Contacts of the helix formed by residues 259 - 274 (chain D) in PDB entry 5DQZ
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 LYS 259 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D PHE 3.4 7.8 + - - +
256D ARG* 3.9 15.8 + - - +
257D SER 4.7 4.5 - - - +
258D SER* 1.3 78.7 - - - +
260D THR* 1.3 64.3 + - - +
261D LEU 3.4 2.5 - - - -
262D ALA* 3.0 28.4 + - + -
263D LYS* 3.2 20.2 + - + +
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Residues in contact with THR 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LEU* 5.1 0.9 - - + -
190D VAL* 4.3 5.8 - - + -
223D ILE* 4.4 14.1 - - + -
254D ILE* 4.4 2.3 - - - +
255D PHE* 3.4 44.8 + - + -
258D SER* 3.2 20.2 + - - -
259D LYS* 1.3 73.3 - - - +
261D LEU* 1.3 59.4 + - - +
263D LYS* 3.2 6.5 + - - +
264D LEU* 2.9 45.9 + - + +
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D MET* 3.6 29.4 - - + -
19D PHE* 3.5 34.3 - - + -
53D MET* 4.1 8.5 - - + -
81D ALA 5.0 0.4 - - - +
82D GLY* 5.4 0.4 - - - -
190D VAL* 4.0 27.0 - - + +
193D ALA* 3.7 21.8 - - + -
194D ALA* 3.7 23.1 - - - +
255D PHE* 5.1 1.6 + - + +
259D LYS 3.4 0.4 - - - -
260D THR* 1.3 78.2 - - - +
262D ALA* 1.3 63.7 + - - +
264D LEU* 3.4 20.0 + - - +
265D ILE* 3.7 10.5 - - + +
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Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL 6.2 0.2 - - - -
17D MET* 5.6 5.8 - - + -
259D LYS* 3.0 30.0 + - + +
261D LEU* 1.3 80.4 - - - +
263D LYS* 1.3 58.2 + - + +
265D ILE* 4.0 7.6 + - - +
266D PRO* 3.2 20.8 - - - +
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Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D SER* 3.6 23.3 + - - +
259D LYS* 3.2 19.1 + - + +
260D THR* 4.1 4.3 - - - +
262D ALA* 1.3 76.9 - - + +
264D LEU* 1.3 65.2 + - - +
265D ILE 3.3 0.9 - - - -
266D PRO* 3.4 15.6 - - - +
267D LEU* 3.7 11.6 + - - +
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D VAL* 3.9 10.8 - - + +
191D THR* 3.7 35.7 - - + +
194D ALA* 3.6 15.0 - - + -
219D ILE* 4.0 23.8 - - + -
223D ILE* 3.6 27.4 - - + -
260D THR* 2.9 32.5 + - + +
261D LEU* 3.6 4.7 - - - +
262D ALA 3.4 0.2 - - - -
263D LYS* 1.3 79.4 - - - +
265D ILE* 1.3 58.5 + - - +
267D LEU* 3.3 14.8 + - + +
268D ILE* 3.1 31.4 + - + +
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Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.9 39.3 - - + +
17D MET* 4.3 7.6 - - + -
194D ALA* 4.0 17.3 - - + +
197D ALA* 3.9 22.9 - - + -
198D ALA* 4.3 17.7 - - + +
261D LEU* 3.7 16.6 - - + +
262D ALA* 4.3 5.4 - - - +
264D LEU* 1.3 73.7 - - - +
266D PRO* 1.4 71.7 - - + +
268D ILE* 3.2 10.1 + - - +
269D GLU* 3.0 31.4 + - + +
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Residues in contact with PRO 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ALA 3.2 21.1 - - - +
263D LYS* 3.4 13.2 - - - +
265D ILE* 1.4 94.2 - - + +
267D LEU* 1.3 55.1 - - - +
269D GLU* 3.4 7.7 + - + +
270D ASP* 2.9 29.8 + - - +
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 4.0 28.7 - - + -
219D ILE* 3.9 28.7 - - + +
222D ILE* 4.1 28.3 - - + -
