Contacts of the helix formed by residues 263 - 275 (chain F) in PDB entry 5UQ9
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 THR 263 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185F MET* 4.4 20.2 - - + -
188F ASN* 3.2 38.3 + - + +
262F GLY* 1.3 71.4 - - - -
264F GLY* 1.3 62.5 + - - +
265F LYS* 3.4 2.5 - - - +
266F TRP* 3.4 32.6 + - + +
267F THR* 3.4 17.5 + - - -
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Residues in contact with GLY 264 (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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188F ASN* 4.4 4.7 - - - +
189F GLY* 4.3 1.5 - - - -
192F TYR* 3.5 36.2 + - - -
260F GLN* 4.0 0.4 + - - -
262F GLY 2.8 10.3 + - - -
263F THR* 1.3 79.7 - - - +
265F LYS* 1.3 60.4 + - - +
267F THR* 3.7 6.4 + - - -
281F ILE* 3.8 11.3 - - - +
285F VAL* 3.3 18.6 - - - +
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Residues in contact with LYS 265 (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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272E LEU* 3.2 30.8 + - + +
273E GLU* 3.9 24.4 + - - +
275E GLY 6.0 0.4 - - - +
260F GLN* 3.2 40.7 + - - +
262F GLY* 5.0 7.4 - - - -
263F THR 4.9 1.6 - - - +
264F GLY* 1.3 73.5 - - - +
266F TRP* 1.3 90.9 + - + +
267F THR 3.1 2.7 - - - -
268F ALA* 3.1 5.9 + - - +
269F ILE* 2.8 36.2 + - + +
285F VAL* 3.9 15.3 - - + -
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Residues in contact with TRP 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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273E GLU* 3.8 29.8 - - + -
185F MET* 3.7 15.0 - - + +
262F GLY* 5.1 1.6 - - - -
263F THR* 3.4 41.5 - - + +
264F GLY 3.4 1.2 - - - -
265F LYS* 1.3 96.4 - - + +
267F THR* 1.3 57.3 + - - +
269F ILE* 3.6 38.2 - - + +
270F SER* 2.8 29.6 + - - -
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Residues in contact with THR 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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185F MET* 2.4 32.5 + - - -
186F VAL* 3.8 25.8 - - + +
189F GLY* 3.3 22.7 + - - -
190F ILE* 4.9 0.7 - - + +
263F THR 3.4 5.6 + - - -
264F GLY 3.7 1.9 + - - -
265F LYS 3.1 0.6 - - - -
266F TRP* 1.3 79.1 - - - +
268F ALA* 1.3 55.9 + - - +
270F SER* 3.4 3.5 + - - -
271F ALA* 3.0 24.9 + - - +
278F VAL* 5.4 4.2 - - + +
281F ILE* 3.7 17.7 - - + -
341F LEU* 3.9 14.9 - - + +
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Residues in contact with ALA 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LEU* 3.7 23.6 - - + -
286E PHE* 4.3 3.7 - - + -
265F LYS 3.1 5.7 + - - +
267F THR* 1.3 76.2 - - - +
269F ILE* 1.3 64.6 + - - +
271F ALA* 3.3 10.1 + - - +
272F LEU* 3.1 25.6 + - - +
278F VAL 5.2 2.0 - - - +
281F ILE* 3.6 16.4 - - + +
282F GLY* 3.8 28.0 - - - +
285F VAL* 4.7 1.6 - - + -
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Residues in contact with ILE 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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269E ILE* 3.7 39.7 - - + +
272E LEU* 3.7 25.8 - - + -
273E GLU* 4.2 12.3 - - + +
265F LYS* 2.8 24.6 + - + +
266F TRP* 3.6 41.5 - - + +
268F ALA* 1.3 73.7 - - - +
270F SER* 1.3 65.8 + - - +
272F LEU* 3.2 8.1 + - - +
273F GLU* 3.0 38.6 + - - +
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Residues in contact with SER 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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106F TYR* 4.4 1.9 + - - -
107F ARG* 5.8 0.4 - - - -
182F PHE* 3.6 17.2 - - - -
185F MET* 3.7 17.6 - - - +
266F TRP 2.8 18.5 + - - -
267F THR 3.6 5.4 - - - -
268F ALA 3.3 0.2 - - - -
269F ILE* 1.3 76.5 - - - +
271F ALA* 1.3 61.3 + - - +
273F GLU* 3.2 13.1 + - - -
274F TYR* 3.0 50.8 + - - -
341F LEU* 3.9 4.8 - - - +
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Residues in contact with ALA 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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286E PHE* 4.1 7.2 - - + -
267F THR 3.0 13.1 + - - +
268F ALA* 3.4 11.7 - - - +
269F ILE 3.2 0.4 - - - -
270F SER* 1.3 77.9 - - - +
272F LEU* 1.3 55.9 + - - +
274F TYR 3.6 0.2 + - - -
275F GLY* 3.0 7.8 + - - -
276F VAL 2.8 46.2 + - - +
278F VAL* 3.6 27.4 - - + -
341F LEU* 4.0 10.9 - - + +
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Residues in contact with LEU 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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265E LYS* 3.1 23.6 - - + +
268E ALA* 3.6 28.0 - - + -
269E ILE* 3.6 28.5 - - + +
272E LEU* 3.7 18.8 - - + -
282E GLY* 4.8 1.3 - - - +
285E VAL* 3.8 28.6 - - + +
286E PHE* 3.5 30.5 - - + -
268F ALA 3.1 16.3 + - - +
269F ILE* 3.2 5.4 + - - +
271F ALA* 1.3 72.6 - - - +
273F GLU* 1.3 66.3 + - - +
275F GLY* 3.2 11.9 + - - +
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Residues in contact with GLU 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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265E LYS* 4.0 21.3 + - - +
269E ILE* 3.9 14.2 - - + +
106F TYR* 4.3 1.9 + - - -
107F ARG* 2.5 34.8 + - - -
269F ILE* 3.0 32.8 + - - +
270F SER* 3.2 14.7 + - - +
272F LEU* 1.3 78.6 - - - +
274F TYR* 1.3 69.1 + - + +
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Residues in contact with TYR 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F TYR* 3.0 23.4 + - - -
107F ARG* 4.1 5.5 + - - -
182F PHE* 4.2 7.7 - + - -
270F SER* 3.0 43.6 + - - +
273F GLU* 1.3 87.8 - - + +
275F GLY* 1.3 63.9 + - - +
276F VAL* 3.9 19.0 - - + +
341F LEU* 4.0 8.1 - - + -
344F GLN* 4.0 23.2 + - + +
345F ALA* 4.6 10.5 - - + -
348F GLU* 3.6 42.6 - - + -
349F PHE* 3.3 28.1 - + - -
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Residues in contact with GLY 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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289E CYS* 3.2 40.2 - - - +
293E LEU* 5.9 2.4 - - - +
271F ALA 3.0 6.0 + - - -
272F LEU* 3.2 11.6 + - - -
273F GLU 3.3 0.8 + - - -
274F TYR* 1.3 80.2 - - - +
276F VAL* 1.3 58.3 + - - +
277F PRO* 3.9 2.4 - - - +
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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