Contacts of the strand formed by residues 248 - 253 (chain F) in PDB entry 2V90
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 ARG 248 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246F LYS* 3.9 7.4 - - + +
247F PRO* 1.3 78.0 - - - +
249F CYS* 1.3 60.5 + - - +
250F LEU* 3.4 19.9 + - + +
289F ALA 3.2 26.1 + - - -
290F GLY* 3.2 26.8 + - - -
291F MET* 4.3 1.0 - - - +
292F GLN* 4.7 2.1 - - - +
326F LEU 3.7 1.4 - - - +
327F THR* 3.3 4.2 - - - -
328F VAL* 2.8 49.4 + - + +
330F ASP* 2.9 41.4 + - - -
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Residues in contact with CYS 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F PRO 4.2 0.6 + - - -
248F ARG* 1.3 70.5 - - - +
250F LEU* 1.3 66.3 + - - +
251F HIS* 4.0 21.1 + - + -
302F GLY* 6.1 2.0 - - - -
325F SER* 2.9 28.9 - - - -
326F LEU 3.5 4.5 - - - -
327F THR* 3.5 21.6 - - + +
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F ARG* 3.4 33.9 - - + +
249F CYS* 1.3 80.3 - - - +
251F HIS* 1.3 64.7 + - - +
252F LEU 4.1 0.6 + - - -
289F ALA* 3.0 38.6 - - + +
291F MET* 3.4 43.7 - - + +
324F VAL 3.9 0.5 - - - +
325F SER* 3.4 3.5 + - - -
326F LEU* 2.8 31.5 + - - +
328F VAL* 4.3 7.4 - - + -
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Residues in contact with HIS 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F CYS* 4.0 25.0 + - + -
250F LEU* 1.3 74.7 - - - +
252F LEU* 1.3 67.7 + - - +
253F GLU* 3.9 10.1 - - - +
289F ALA* 4.9 3.3 - - - +
324F VAL 3.5 3.8 - - - +
325F SER* 3.7 26.8 + - - -
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Residues in contact with LEU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F LEU 5.0 0.2 - - - +
251F HIS* 1.3 79.9 - - - +
253F GLU* 1.3 64.1 + - - +
254F LYS 4.1 0.2 - - - -
259F PHE* 3.6 33.0 - - + -
285F PRO* 3.6 18.8 - - + +
286F ALA* 3.9 20.2 - - + +
289F ALA* 3.5 32.1 - - + -
291F MET* 4.2 10.1 - - + -
322F SER 4.0 0.2 - - - +
323F CYS* 3.3 4.9 - - - +
324F VAL* 2.7 39.7 + - + +
326F LEU* 3.4 32.3 - - + -
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Residues in contact with GLU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F HIS* 3.9 12.0 - - - +
252F LEU* 1.3 75.4 - - - +
254F LYS* 1.3 65.7 + - - +
255F GLY 3.9 0.2 + - - -
259F PHE* 4.1 1.3 - - - -
285F PRO* 3.2 21.6 - - - +
322F SER 3.5 4.7 - - - +
323F CYS* 3.5 26.2 - - - -
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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