223D ILE* 4.2 16.4 - - + -
263D LYS 3.7 10.0 + - - +
264D LEU* 3.3 13.9 + - + +
265D ILE 3.2 0.8 - - - -
266D PRO* 1.3 79.7 - - - +
268D ILE* 1.3 55.5 + - - +
270D ASP* 3.2 9.1 + - - +
271D VAL* 2.9 37.0 + - + +
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Residues in contact with ILE 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D THR* 4.9 0.4 - - + +
194D ALA* 4.0 15.7 - - + +
195D ILE* 3.8 35.2 - - + +
198D ALA* 4.7 3.6 - - + -
200D TYR* 4.0 30.3 - - + -
215D PHE* 4.2 18.6 - - + -
219D ILE* 3.9 28.5 - - + -
264D LEU* 3.1 19.5 + - + +
265D ILE* 3.2 8.7 + - - +
267D LEU* 1.3 75.2 - - - +
269D GLU* 1.3 63.4 + - - +
271D VAL* 3.2 8.8 + - - +
272D LEU* 3.0 23.0 + - + +
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Residues in contact with GLU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LYS* 3.2 18.8 + - - -
101D TYR* 4.8 6.1 + - - -
198D ALA* 4.0 4.9 - - - +
200D TYR* 3.0 40.3 + - - -
265D ILE* 3.0 28.6 + - + +
266D PRO* 3.8 7.4 - - + +
268D ILE* 1.3 78.4 - - + +
270D ASP* 1.3 55.5 + - - +
272D LEU* 3.6 3.6 + - - +
273D ALA* 2.9 30.0 + - - +
279D PRO* 5.2 9.4 - - - +
280D PRO* 5.8 0.7 - - - +
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Residues in contact with ASP 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LYS* 3.6 27.8 + - - -
122D LEU* 4.4 12.4 - - - +
266D PRO 2.9 18.2 + - - +
267D LEU* 3.4 9.9 - - - +
268D ILE 3.1 0.2 - - - -
269D GLU* 1.3 74.0 - - - +
271D VAL* 1.3 66.8 + - - +
273D ALA* 3.0 8.6 + - - +
274D ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL* 3.8 22.8 - - + +
118D LYS* 4.4 8.9 - - - +
119D MET* 3.7 27.8 - - + -
122D LEU* 3.7 25.1 - - + -
215D PHE* 4.9 2.7 - - + -
219D ILE* 4.2 14.8 - - + -
222D ILE* 4.1 16.4 - - + -
267D LEU* 2.9 19.0 + - + +
268D ILE* 3.4 9.9 - - - +
270D ASP* 1.3 78.8 - - - +
272D LEU* 1.3 69.0 + - + +
274D ALA* 3.3 15.9 - - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 3.2 26.2 + - + -
102D GLN* 4.8 5.8 - - + -
105D LEU* 3.5 19.6 - - + +
115D VAL* 4.4 2.5 - - + +
200D TYR* 3.4 49.8 - - + +
206D PHE* 3.6 38.1 - - + -
215D PHE* 4.1 11.7 - - + -
268D ILE* 3.0 22.1 + - + +
269D GLU* 4.0 4.0 - - - +
271D VAL* 1.3 77.4 - - + +
273D ALA* 1.3 66.3 + - - +
275D GLY* 3.1 12.1 + - - -
277D ILE 5.4 0.3 - - - +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 3.4 12.5 + - - +
269D GLU 2.9 20.7 + - - +
270D ASP* 3.0 13.0 + - - +
272D LEU* 1.3 75.5 - - - +
274D ALA* 1.3 58.2 + - - +
275D GLY 3.0 5.8 + - - -
276D GLU* 3.0 15.2 + - - +
277D ILE 4.5 4.5 + - - +
279D PRO* 5.1 10.3 - - + -
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Residues in contact with ALA 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 3.5 21.4 - - - +
115D VAL* 4.7 0.7 - - - -
118D LYS* 3.4 37.9 - - + -
270D ASP* 3.0 7.0 + - - +
271D VAL 3.3 15.5 - - - +
272D LEU 3.1 0.8 - - - -
273D ALA* 1.3 76.5 - - - +
275D GLY* 1.3 59.2 + - - +
276D GLU* 3.0 13.6 + - - +
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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