Contacts of the helix formed by residues 264 - 274 (chain D) in PDB entry 3K75
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 GLN 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D SER* 4.3 13.7 + - - -
260D ILE* 3.9 10.5 - - + +
261D PRO* 2.9 33.4 + - + +
263D ASP* 1.3 92.7 + - - +
265D TYR* 1.3 63.9 + - - +
266D TYR 3.5 2.2 - - - -
267D CYS* 3.3 7.6 + - - +
268D GLY* 3.1 16.6 + - - -
295D GLU 4.4 1.2 - - - +
296D TYR* 3.4 52.8 - - + +
297D THR* 4.1 10.8 - - + +
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Residues in contact with TYR 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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174D ILE* 3.2 28.0 + - + +
176D THR* 2.7 42.7 + - - -
194D LEU* 3.2 30.6 + - + +
195D LEU 4.0 2.9 - - - -
196D THR* 3.4 31.9 - - + +
260D ILE* 4.0 11.6 - - + +
261D PRO 3.0 9.2 + - - +
262D LYS* 3.2 17.7 + - + +
263D ASP 3.6 0.2 - - - -
264D GLN* 1.3 77.1 - - - +
266D TYR* 1.3 91.0 + + + +
267D CYS 3.1 0.2 - - - -
268D GLY* 2.9 5.0 + - - -
269D VAL* 2.9 36.0 + - + +
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Residues in contact with TYR 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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174D ILE* 3.9 22.3 - - + +
176D THR* 5.6 1.6 - - - -
262D LYS* 4.6 14.0 + - + -
264D GLN 3.5 0.2 - - - -
265D TYR* 1.3 100.6 - + + +
267D CYS* 1.3 60.9 + - - +
268D GLY 3.3 0.2 - - - -
269D VAL* 3.9 13.5 - - + -
270D LEU* 3.2 17.5 + - - +
313D VAL* 3.9 13.3 + - + +
314D ASP* 3.3 40.6 + - - -
315D SER* 3.6 28.5 - - - -
316D GLU* 3.9 11.3 - - + +
319D ILE* 3.4 14.9 - - - +
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Residues in contact with CYS 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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264D GLN* 3.3 5.5 + - - +
265D TYR 3.1 0.8 - - - -
266D TYR* 1.3 76.0 - - - +
268D GLY* 1.3 60.5 + - - +
270D LEU* 3.5 4.6 + - - +
271D TYR* 3.1 25.5 + - - +
293D ILE* 5.4 3.8 - - - +
294D ASN 4.2 5.2 - - - +
295D GLU 3.2 15.1 - - - +
296D TYR 3.3 19.7 - - - +
297D THR* 3.6 31.6 - - - +
298D ILE* 4.1 4.9 - - - -
313D VAL* 4.6 13.7 - - - +
319D ILE* 4.1 23.1 - - - -
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Residues in contact with GLY 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 3.6 9.9 - - - -
260D ILE* 4.4 8.3 - - - -
264D GLN 3.1 9.6 + - - -
265D TYR 2.9 7.4 + - - -
267D CYS* 1.3 75.3 - - - +
269D VAL* 1.3 58.5 + - - +
271D TYR* 3.3 1.8 + - - +
272D PHE* 2.8 45.1 + - - -
295D GLU* 3.3 10.7 + - - -
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Residues in contact with VAL 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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176D THR* 4.2 9.0 - - + +
178D CYS* 4.1 11.7 - - - -
182D ARG* 3.5 17.3 - - - +
194D LEU* 3.6 16.8 - - + +
265D TYR* 2.9 44.7 + - + +
266D TYR* 4.2 12.6 - - + +
268D GLY* 1.3 73.0 - - - +
270D LEU* 1.3 64.3 + - - +
273D THR* 2.7 40.2 + - - +
316D GLU* 3.4 21.3 - - + +
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Residues in contact with LEU 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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266D TYR 3.2 17.6 + - - +
267D CYS* 3.5 7.2 - - - +
269D VAL* 1.3 78.9 - - - +
271D TYR* 1.3 54.0 + - - +
273D THR* 3.8 0.9 - - - -
274D GLY* 2.8 35.5 + - - -
278D PHE* 4.2 8.7 - - + -
279D ASN* 3.8 5.2 - - - +
282D MET* 3.9 38.1 - - + -
293D ILE* 4.4 16.8 - - + -
316D GLU* 3.7 12.8 + - + +
319D ILE* 3.8 27.1 - - + -
320D PHE* 4.7 5.8 - - + -
333D ARG* 3.6 23.5 + - - +
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Residues in contact with TYR 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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267D CYS 3.1 14.1 + - - +
268D GLY 3.7 3.4 - - - +
269D VAL 3.3 0.2 - - - -
270D LEU* 1.3 80.9 - - - +
272D PHE* 1.3 97.1 + + - +
273D THR 3.8 0.2 + - - -
274D GLY 3.8 1.0 + - - -
279D ASN* 3.0 28.0 + - - +
283D ARG* 3.8 31.4 - - - -
294D ASN 5.1 1.6 - - - +
295D GLU* 3.6 41.2 + - + -
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Residues in contact with PHE 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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178D CYS* 3.9 6.5 - - + -
179D GLY* 3.1 20.1 + - - -
192D ASP* 4.2 18.0 - - - +
194D LEU* 3.8 22.7 - - + -
258D ARG* 3.6 47.1 - - - -
260D ILE* 4.9 4.5 - - + -
268D GLY* 2.8 31.4 + - - +
269D VAL 4.4 0.2 - - - +
271D TYR* 1.3 93.2 - + - +
273D THR* 1.3 62.8 + - - +
295D GLU* 3.2 39.9 - - + -
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Residues in contact with THR 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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178D CYS* 3.7 3.5 - - - -
179D GLY* 3.8 8.5 - - - +
182D ARG* 2.7 62.3 + - + +
183D ARG* 2.8 29.3 + - + -
269D VAL* 2.7 28.5 + - - +
270D LEU 3.8 2.0 - - - -
272D PHE* 1.3 74.3 - - - +
274D GLY* 1.3 75.1 - - - +
330D PRO* 4.2 6.3 - - + -
333D ARG* 4.3 7.2 - - - +
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Residues in contact with GLY 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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183D ARG* 2.7 26.4 + - - -
270D LEU 2.8 12.0 + - - -
271D TYR 3.8 1.2 + - - -
272D PHE 3.5 1.8 - - - -
273D THR* 1.3 93.2 - - - +
275D SER* 1.3 55.6 + - - -
278D PHE* 4.5 5.4 - - - -
279D ASN* 3.1 27.6 - - - -
333D ARG* 4.7 6.1 - - - -
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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