 5.5 - - - +
503B MN 2.2 31.6 + - - -
504B MN 3.8 0.7 + - - -
2002B RNS 3.2 2.3 + - - -
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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