Contacts of the strand formed by residues 336 - 339 (chain C) 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 GLU 336 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A PRO* 3.7 24.1 - - - +
283A GLY* 3.5 14.1 + - - +
287A LYS* 4.3 15.3 - - + +
288A LYS* 2.9 25.7 + - + -
333C ALA* 4.5 14.0 - - - +
334C ASP 3.6 0.6 - - - -
335C ARG* 1.3 78.9 - - - +
337C THR* 1.3 61.7 + - - +
262E LEU* 3.5 19.2 - - + +
263E LEU 3.1 11.2 - - - +
264E ARG* 2.8 47.1 + - + +
278E TRP* 5.0 0.5 - - - -
310E HIS* 3.6 0.2 + - - -
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Residues in contact with THR 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLY* 3.6 8.0 - - - +
288A LYS* 2.6 25.6 + - - +
336C GLU* 1.3 69.3 - - - +
338C SER* 1.3 73.7 + - - +
339C VAL* 3.7 17.2 + - + +
262E LEU* 3.7 4.2 - - - +
263E LEU* 2.8 34.1 + - - +
310E HIS* 3.0 21.1 + - - -
311E GLU* 4.9 1.6 + - - -
314E VAL* 4.0 21.4 - - + +
318E GLN* 5.5 2.9 - - - +
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLN* 3.1 25.4 + - - -
282A PRO 4.1 9.6 - - - -
283A GLY* 3.0 12.6 + - - +
284A LEU* 3.7 29.4 - - - +
337C THR* 1.3 77.5 - - - +
339C VAL* 1.3 68.0 + - - +
261E PHE 3.5 11.6 + - - -
262E LEU* 3.7 7.2 + - - +
281E ASP* 4.9 6.4 + - - -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLN* 4.3 12.6 + - - +
337C THR* 3.8 20.6 - - + +
338C SER* 1.3 82.3 + - - +
254E LYS* 5.7 0.2 - - - +
257E GLN 4.6 0.9 - - - +
258E GLY* 3.6 9.3 - - - -
259E PHE* 2.8 39.7 + - + -
260E GLY* 3.0 24.1 + - - -
261E PHE* 2.9 60.7 + - + +
263E LEU* 5.3 2.0 - - + -
314E VAL* 4.5 17.0 - - + -
317E ILE* 4.6 16.8 - - + -
318E GLN* 5.1 8.7 - - + +
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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