Contacts of the helix formed by residues 259 - 274 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C PHE 3.1 7.2 + - - -
256C ARG* 3.4 12.8 + - - +
257C SER 3.2 6.8 - - - +
258C SER* 1.3 80.8 - - - +
260C THR* 1.3 64.7 + - - +
261C LEU 3.4 2.7 - - - -
262C ALA* 3.1 30.5 + - + +
263C LYS* 3.1 25.9 + - - +
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Residues in contact with THR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 5.2 0.2 - - + -
190C VAL* 5.1 4.9 - - + -
223C ILE* 4.1 20.2 - - + -
227C THR* 4.4 4.7 + - - +
255C PHE* 3.0 43.2 + - + -
258C SER* 3.1 20.8 + - - -
259C LYS* 1.3 73.9 - - - +
261C LEU* 1.3 60.1 + - + +
263C LYS* 3.0 6.7 + - - +
264C LEU* 2.9 50.4 + - + +
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.1 33.0 - - + +
12C LYS* 4.2 15.4 + - - +
14C ARG 3.2 27.6 - - - +
15C VAL 4.0 1.3 - - - +
16C SER* 3.6 27.4 - - - +
50C ALA* 4.2 19.3 - - + -
190C VAL* 4.3 23.8 - - + -
255C PHE* 4.7 5.1 + - + +
259C LYS 3.4 0.4 - - - -
260C THR* 1.3 81.6 - - + +
262C ALA* 1.3 61.3 + - - +
263C LYS 3.6 0.3 + - - -
264C LEU* 3.9 15.4 + - + +
265C ILE* 4.8 5.2 + - - +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 4.0 23.3 + - + +
259C LYS* 3.1 35.7 + - + +
261C LEU* 1.3 81.7 - - - +
263C LYS* 1.3 60.7 + - + +
266C PRO* 3.4 21.0 - - - +
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C SER* 3.2 29.7 + - - +
259C LYS* 3.2 21.7 - - + +
260C THR* 3.0 6.0 + - - +
262C ALA* 1.3 80.8 - - + +
264C LEU* 1.3 58.5 + - - +
265C ILE 3.5 1.6 - - - -
266C PRO* 3.4 7.1 - - + +
267C LEU* 2.9 33.6 + - + +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 5.8 0.4 - - + -
187C LEU* 5.9 0.2 - - + -
190C VAL* 3.8 22.4 - - + +
191C THR* 4.1 15.3 - - + +
194C ALA* 3.7 27.8 - - + -
219C ILE* 4.1 23.8 - - + -
223C ILE* 4.3 18.6 - - + -
260C THR* 2.9 34.6 + - + +
261C LEU* 3.9 12.3 + - + +
262C ALA 3.6 0.8 - - - -
263C LYS* 1.3 78.3 - - - +
265C ILE* 1.3 62.3 + - + +
267C LEU* 3.4 9.2 + - + +
268C ILE* 3.0 31.4 + - + +
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.7 11.4 - - + -
98C LYS* 6.0 0.2 - - - +
194C ALA* 4.0 20.6 - - + +
197C ALA* 4.3 6.1 - - + -
198C ALA* 3.9 30.3 - - + +
261C LEU 4.8 4.7 + - - +
264C LEU* 1.3 74.3 - - + +
266C PRO* 1.4 74.7 - - + +
268C ILE* 3.2 7.2 + - - +
269C GLU* 2.9 33.9 + - + +
299C ASP* 3.5 35.0 - - + +
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Residues in contact with PRO 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ALA 3.4 24.7 - - - +
263C LYS* 3.4 9.4 - - + +
265C ILE* 1.4 95.2 - - + +
267C LEU* 1.3 55.5 + - - +
269C GLU* 3.7 6.9 - - + +
270C ASP* 2.9 32.4 + - - +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LEU* 4.3 25.6 - - + -
