Contacts of the helix formed by residues 305 - 318 (chain D) in PDB entry 6CET
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 305 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLN* 4.6 8.1 - - - +
221D PHE* 3.4 27.8 - - - -
222D SER* 3.1 31.6 + - - -
223D ARG* 3.3 34.5 - - - +
253D ASP* 3.4 13.5 + - - +
255D TYR* 4.9 1.6 + - - +
298D ASN* 5.6 1.4 + - - +
304D GLY* 1.3 73.1 - - - -
306D TYR* 1.3 65.3 + - - +
307D LEU 3.6 1.3 - - - -
308D GLU* 3.7 15.9 + - - +
309D ALA* 3.3 19.1 + - - +
838D ARG* 4.9 1.8 + - - +
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Residues in contact with TYR 306 (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 GLN* 6.0 4.5 - - + -
221D PHE* 4.9 8.1 - + - -
304D GLY* 3.5 2.9 - - - -
305D ASN* 1.3 78.1 + - - +
307D LEU* 1.3 79.3 + - + +
309D ALA* 2.8 24.2 + - - +
310D ILE* 3.1 33.4 + - + +
335D VAL* 3.5 31.3 - - + +
337D THR* 5.3 4.3 - - + -
343D PHE* 3.6 57.9 - + + -
365D ASP* 3.2 31.9 + - - +
380D PHE* 4.3 15.0 - + - -
403D ILE* 3.3 21.5 - - + +
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Residues in contact with LEU 307 (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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306D TYR* 1.3 93.9 - - + +
308D GLU* 1.3 56.5 + - - +
310D ILE* 3.4 15.3 + - + -
311D ASN* 2.9 27.4 + - + +
345D VAL* 4.2 25.6 - - + -
349D LEU* 3.7 32.3 - - + +
350D MET* 4.4 5.2 - - + +
353D THR* 3.7 38.1 - - + +
380D PHE* 4.9 12.8 - - + -
402D TRP* 5.2 11.4 - - + +
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Residues in contact with GLU 308 (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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223D ARG* 3.5 27.7 + - - -
238D ASN* 5.4 4.2 + - - -
251D TYR* 4.3 8.0 + - - -
253D ASP* 3.9 4.2 - - - +
304D GLY 5.2 0.4 - - - +
305D ASN* 3.8 10.3 - - - +
306D TYR 3.1 0.2 - - - -
307D LEU* 1.3 78.4 - - - +
309D ALA* 1.3 57.0 + - - +
311D ASN* 3.1 9.7 + - - +
312D LEU* 2.9 27.0 + - - +
345D VAL* 6.0 1.8 - - + -
349D LEU* 4.0 22.2 - - + +
818D LYS* 3.9 1.3 + - - +
838D ARG* 2.6 57.8 + - - +
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Residues in contact with ALA 309 (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 PHE* 3.2 35.9 - - + -
221D PHE* 4.5 17.5 - - + -
255D TYR* 4.4 11.4 + - + +
305D ASN 3.3 9.7 + - - +
306D TYR 2.8 10.3 + - - +
308D GLU* 1.3 75.5 - - - +
310D ILE* 1.3 66.0 + - + +
312D LEU* 3.3 11.8 - - + +
313D SER 3.0 17.7 + - - -
335D VAL* 6.1 0.4 - - + -
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Residues in contact with ILE 310 (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 PHE* 5.0 0.4 - - - -
306D TYR* 3.1 70.9 + - + +
307D LEU* 3.8 17.9 - - + +
309D ALA* 1.3 75.7 - - + +
311D ASN* 1.3 56.8 + - - +
313D SER* 2.4 28.1 + - - +
314D PHE* 2.9 40.0 + - + -
333D SER* 6.0 3.6 - - - -
335D VAL* 3.7 23.6 - - + -
353D THR* 5.6 2.7 - - + -
363D GLY* 5.6 9.6 - - - -
402D TRP* 6.1 2.9 - - - +
403D ILE* 6.1 2.0 - - + -
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Residues in contact with ASN 311 (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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307D LEU* 2.9 15.4 + - + +
308D GLU* 3.1 12.3 + - - +
310D ILE* 1.3 77.9 - - - +
312D LEU* 1.3 56.9 + - - +
314D PHE* 3.2 6.9 + - - +
315D ASN* 2.9 23.9 + - - +
349D LEU* 4.7 11.8 - - - +
352D LEU* 3.7 14.0 - - - +
353D THR* 3.6 26.3 - - + +
356D ARG* 3.0 27.7 - - - +
818D LYS* 3.5 25.6 + - - +
