Contacts of the helix formed by residues 268 - 278 (chain F) in PDB entry 2F9K
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 SER 268 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F TYR* 3.7 1.1 - - - -
244F ASP* 3.6 17.7 + - - +
261F ASP* 4.4 23.3 + - - -
266F LYS* 2.8 15.1 + - - -
267F CYS* 1.3 73.0 - - - +
269F TRP* 1.3 67.9 + - - +
270F LEU* 2.9 23.5 + - - +
271F VAL* 3.2 9.4 - - - +
272F VAL* 3.1 25.3 + - - +
290F TYR* 4.2 6.3 - - - -
305F TYR* 5.5 0.7 - - - -
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Residues in contact with TRP 269 (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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190F GLU* 4.6 7.5 + - - -
193F TYR* 3.2 33.0 - + - +
241F ILE* 3.4 46.0 - - + +
244F ASP* 3.0 16.0 + - + +
245F TYR* 5.3 0.9 - - + -
268F SER* 1.3 74.0 + - - +
270F LEU* 1.3 84.5 + - + +
272F VAL* 3.3 5.5 + - + +
273F GLN* 3.0 62.3 + - + +
310F LEU* 4.6 2.9 - - + -
313F VAL* 3.9 9.9 - - + -
314F PHE* 3.7 46.2 - + + -
317F TYR* 4.2 25.2 - + + -
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Residues in contact with LEU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ASP 3.7 22.2 - - - +
245F TYR* 4.2 14.1 - - + -
248F LEU* 3.9 22.4 - - + -
249F PHE* 3.9 28.0 - - + -
268F SER* 2.9 11.5 + - - +
269F TRP* 1.3 99.9 - - + +
271F VAL* 1.3 56.5 + - - +
273F GLN* 3.2 2.1 + - - +
274F CYS* 2.9 28.1 + - - +
305F TYR* 3.6 15.9 - - + +
310F LEU* 3.5 30.5 - - + +
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Residues in contact with VAL 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F LEU* 4.5 0.7 - - + -
188F PHE* 3.6 33.9 - - + -
266F LYS 3.8 2.2 - - - +
268F SER* 3.2 30.0 + - - +
270F LEU* 1.3 78.3 - - - +
272F VAL* 1.3 63.3 + - + +
274F CYS* 3.4 2.6 + - - +
275F LEU* 2.9 33.9 + - + +
286F LEU* 3.9 22.0 - - + -
290F TYR* 3.6 26.7 - - + +
305F TYR* 3.2 21.6 + - - +
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Residues in contact with VAL 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F PHE 3.9 20.0 - - - +
189F THR* 4.1 11.2 - - - +
190F GLU* 4.0 30.1 - - + +
193F TYR* 4.3 9.4 - - + -
267F CYS* 4.1 16.4 - - - -
268F SER 3.1 16.1 + - - +
269F TRP* 3.5 10.8 - - + +
271F VAL* 1.3 85.9 - - + +
273F GLN* 1.3 70.0 + - - +
275F LEU* 3.4 4.8 + - - +
276F GLN* 3.2 33.0 + - + +
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Residues in contact with GLN 273 (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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190F GLU* 3.7 23.2 + - - -
269F TRP* 3.0 64.8 + - + +
270F LEU 3.8 3.6 - - - +
272F VAL* 1.3 76.0 - - - +
274F CYS* 1.3 65.2 + - - +
276F GLN* 3.3 26.5 + - - +
277F ARG* 3.1 50.1 + - - +
310F LEU* 4.0 16.2 - - + -
313F VAL* 4.0 2.9 - - + +
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Residues in contact with CYS 274 (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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270F LEU 2.9 14.5 + - - +
271F VAL* 3.4 9.4 - - - +
273F GLN* 1.3 76.5 - - - +
275F LEU* 1.3 58.5 + - - +
277F ARG* 2.9 2.9 + - - +
278F ALA* 2.9 35.6 + - - +
286F LEU* 4.0 13.9 - - - -
304F LEU* 3.8 26.5 - - - -
305F TYR* 3.5 29.8 - - + -
308F LEU* 3.9 18.0 - - - +
310F LEU* 4.0 6.9 - - + +
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Residues in contact with LEU 275 (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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185F LEU* 3.4 33.7 - - + +
188F PHE* 3.5 31.9 - - + +
271F VAL* 2.9 20.7 + - + +
272F VAL 3.6 4.9 - - - +
274F CYS* 1.3 75.9 - - - +
276F GLN* 1.3 62.8 + - + +
277F ARG 3.3 0.7 + - - -
278F ALA* 3.9 11.3 + - + +
283F TYR* 3.8 35.0 - - + -
286F LEU* 3.7 22.9 - - + -
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Residues in contact with GLN 276 (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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190F GLU* 3.5 35.1 + - - +
272F VAL* 3.2 18.0 + - + +
273F GLN* 3.6 30.5 + - - +
274F CYS 3.2 1.0 - - - -
275F LEU* 1.3 78.1 - - + +
277F ARG* 1.3 66.4 + - + +
278F ALA 5.4 0.2 - - - -
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Residues in contact with ARG 277 (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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273F GLN* 3.1 45.2 + - - +
274F CYS 2.9 3.8 + - - +
276F GLN* 1.3 89.4 + - + +
278F ALA* 1.3 65.9 + - - +
279F THR* 3.7 3.3 + - - +
282F GLN* 4.2 0.3 - - - +
308F LEU* 4.0 31.0 + - + +
310F LEU* 4.1 15.0 - - - -
313F VAL* 3.3 36.9 - - - +
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Residues in contact with ALA 278 (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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274F CYS* 2.9 23.1 + - - +
275F LEU* 3.9 10.5 + - + +
276F GLN 3.8 0.7 - - - -
277F ARG* 1.3 79.6 - - - +
279F THR* 1.3 66.3 + - - +
280F PRO* 4.6 0.3 - - - +
282F GLN* 3.3 26.7 - - + -
283F TYR* 3.9 14.3 - - + +
286F LEU* 6.0 0.4 - - + -
308F LEU* 4.4 7.6 - - + -
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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