219C ILE* 3.8 29.6 - - + +
222C ILE* 4.3 20.4 - - + -
223C ILE* 4.3 22.7 - - + -
263C LYS* 2.9 23.0 + - + +
264C LEU* 3.5 11.9 - - + +
266C PRO* 1.3 76.7 - - - +
268C ILE* 1.3 56.5 + - - +
270C ASP* 3.3 6.2 + - - +
271C VAL* 2.9 38.7 + - + +
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Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ALA* 4.2 9.9 - - + +
195C ILE* 3.8 37.0 - - + +
198C ALA* 4.8 3.8 - - + -
200C TYR* 3.8 32.3 - - + -
215C PHE* 4.1 17.0 - - + -
219C ILE* 3.9 29.4 - - + -
264C LEU* 3.0 22.8 + - + +
265C ILE* 3.6 8.5 - - - +
267C LEU* 1.3 75.9 - - - +
269C GLU* 1.3 63.1 + - - +
271C VAL* 3.3 7.1 + - - +
272C LEU* 3.0 26.0 + - + +
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LYS* 2.7 31.5 + - - -
101C TYR* 4.6 6.2 + - - -
198C ALA* 4.4 3.6 - - - +
200C TYR* 2.9 29.0 + - + -
265C ILE* 2.9 30.5 + - + +
266C PRO* 3.7 7.2 - - + +
268C ILE* 1.3 76.2 - - - +
270C ASP* 1.3 57.5 + - - +
272C LEU* 3.6 3.5 + - - +
273C ALA* 2.9 29.2 + - - +
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS* 3.6 28.1 + - - +
122C LEU* 4.1 13.7 - - + +
266C PRO 2.9 18.4 + - - +
267C LEU* 3.6 6.5 - - - +
269C GLU* 1.3 75.6 - - - +
271C VAL* 1.3 67.0 + - - +
273C ALA* 3.0 17.3 + - - +
274C ALA* 3.0 14.0 + - - +
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C VAL* 3.7 19.3 - - + +
118C LYS* 4.2 8.4 - - - +
119C MET* 3.7 37.5 - - + -
122C LEU* 3.7 22.2 - - + -
215C PHE* 5.0 0.2 - - + -
219C ILE* 4.4 9.0 - - + -
222C ILE* 3.8 21.3 - - + -
267C LEU* 2.9 22.9 + - + +
268C ILE* 3.5 7.2 - - - +
270C ASP* 1.3 77.5 - - - +
272C LEU* 1.3 67.5 + - + +
274C ALA* 3.4 15.4 + - - +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 3.1 27.6 + - + -
102C GLN* 4.8 5.6 - - + -
105C LEU* 3.5 19.4 - - + +
115C VAL* 4.3 3.4 - - + +
200C TYR* 3.4 50.7 - - + +
206C PHE* 3.7 36.8 - - + -
215C PHE* 4.0 14.4 - - + -
268C ILE* 3.0 21.7 + - + +
269C GLU* 4.0 3.4 - - - +
271C VAL* 1.3 77.7 - - + +
273C ALA* 1.3 66.2 + - - +
275C GLY* 3.0 13.2 + - - -
277C ILE 5.5 0.2 - - - +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 3.2 10.9 + - - +
269C GLU 2.9 20.6 + - - +
270C ASP* 3.0 14.1 + - - +
272C LEU* 1.3 71.1 - - - +
274C ALA* 1.3 57.4 + - - +
275C GLY 2.9 11.0 + - - -
276C GLU* 2.9 17.5 + - - +
277C ILE 4.5 2.1 + - - -
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LYS* 3.6 22.6 - - - +
118C LYS* 3.3 43.5 - - + -
270C ASP* 3.0 6.8 + - - +
271C VAL 3.5 8.1 - - - +
272C LEU 3.1 0.8 - - - -
273C ALA* 1.3 75.3 - - - +
275C GLY* 1.3 59.5 + - - +
276C GLU* 3.0 12.9 + - - +
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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