Contacts of the helix formed by residues 263 - 273 (chain S) in PDB entry 5GJQ
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 LEU 263 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N SER* 5.7 3.1 - - - +
37N GLU* 4.6 14.6 - - - +
258S TYR* 3.2 35.6 + - + +
259S LEU* 4.1 2.4 - - - +
261S TYR* 4.9 6.5 - - + -
262S SER* 1.3 81.7 - - - +
264S TYR* 1.3 59.9 + - - +
265S ASP* 3.8 15.0 - - - +
266S GLN* 4.3 11.4 - - + -
267S ALA* 3.9 3.5 + - - +
172T LYS* 6.1 4.9 - - + -
214T ARG* 6.2 0.9 - - + -
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Residues in contact with TYR 264 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259S LEU* 4.7 2.5 - - + -
262S SER 3.3 8.5 + - - +
263S LEU* 1.3 72.5 - - - +
265S ASP* 1.3 54.7 + - - +
266S GLN 3.4 0.4 - - - -
267S ALA* 3.1 7.9 + - - +
268S GLU* 2.7 31.2 + - - +
295S ILE* 3.7 34.4 - - + +
298S ILE* 4.5 21.3 - - + -
299S GLN* 3.6 32.3 - - + -
210T THR* 5.5 7.2 - - - +
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Residues in contact with ASP 265 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N GLU* 5.4 8.1 - - - +
40N GLU* 6.0 6.1 - - + +
263S LEU* 3.8 15.1 - - - +
264S TYR* 1.3 74.5 + - - +
266S GLN* 1.3 79.1 + - - +
268S GLU* 2.4 46.0 + - + +
269S LYS* 2.8 10.0 + - + +
299S GLN* 4.5 3.1 - - - +
172T LYS* 5.8 2.1 + - - -
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Residues in contact with GLN 266 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N ALA* 3.4 38.5 - - + +
37N GLU* 4.1 21.1 - - + +
228S ARG* 5.5 4.5 - - - +
258S TYR* 4.1 16.4 - - + -
263S LEU* 4.3 14.1 - - + -
264S TYR 3.4 0.2 - - - -
265S ASP* 1.3 91.1 + - - +
267S ALA* 1.3 58.6 + - - +
269S LYS* 3.8 1.3 + - - +
270S LEU* 2.9 29.3 + - + +
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Residues in contact with ALA 267 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255S LEU* 4.0 15.3 - - + +
258S TYR* 3.8 29.2 - - + -
259S LEU* 4.3 10.8 - - + -
263S LEU 3.9 2.9 + - - +
264S TYR* 3.1 9.9 + - - +
265S ASP 3.1 0.4 - - - -
266S GLN* 1.3 77.8 - - - +
268S GLU* 1.3 59.4 + - - +
270S LEU* 3.1 10.0 - - - +
271S VAL* 2.9 32.8 + - - +
295S ILE* 4.7 8.1 - - + -
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Residues in contact with GLU 268 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264S TYR 2.7 12.0 + - - +
265S ASP* 2.4 47.3 + - + +
267S ALA* 1.3 68.1 - - - +
269S LYS* 1.3 72.5 + - + +
271S VAL* 2.8 24.7 + - - +
272S SER* 2.9 15.1 + - - +
295S ILE* 4.1 15.0 - - + +
299S GLN* 3.0 32.3 - - - +
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Residues in contact with LYS 269 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N TRP* 5.6 0.4 - - - -
36N ALA 4.3 16.2 - - - +
39N SER* 4.4 11.0 - - - -
40N GLU* 3.9 28.5 - - + -
71N LEU* 4.3 3.7 - - + +
265S ASP* 2.8 14.8 + - + +
266S GLN* 4.3 0.4 - - - +
268S GLU* 1.3 87.7 - - + +
270S LEU* 1.3 62.5 + - - +
272S SER* 3.1 23.2 + - - +
273S LYS* 3.2 17.5 + - - +
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Residues in contact with LEU 270 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N TRP* 4.7 3.1 - - + -
36N ALA* 5.2 4.0 - - + +
254S LEU* 5.8 5.8 - - + -
255S LEU* 4.1 18.8 - - + -
266S GLN* 2.9 22.7 + - + +
267S ALA* 3.1 14.1 - - - +
269S LYS* 1.3 75.2 - - - +
271S VAL* 1.3 61.7 + - + +
273S LYS* 3.1 38.7 - - - +
274S SER* 3.0 19.1 + - - +
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Residues in contact with VAL 271 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255S LEU* 4.9 12.1 - - + -
267S ALA 2.9 17.7 + - - +
268S GLU* 2.8 16.0 + - - +
270S LEU* 1.3 73.1 - - + +
272S SER* 1.3 55.4 + - - +
274S SER* 2.7 38.2 + - - +
288S TYR* 4.4 24.3 + - + +
292S THR* 5.6 5.8 - - - +
295S ILE* 4.4 16.2 - - + -
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Residues in contact with SER 272 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N LEU* 5.8 1.6 - - - -
268S GLU* 2.9 15.9 + - - +
269S LYS* 3.1 19.4 + - - +
271S VAL* 1.3 78.1 - - - +
273S LYS* 1.3 58.3 + - - +
274S SER 3.6 3.1 + - - +
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Residues in contact with LYS 273 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N TRP* 2.0 52.6 - - + -
70N HIS* 2.0 28.2 + - - +
71N LEU* 2.8 53.9 - - + +
72N GLY* 4.1 4.3 + - - -
235S LEU* 5.9 5.3 - - - +
269S LYS 3.2 5.8 + - - +
270S LEU* 3.1 30.7 + - - +
272S SER* 1.3 76.0 - - - +
274S SER* 1.3 66.7 + - - +
275S VAL 3.8 1.0 + - - -
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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