Contacts of the helix formed by residues 265 - 275 (chain F) in PDB entry 4P0S
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 GLY 265 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263F MET* 2.9 1.0 - - - +
264F GLU* 1.3 83.9 - - - +
266F GLY* 1.3 66.0 + - - +
267F GLY 3.1 2.7 - - - -
268F GLN* 2.8 22.1 + - - +
269F LEU* 3.0 12.2 + - - +
429F TRP* 3.7 38.0 - - - +
432F LEU* 5.3 1.0 - - - +
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Residues in contact with GLY 266 (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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270B LEU* 5.9 0.4 - - - -
260F LEU* 4.6 3.1 - - - -
261F LEU* 3.4 38.5 - - - +
263F MET* 2.9 12.7 + - - +
265F GLY* 1.3 75.2 - - - +
267F GLY* 1.3 58.5 + - - +
269F LEU* 3.0 12.5 + - - +
270F LEU* 2.9 28.4 + - - +
429F TRP* 5.2 0.6 - - - -
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Residues in contact with GLY 267 (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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267B GLY 3.7 9.6 - - - +
268B GLN* 5.1 0.7 - - - -
270B LEU* 5.2 2.6 - - - +
271B GLY* 3.2 35.4 - - - -
274B GLN* 3.1 11.9 + - - +
265F GLY 3.1 1.2 - - - -
266F GLY* 1.3 71.7 - - - +
268F GLN* 1.3 64.2 + - - +
269F LEU 3.0 1.6 - - - -
270F LEU* 4.5 1.8 - - - -
271F GLY* 3.0 22.3 + - - -
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Residues in contact with GLN 268 (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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271B GLY* 4.6 0.6 - - - -
264F GLU 5.7 0.4 - - - +
265F GLY* 2.8 16.5 + - - +
267F GLY* 1.3 73.3 - - - +
269F LEU* 1.3 57.4 + - - +
271F GLY* 3.6 1.5 + - - -
272F ALA* 3.1 27.4 + - - +
429F TRP* 4.5 14.2 - - + +
430F LYS* 3.6 41.1 + - + +
433F ALA* 4.2 12.2 - - + +
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Residues in contact with LEU 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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256F LEU* 4.7 9.6 - - + -
260F LEU* 4.5 27.1 - - + -
261F LEU* 5.6 0.9 - - + -
265F GLY 3.0 9.0 + - - +
266F GLY* 3.1 14.4 - - - +
268F GLN* 1.3 74.8 - - - +
270F LEU* 1.3 68.7 + - - +
271F GLY 3.0 2.0 + - - -
272F ALA* 3.1 12.0 + - - +
273F LEU* 3.1 20.1 + - + +
315F LEU* 5.5 0.7 - - + -
432F LEU* 3.7 30.5 - - + -
433F ALA* 4.4 12.3 - - - +
436F THR* 3.3 38.1 - - + +
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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
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261B LEU* 4.9 6.1 - - + +
266B GLY 4.1 1.8 - - - -
267B GLY* 3.0 37.2 - - - +
270B LEU* 6.0 2.0 - - + -
256F LEU* 4.3 17.7 - - + -
261F LEU* 4.3 20.8 - - + +
266F GLY 2.9 13.4 + - - +
267F GLY* 4.3 1.1 - - - +
269F LEU* 1.3 79.4 - - - +
271F GLY* 1.3 63.1 + - - +
273F LEU* 3.2 7.7 + - + +
274F GLN* 3.0 37.3 + - - +
280F CYS* 3.8 32.1 - - + -
282F ILE* 4.4 15.9 - - + -
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Residues in contact with GLY 271 (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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267B GLY 4.6 1.0 - - - -
268B GLN* 4.9 12.1 - - - -
267F GLY 3.0 18.0 + - - -
268F GLN* 3.8 1.6 - - - -
269F LEU 3.0 0.2 - - - -
270F LEU* 1.3 77.7 - - - +
272F ALA* 1.3 62.3 + - - +
274F GLN* 3.1 22.7 + - - +
275F THR* 3.3 13.1 + - - -
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Residues in contact with ALA 272 (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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268F GLN* 3.1 17.7 + - + +
269F LEU 3.1 3.3 + - - +
271F GLY* 1.3 73.4 - - - +
273F LEU* 1.3 62.2 + - + +
275F THR* 3.2 24.3 - - - -
276F MET* 4.0 3.6 + - - +
430F LYS* 6.1 2.2 - - - +
433F ALA* 4.5 15.5 - - + +
434F ASP* 5.5 2.5 - - - +
437F CYS* 3.7 30.8 - - - -
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Residues in contact with LEU 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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254F VAL* 3.7 39.3 - - + -
256F LEU* 4.8 7.4 - - + -
269F LEU* 3.1 18.0 + - + +
270F LEU* 3.4 11.9 - - + +
272F ALA* 1.3 78.6 - - - +
274F GLN* 1.3 61.0 + - - +
276F MET* 3.2 30.1 + - + +
278F CYS* 3.1 23.8 - - - -
280F CYS* 4.2 11.4 - - - -
433F ALA 5.1 0.4 - - - +
436F THR* 3.6 40.8 - - + +
437F CYS* 3.9 9.2 - - - +
440F THR* 3.9 5.2 - - - +
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Residues in contact with GLN 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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261B LEU 5.3 0.4 + - - -
263B MET 3.9 6.3 + - - -
264B GLU* 3.2 34.4 + - + +
265B GLY* 4.1 1.4 - - - -
267B GLY* 3.3 24.4 - - - +
268B GLN* 3.8 21.5 + - - +
270F LEU* 3.0 26.2 + - - +
271F GLY* 3.1 9.7 + - - +
273F LEU* 1.3 74.1 - - - +
275F THR* 1.3 57.7 + - - +
276F MET 2.8 15.7 - - - +
278F CYS 4.7 7.1 - - - +
280F CYS* 4.5 15.5 - - - +
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Residues in contact with THR 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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271F GLY 3.3 14.8 + - - -
272F ALA* 3.2 18.1 + - - -
274F GLN* 1.3 76.5 - - - +
276F MET* 1.3 59.2 + - + +
277F GLU* 4.1 1.7 + - - +
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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