Contacts of the helix formed by residues 253 - 267 (chain D) in PDB entry 6Q2N
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 ASN 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D ARG* 4.5 11.4 + - - +
249D SER 4.0 9.4 - - - +
250D CYS* 2.9 21.6 + - - +
251D LYS 3.2 0.2 - - - -
252D THR* 1.3 80.3 - - - +
254D TYR* 1.3 73.8 + - - +
255D ILE* 3.8 8.4 + - - +
256D CYS* 3.6 22.2 - - + +
257D ARG* 3.3 19.3 + - - -
295D THR* 4.1 5.1 - - - -
296D VAL* 3.7 26.8 - - + +
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Residues in contact with TYR 254 (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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252D THR 4.5 0.2 + - - -
253D ASN* 1.3 74.6 + - - +
255D ILE* 1.3 82.6 + - + +
257D ARG* 3.1 40.9 + - - +
258D SER* 3.0 25.0 + - - -
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Residues in contact with ILE 255 (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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197D ARG* 3.7 33.4 - - - +
253D ASN* 3.8 6.9 + - - +
254D TYR* 1.3 89.5 - - + +
256D CYS* 1.3 63.3 + - - +
258D SER* 3.2 10.1 - - - -
259D ARG* 3.0 60.7 + - - +
295D THR* 3.8 4.7 - - + -
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Residues in contact with CYS 256 (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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250D CYS* 2.0 49.1 - - - -
253D ASN* 3.6 22.9 - - + +
254D TYR 3.2 0.2 - - - -
255D ILE* 1.3 77.9 - - - +
257D ARG* 1.3 55.1 + - - +
259D ARG* 3.1 5.8 + - - +
260D LEU* 2.9 28.6 + - - +
292D LEU* 4.7 1.0 - - - +
295D THR* 3.3 34.9 - - - +
296D VAL* 3.6 2.7 - - - -
297D MET* 3.6 19.5 - - - -
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Residues in contact with ARG 257 (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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250D CYS* 3.9 7.6 - - - +
251D LYS* 3.8 30.0 + - + +
252D THR 5.3 0.2 - - - -
253D ASN 3.3 30.1 + - - +
254D TYR* 3.1 44.8 + - - +
256D CYS* 1.3 74.9 - - - +
258D SER* 1.3 59.6 + - - +
260D LEU* 4.3 9.2 - - + -
261D ALA* 2.9 33.4 + - + +
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Residues in contact with SER 258 (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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254D TYR* 3.0 17.8 + - - -
255D ILE* 3.2 14.8 - - - -
257D ARG* 1.3 77.5 - - - +
259D ARG* 1.3 69.7 + - - +
261D ALA* 3.9 3.4 - - - +
262D ASP* 3.0 37.0 + - - +
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Residues in contact with ARG 259 (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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197D ARG* 4.4 17.3 + - - +
200D PHE* 5.4 9.1 + - - +
201D ASP* 5.4 8.9 + - - +
255D ILE* 3.0 41.8 + - - +
256D CYS* 3.1 4.5 + - - +
258D SER* 1.3 83.6 + - - +
260D LEU* 1.3 58.2 + - - +
262D ASP* 3.4 13.2 + - - +
263D PHE* 3.0 23.2 + - - +
287D LEU 5.4 1.1 - - - -
288D ALA 4.4 2.3 - - - +
290D SER 4.7 1.2 + - - -
291D GLY* 2.3 55.4 + - - +
292D LEU* 3.5 34.6 - - + +
293D ILE 3.8 10.5 + - - -
295D THR* 4.4 8.0 - - + +
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Residues in contact with LEU 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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247D GLN* 4.7 16.6 - - + +
250D CYS* 3.8 22.7 - - + -
251D LYS* 5.6 5.6 - - + -