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Residues in contact with LEU 312 (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 PHE* 3.9 20.0 - - + -
219D VAL* 6.3 1.8 - - + -
255D TYR* 3.2 41.1 - - + +
308D GLU 2.9 11.0 + - - +
309D ALA* 3.3 14.8 - - + +
311D ASN* 1.3 74.1 - - - +
313D SER* 1.3 63.3 + - - +
315D ASN* 3.1 6.7 + - + +
316D VAL* 2.9 38.2 + - + +
818D LYS* 3.6 13.4 - - - +
836D TYR* 3.6 5.6 - - - +
838D ARG* 3.4 16.4 - - - +
1434D PRO* 4.9 15.7 - - + +
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Residues in contact with SER 313 (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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172D TYR* 4.7 8.7 - - - -
174D PHE* 4.2 16.2 - - - -
309D ALA 3.0 13.3 + - - -
310D ILE* 2.4 31.9 + - - +
312D LEU* 1.3 81.1 - - - +
314D PHE* 1.3 60.1 + - - +
316D VAL* 3.2 8.3 + - - +
317D PHE* 2.9 36.2 + - - -
333D SER* 3.8 26.3 + - - -
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Residues in contact with PHE 314 (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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310D ILE* 2.9 41.4 + - + -
311D ASN* 3.4 12.1 - - - +
313D SER* 1.3 86.6 + - - +
315D ASN* 1.3 55.8 + - - +
316D VAL 3.1 0.2 - - - -
317D PHE* 4.1 4.9 - + + +
318D ASP* 2.9 32.8 + - + +
333D SER* 6.4 0.7 - - - -
353D THR* 5.3 7.0 - - + -
356D ARG* 3.2 42.4 + - + +
357D MET* 3.6 31.2 - - + -
360D ASN* 3.6 11.7 - - + -
362D ILE* 3.6 36.6 - - + -
363D GLY* 4.9 7.4 - - - -
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Residues in contact with ASN 315 (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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311D ASN 2.9 16.1 + - - +
312D LEU* 3.1 12.0 + - + +
314D PHE* 1.3 72.3 - - - +
316D VAL* 1.3 57.6 + - - +
318D ASP* 2.8 28.0 + - - +
319D LYS* 4.6 17.6 - - - +
356D ARG* 3.2 10.4 + - - +
816D GLN* 5.8 3.4 - - - +
818D LYS* 3.3 37.6 - - + +
820D GLN* 5.4 5.4 - - - +
1434D PRO* 4.7 12.3 - - + +
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Residues in contact with VAL 316 (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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172D TYR* 3.5 36.1 - - + +
312D LEU* 2.9 21.0 + - + +
313D SER* 3.6 8.5 - - - +
314D PHE 3.1 0.4 - - - -
315D ASN* 1.3 76.4 - - - +
317D PHE* 1.3 64.0 + - - +
318D ASP 3.2 2.8 + - - -
319D LYS* 3.4 21.5 + - - +
320D HIS* 3.7 1.2 + - - -
1433D ASP* 5.3 6.5 - - - +
1434D PRO* 3.7 30.3 - - + -
1435D LEU* 4.7 15.7 - - + -
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Residues in contact with PHE 317 (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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170D MET* 4.2 12.6 - - + -
172D TYR* 3.5 45.3 - + - -
313D SER 2.9 26.4 + - - +
314D PHE* 3.3 7.4 + + + +
316D VAL* 1.3 75.1 - - - +
318D ASP* 1.3 53.8 + - - +
319D LYS 3.3 0.2 - - - -
320D HIS* 2.4 40.8 + - + -
331D GLN* 3.2 47.5 - - + +
332D MET 4.1 7.4 - - - -
333D SER* 3.2 26.2 - - - -
360D ASN* 5.4 3.4 + - - +
362D ILE* 3.6 28.7 - - + -
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Residues in contact with ASP 318 (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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314D PHE 2.9 16.0 + - - +
315D ASN* 2.8 41.8 + - - +
317D PHE* 1.3 73.6 - - - +
319D LYS* 1.3 78.9 + - - +
320D HIS* 3.2 6.7 + - - -
321D TYR* 3.5 4.9 - - - -
356D ARG* 3.0 16.1 + - - +
360D ASN* 5.9 2.7 - - - +
816D GLN* 4.2 14.6 - - + +
1291D ARG* 3.5 24.9 + - - -
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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