Contacts of the helix formed by residues 262 - 275 (chain A) 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 GLY 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A TYR* 4.3 3.2 + - - -
260A GLN* 3.5 6.3 - - - +
261A LYS* 1.3 80.9 - - - +
263A THR* 1.3 62.0 + - - +
264A GLY 3.0 6.7 + - - -
265A LYS* 3.2 27.6 - - - +
266A TRP* 3.0 38.4 + - - -
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Residues in contact with THR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 4.1 18.6 - - + +
185A MET* 3.8 14.7 - - + +
188A ASN* 3.0 43.0 + - - +
189A GLY 4.4 0.7 + - - -
192A TYR* 4.5 5.9 + - - -
261A LYS* 3.8 3.0 - - - +
262A GLY* 1.3 75.3 + - - +
264A GLY* 1.3 59.1 + - - +
266A TRP* 3.9 28.7 - - + -
267A THR* 2.8 28.1 + - - -
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Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLY* 4.8 3.4 - - - -
192A TYR* 3.5 41.4 + - - -
262A GLY 3.0 2.0 + - - -
263A THR* 1.3 77.9 + - - +
265A LYS* 1.3 64.4 + - - +
267A THR* 3.3 14.1 + - - -
268A ALA 3.4 8.0 + - - -
281A ILE* 4.4 1.6 - - - +
285A VAL* 3.4 15.9 - - - +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLN* 4.5 13.8 + - + +
262A GLY* 3.2 23.5 - - - +
264A GLY* 1.3 71.4 - - - +
266A TRP* 1.3 76.3 + - + +
268A ALA* 3.1 4.6 + - - +
269A ILE* 2.7 45.4 + - + +
285A VAL* 4.0 23.3 - - + +
272B LEU* 3.6 32.3 + - + +
273B GLU* 4.2 17.5 + - - +
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Residues in contact with TRP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN 3.9 20.0 - - - -
104A SER 4.8 0.9 - - - -
105A GLU* 3.4 55.5 + - + -
185A MET* 3.6 24.7 - - + +
261A LYS 4.8 5.8 - - - -
262A GLY* 3.0 25.6 + - - +
263A THR* 3.9 25.8 - - + +
264A GLY 3.3 0.2 - - - -
265A LYS* 1.3 97.3 - - + +
267A THR* 1.3 56.7 + - - +
269A ILE* 3.9 12.9 - - + +
270A SER* 2.9 29.3 + - - -
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A MET* 2.7 35.2 + - - +
186A VAL* 4.2 16.8 - - + +
189A GLY* 3.8 10.1 - - - -
263A THR 2.8 9.2 + - - -
264A GLY 3.3 8.4 + - - -
265A LYS 3.2 0.6 - - - -
266A TRP* 1.3 78.9 - - - +
268A ALA* 1.3 57.3 + - - +
270A SER* 3.3 3.5 + - - -
271A ALA* 3.0 26.2 + - - +
278A VAL* 5.2 3.6 - - + -
281A ILE* 4.1 17.9 - - + -
341A LEU* 3.7 22.1 - - + +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLY 3.4 8.0 + - - +
265A LYS* 3.1 5.2 + - - +
267A THR* 1.3 76.2 - - - +
269A ILE* 1.3 66.5 + - - +
271A ALA* 3.4 7.2 + - - +
272A LEU* 3.1 27.7 + - - +
278A VAL* 5.6 1.6 - - - -
281A ILE* 4.5 4.7 - - + +
282A GLY* 4.0 24.7 - - - +
285A VAL* 4.7 1.8 - - + -
272B LEU* 3.6 28.5 - - + -
286B PHE* 4.5 4.9 - - + -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 6.2 0.2 - - - +
265A LYS* 2.7 35.4 + - + +
266A TRP* 3.9 13.2 - - + +
268A ALA* 1.3 68.9 - - - +
270A SER* 1.3 65.3 + - - +
272A LEU* 3.3 6.5 + - - +
273A GLU* 3.0 42.1 + - + +
269B ILE* 4.0 19.9 - - + +
272B LEU* 3.7 26.2 - - + -
273B GLU* 4.0 29.4 - - + +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 4.1 8.6 + - - -
107A ARG* 5.8 0.2 - - - -
182A PHE* 3.5 25.9 - - - -
185A MET* 4.1 14.4 - - - -
266A TRP 2.9 19.0 + - - -
267A THR 3.6 5.2 - - - -
268A ALA 3.3 0.2 - - - -
269A ILE* 1.3 76.6 - - - +
271A ALA* 1.3 62.9 + - - +
273A GLU* 3.4 11.3 + - - +
274A TYR* 3.2 35.3 + - - +
341A LEU* 3.8 6.2 - - - +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A THR 3.0 14.0 + - - +
268A ALA* 3.6 8.7 - - - +
269A ILE 3.2 0.2 - - - -
270A SER* 1.3 76.8 - - - +
272A LEU* 1.3 57.3 + - - +
274A TYR 3.7 0.2 - - - -
275A GLY* 2.9 9.7 + - - -
276A VAL* 2.9 45.0 + - - +
278A VAL* 3.6 27.1 - - + -
341A LEU* 3.9 11.4 - - + +
286B PHE* 4.0 6.5 - - + -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA 3.1 10.9 + - - +
269A ILE 3.3 4.0 + - - +
271A ALA* 1.3 76.0 - - - +
273A GLU* 1.3 63.4 + - - +
275A GLY* 3.4 10.3 + - - -
260B GLN 5.3 1.0 - - - +
265B LYS* 3.1 23.6 - - + +
268B ALA* 3.7 21.8 - - + -
269B ILE* 3.7 26.5 - - + -
272B LEU* 3.6 29.8 - - + -
282B GLY* 4.7 2.7 - - - +
285B VAL* 3.7 31.3 - - + +
286B PHE* 3.5 31.4 - - + -
289B CYS* 5.4 1.3 - - - -
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 4.4 1.0 + - - -
107A ARG* 2.4 36.9 + - - -
269A ILE* 3.0 36.7 + - - +
270A SER* 3.8 11.0 - - - +
271A ALA 3.3 0.2 - - - -
272A LEU* 1.3 79.5 - - - +
274A TYR* 1.3 75.1 + - + +
275A GLY 3.6 0.3 + - - -
260B GLN 5.5 1.6 - - - +
261B LYS* 5.0 9.4 + - - +
265B LYS* 4.2 17.3 + - - +
266B TRP* 4.9 14.4 - - + -
269B ILE* 4.0 15.7 - - + +
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 3.5 20.4 + + - -
107A ARG* 4.0 8.9 + - - -
182A PHE* 5.0 1.8 - + - -
270A SER* 3.2 27.8 + - - +
273A GLU* 1.3 92.3 - - + +
275A GLY* 1.3 62.2 + - - +
276A VAL* 3.5 7.5 + - + +
341A LEU* 5.1 5.6 - - + -
344A GLN* 3.8 33.1 + - + +
345A ALA* 5.2 4.9 - - - -
348A GLU* 3.9 33.8 - - + +
349A PHE* 3.1 38.8 - + - -
260B GLN* 4.1 7.2 + - - -
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA 2.9 7.0 + - - -
272A LEU 3.4 5.7 + - - -
273A GLU 3.3 4.9 + - - -
274A TYR* 1.3 79.4 - - - +
276A VAL* 1.3 60.2 + - - +
277A PRO* 4.0 2.6 - - - +
344A GLN* 4.9 1.4 + - - -
260B GLN* 3.7 25.5 + - - -
289B CYS* 3.4 37.4 - - - +
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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