256D CYS 2.9 15.8 + - - +
257D ARG* 4.0 7.6 - - + +
258D SER 3.2 0.2 - - - -
259D ARG* 1.3 76.0 - - - +
261D ALA* 1.3 59.4 + - - +
263D PHE* 3.2 3.8 + - + +
264D PHE* 2.9 37.9 + - + +
292D LEU* 3.7 17.7 - - + +
297D MET* 4.2 20.2 - - + -
328D PHE* 4.4 22.7 - - + -
332D PHE* 4.4 14.8 - - + -
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Residues in contact with ALA 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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257D ARG* 2.9 20.9 + - + +
258D SER* 4.0 3.8 - - - +
260D LEU* 1.3 73.6 - - - +
262D ASP* 1.3 58.5 + - - +
264D PHE* 3.5 11.4 + - - +
265D THR* 2.5 37.8 + - - +
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Residues in contact with ASP 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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258D SER* 3.0 32.5 + - - +
259D ARG* 3.4 16.6 - - - +
261D ALA* 1.3 77.1 - - - +
263D PHE* 1.3 56.7 + - - +
265D THR* 3.0 6.1 + - - -
266D ASN* 2.6 49.6 + - - +
287D LEU 4.9 5.4 - - - +
288D ALA* 4.1 8.5 - - - -
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Residues in contact with PHE 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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259D ARG 3.0 16.9 + - - +
260D LEU* 3.2 6.7 + - + +
262D ASP* 1.3 73.1 - - - +
264D PHE* 1.3 65.2 + - - +
265D THR 3.3 0.3 + - - -
266D ASN 3.4 7.8 + - - -
267D CYS* 3.7 27.1 + - + -
288D ALA* 3.5 20.0 - - + -
289D TYR* 3.5 35.2 - + + -
292D LEU* 3.6 20.2 - - + -
331D PHE* 3.7 30.1 - + - -
332D PHE* 3.7 34.3 - + + -
335D ASN* 5.1 1.8 - - - -
338D LEU* 3.6 24.2 - - + -
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Residues in contact with PHE 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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247D GLN* 5.3 5.6 - - - -
260D LEU* 2.9 19.8 + - + +
261D ALA* 3.5 15.5 - - - +
263D PHE* 1.3 77.3 - - - +
265D THR* 1.3 60.0 + - - +
268D GLN* 3.4 26.9 + - - +
328D PHE* 3.6 35.9 - + - -
331D PHE* 4.0 25.8 - + - -
76F TYR* 4.7 3.1 - - - -
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Residues in contact with THR 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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261D ALA* 2.5 21.2 + - - +
262D ASP* 3.0 12.1 + - - -
264D PHE* 1.3 78.8 - - - +
266D ASN* 1.3 70.2 + - - +
268D GLN* 4.3 1.6 - - - +
76F TYR* 3.2 42.1 + - + -
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Residues in contact with ASN 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 ASP* 2.6 39.8 + - - +
263D PHE 3.4 1.8 + - - -
265D THR* 1.3 88.3 - - - +
267D CYS* 1.3 60.5 + - - +
268D GLN* 3.1 9.7 + - - +
281D ASN* 4.8 10.0 - - - +
284D ASP* 3.0 51.9 + - - +
285D CYS* 3.8 6.7 - - - +
287D LEU 5.0 0.6 - - - -
288D ALA* 3.4 12.5 - - + +
337D CYS* 4.9 3.3 - - - -
76F TYR* 4.8 2.6 + - - -
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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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263D PHE* 3.7 28.2 + - + -
266D ASN* 1.3 77.1 - - - +
268D GLN* 1.3 61.3 + - - +
269D PRO* 3.3 0.5 - - - +
285D CYS* 2.0 65.5 - - - -
288D ALA* 4.3 0.2 - - - -
331D PHE* 4.9 2.1 - - - -
335D ASN* 2.3 46.2 + - - +
337D CYS* 3.4 9.2 - - - +
338D LEU* 4.0 11.0 - - + +
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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