Contacts of the helix formed by residues 267 - 281 (chain A) in PDB entry 2QK9
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 PHE 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A TYR* 3.2 46.9 - + - -
163A TYR* 5.7 1.1 - + - -
261A VAL* 5.5 1.3 - - + -
265A SER* 3.0 16.8 + - - +
266A GLY* 1.3 78.0 - - - +
268A ILE* 1.3 87.8 + - + +
269A GLY* 3.2 22.7 - - - -
270A ASN* 2.8 16.5 + - + +
271A GLU* 3.1 9.9 + - - +
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Residues in contact with ILE 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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163A TYR* 3.9 23.6 - - + +
166A PRO* 6.1 2.2 - - + -
266A GLY 3.3 4.1 + - - -
267A PHE* 1.3 95.0 - - + +
269A GLY* 1.3 66.9 + - - +
271A GLU* 4.6 13.2 - - + +
272A GLU* 3.0 43.1 + - + +
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Residues in contact with GLY 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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143A TYR* 3.5 15.7 - - - +
163A TYR* 3.7 26.2 - - - -
267A PHE* 2.9 18.3 + - - -
268A ILE* 1.3 82.1 - - - +
270A ASN* 1.3 62.3 + - - +
273A ALA* 3.2 24.6 + - - +
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Residues in contact with ASN 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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143A TYR* 3.8 7.6 - - - -
144A THR 5.3 4.9 + - - -
145A ASP* 5.3 2.0 + - - +
210A ASN* 3.1 30.7 + - - +
261A VAL* 4.1 15.7 - - + +
262A PRO 3.3 7.4 - - - +
263A GLY 3.0 22.6 - - - +
265A SER* 3.1 33.6 - - - +
267A PHE* 2.8 13.3 + - + +
269A GLY* 1.3 73.7 - - - +
271A GLU* 1.3 62.6 + - - +
273A ALA* 3.4 3.7 + - - +
274A ASP* 3.0 27.4 + - - +
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Residues in contact with GLU 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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265A SER 3.8 15.4 - - - +
266A GLY* 3.6 24.9 - - - +
267A PHE 3.1 7.4 + - - +
268A ILE* 4.0 17.8 - - + +
270A ASN* 1.3 76.5 - - - +
272A GLU* 1.3 53.4 + - - +
274A ASP* 3.3 7.2 + - - +
275A ARG* 2.7 35.8 + - - +
21C A 3.9 17.5 + - - -
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Residues in contact with GLU 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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163A TYR* 3.4 33.8 - - + -
171A ASN* 5.1 2.6 + - - -
268A ILE* 3.0 34.7 + - + +
271A GLU* 1.3 74.6 - - - +
273A ALA* 1.3 58.5 + - - +
275A ARG* 2.6 45.0 + - - +
276A LEU* 2.7 54.5 + - - +
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Residues in contact with ALA 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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143A TYR* 3.8 24.2 - - + +
144A THR 4.0 6.5 - - - +
145A ASP* 3.7 17.4 - - + +
161A GLY* 3.6 10.0 - - - +
163A TYR* 4.2 8.4 - - + +
269A GLY 3.2 17.6 + - - +
270A ASN* 3.7 5.4 - - - +
272A GLU* 1.3 78.6 - - - +
274A ASP* 1.3 58.5 + - - +
276A LEU* 3.3 6.3 + - - +
277A ALA* 2.9 28.2 + - - +
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Residues in contact with ASP 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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145A ASP* 3.3 20.5 - - - +
210A ASN* 6.3 0.2 - - - +
263A GLY 5.7 0.9 - - - +
270A ASN* 3.0 20.9 + - - +
271A GLU* 3.5 7.1 - - - +
273A ALA* 1.3 75.3 - - - +
275A ARG* 1.3 68.9 + - - +
277A ALA* 3.1 3.8 + - - +
278A ARG* 2.5 64.0 + - - +
10B C 4.5 8.3 + - - -
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Residues in contact with ARG 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 GLU 2.7 21.6 + - - +
272A GLU* 2.6 55.0 + - - +
274A ASP* 1.3 78.5 + - - +
276A LEU* 1.3 83.8 + - - +
278A ARG* 3.4 7.8 + - + +
279A GLU* 3.1 40.4 + - + +
1001A FLC 4.9 5.7 + - - -
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Residues in contact with LEU 276 (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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161A GLY* 4.0 1.8 - - - -
162A VAL 3.7 25.4 - - - +
163A TYR* 4.5 2.9 - - + -
171A ASN* 4.1 20.9 - - + +
172A VAL* 3.4 23.8 - - - +
173A GLY* 3.1 12.3 - - - +
272A GLU* 2.7 35.9 + - - +
273A ALA 3.5 4.7 - - - +
275A ARG* 1.3 103.5 - - - +
277A ALA* 1.3 65.6 + - - +
279A GLU* 3.1 4.9 + - + +
280A GLY 2.9 18.2 + - - -
1001A FLC 4.6 11.2 - - - +
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Residues in contact with ALA 277 (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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145A ASP* 3.5 28.7 - - - +
147A CYS* 3.5 22.1 - - - +
159A GLY* 3.6 16.0 - - - +
160A ILE 3.7 12.6 - - - -
161A GLY* 3.9 0.6 - - - -
273A ALA 2.9 10.6 + - - +
274A ASP 3.1 8.0 + - - +
276A LEU* 1.3 75.1 - - - +
278A ARG* 1.3 64.0 + - - +
280A GLY* 3.1 3.5 + - - -
281A ALA 3.0 18.4 + - - -
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Residues in contact with ARG 278 (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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145A ASP* 5.0 0.2 + - - -
147A CYS* 3.8 18.7 - - - +
149A SER* 5.9 1.6 - - - -
274A ASP* 2.5 51.8 + - - +
275A ARG* 3.7 7.0 - - - +
277A ALA* 1.3 77.8 - - - +
279A GLU* 1.3 67.7 + - - +
281A ALA* 3.3 12.1 + - + +
282A LYS* 3.6 16.9 + - - +
10B C 5.4 2.2 + - - -
11B C 2.7 45.7 + - - -
20C G 6.0 1.6 - - - -
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Residues in contact with GLU 279 (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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275A ARG* 3.1 39.8 + - + +
276A LEU* 3.1 8.7 + - - +
278A ARG* 1.3 78.6 - - - +
280A GLY* 1.3 64.2 + - - +
282A LYS* 2.7 60.8 + - - +
283A GLN* 4.1 5.7 + - - +
1001A FLC 3.8 37.7 - - - +
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Residues in contact with GLY 280 (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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173A GLY 3.6 28.4 - - - -
174A ILE* 3.6 7.2 - - - -
175A ARG* 3.5 11.4 + - - +
276A LEU 2.9 11.1 + - - -
277A ALA 3.1 4.2 + - - -
279A GLU* 1.3 77.4 - - - +
281A ALA* 1.3 56.6 + - - +
282A LYS 3.0 0.2 - - - -
283A GLN* 2.8 35.1 + - - +
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Residues in contact with ALA 281 (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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147A CYS* 4.2 7.2 - - - -
149A SER* 5.3 2.9 - - - +
157A ARG* 2.9 47.1 + - + +
158A ALA 3.9 21.1 - - - -
159A GLY* 4.0 2.1 - - - +
175A ARG* 3.8 12.1 - - - +
277A ALA 3.0 11.0 + - - +
278A ARG* 3.7 10.1 - - + +
279A GLU 3.3 0.6 - - - -
280A GLY* 1.3 75.7 - - - +
282A LYS* 1.3 57.1 + - - +
283A GLN 3.1 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