Contacts of the helix formed by residues 312 - 327 (chain D) in PDB entry 6NFJ
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 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309D ARG* 3.6 28.1 + - + +
311D GLU* 1.3 77.9 - - - +
313D THR* 1.3 65.8 + - - +
314D MET* 4.5 1.3 - - + +
315D ASP* 3.6 23.1 - - + +
316D ILE* 3.5 23.0 + - - +
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Residues in contact with THR 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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311D GLU 4.7 4.7 - - - +
312D ASN* 1.3 73.8 - - - +
314D MET* 1.3 70.0 + - - +
316D ILE* 3.2 24.5 - - - +
317D PHE* 3.4 8.7 + - - +
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Residues in contact with MET 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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312D ASN* 3.5 1.6 - - + +
313D THR* 1.3 82.8 + - - +
315D ASP* 1.3 61.3 + - - +
316D ILE 3.5 0.2 - - - -
317D PHE* 3.9 12.5 - - + +
318D LYS* 3.1 24.6 + - - +
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Residues in contact with ASP 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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307D PRO* 3.9 13.0 - - + -
308D GLN* 3.6 6.1 - - - +
309D ARG* 3.2 23.3 + - - +
312D ASN* 3.6 23.6 + - + +
313D THR 3.3 1.0 - - - -
314D MET* 1.3 82.9 - - - +
316D ILE* 1.3 59.3 + - - +
318D LYS* 3.5 3.8 + - - +
319D CYS* 3.2 28.1 + - - -
390D GLN* 3.2 31.9 + - - +
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Residues in contact with ILE 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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58D ARG* 4.6 22.3 - - + +
61D TRP* 3.9 31.9 - - + +
62D SER 6.2 4.3 - - - -
307D PRO* 3.8 25.8 - - + -
309D ARG 5.2 0.4 - - - +
310D SER 5.3 3.6 - - - +
311D GLU* 5.3 2.0 - - - -
312D ASN 3.5 14.8 + - - +
313D THR* 3.2 19.1 - - - +
315D ASP* 1.3 74.6 - - - +
317D PHE* 1.3 69.7 + - + +
318D LYS 3.2 0.2 - - - -
319D CYS* 3.2 9.8 + - - +
320D GLN* 3.1 19.8 + - - +
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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
----------------------------------------------------------
58D ARG* 6.4 0.2 - - - -
313D THR 3.4 12.9 + - - +
314D MET* 3.9 10.3 - - + +
315D ASP 3.4 0.4 - - - -
316D ILE* 1.3 85.6 - - + +
318D LYS* 1.3 64.1 + - - +
320D GLN* 3.3 24.0 + - + +
321D GLN* 3.3 19.0 + - + +
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Residues in contact with LYS 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 MET 3.1 18.5 + - - +
315D ASP* 3.6 8.7 - - - +
316D ILE 3.2 0.4 - - - -
317D PHE* 1.3 79.1 - - + +
319D CYS* 1.3 62.7 + - - +
321D GLN* 3.7 5.2 + - - +
322D SER* 3.4 15.1 + - - -
388D MET* 3.6 28.1 - - + +
390D GLN* 4.2 19.3 - - - +
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Residues in contact with CYS 319 (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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61D TRP* 3.8 18.6 - - + -
305D ILE* 3.6 27.8 - - + +
306D GLU* 3.7 2.9 - - - -
307D PRO* 3.5 35.0 - - - -
315D ASP 3.2 20.8 + - - -
316D ILE* 3.2 10.9 + - - +
317D PHE 3.2 0.6 - - - -
318D LYS* 1.3 75.9 - - - +
320D GLN* 1.3 63.8 + - - +
322D SER* 3.1 12.7 + - - -
323D MET* 3.2 18.7 + - - +
390D GLN* 4.2 6.3 - - - -
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Residues in contact with GLN 320 (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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55D GLY* 3.8 28.6 - - - +
57D GLY 4.8 0.4 - - - +
58D ARG* 3.5 26.9 + - + -
61D TRP* 3.5 10.5 - - + -
316D ILE 3.1 11.8 + - - +
317D PHE* 3.3 22.2 + - + +
319D CYS* 1.3 77.9 - - - +
321D GLN* 1.3 61.7 + - - +
323D MET* 3.5 2.5 + - - +
324D VAL* 3.1 36.7 + - + +
402D TRP* 3.4 35.8 + - - +
406D GLU* 6.0 0.2 - - - +
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Residues in contact with GLN 321 (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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317D PHE* 3.3 18.1 + - + +
318D LYS* 4.0 9.4 - - - +
319D CYS 3.3 0.4 - - - -
320D GLN* 1.3 79.8 - - - +
322D SER* 1.3 57.6 + - - +
324D VAL* 4.1 7.1 - - - +
325D SER* 2.9 31.4 + - - -
388D MET* 4.4 16.7 - - + +
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Residues in contact with SER 322 (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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303D HIS* 2.9 25.5 + - - -
305D ILE* 3.9 16.4 - - - +
318D LYS 3.4 11.5 + - - -
319D CYS* 3.1 11.0 + - - -
321D GLN* 1.3 76.4 - - - +
323D MET* 1.3 63.6 + - - +
325D SER* 2.7 20.5 + - - -
326D VAL* 3.4 14.6 - - - +
386D ALA 3.2 21.9 + - - -
388D MET* 4.2 7.6 - - - +
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Residues in contact with MET 323 (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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61D TRP* 4.5 8.3 - - + -
302D SER* 4.1 16.6 - - - -
303D HIS* 3.2 44.9 - - - +
304D TRP* 3.8 35.0 - - + -
305D ILE* 4.8 5.2 - - + -
319D CYS 3.2 14.1 + - - +
320D GLN 4.1 1.8 - - - +
322D SER* 1.3 76.3 - - - +
324D VAL* 1.3 57.1 + - - +
326D VAL* 5.1 0.9 - - - -
327D LEU* 2.6 37.4 + - + +
328D GLY 3.1 3.5 + - - -
399D ALA* 5.9 1.8 - - + -
402D TRP* 3.6 40.8 - - + +
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Residues in contact with VAL 324 (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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54D SER* 5.1 8.1 - - - +
320D GLN* 3.1 38.4 + - + +
321D GLN* 4.1 7.2 - - - +
323D MET* 1.3 76.9 - - - +
325D SER* 1.3 59.7 + - - +
328D GLY* 3.7 7.9 - - - +
329D TRP* 2.9 29.8 + - - -
332D ASN* 5.2 1.8 - - - +
341D PRO* 3.7 34.3 - - + -
343D GLY* 5.4 4.3 - - - -
344D MET* 4.0 15.6 - - + +
402D TRP* 4.4 8.1 - - + -
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Residues in contact with SER 325 (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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243D TYR* 4.1 2.6 - - - -
247D TRP* 6.0 1.2 - - - -
321D GLN 2.9 17.1 + - - -
322D SER* 2.7 24.4 + - - -
324D VAL* 1.3 78.1 - - - +
326D VAL* 1.3 63.7 + - - +
329D TRP* 3.8 22.7 - - - +
344D MET* 4.5 14.7 - - - +
386D ALA* 5.2 6.3 + - - +
388D MET* 4.6 9.9 - - - +
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Residues in contact with VAL 326 (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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243D TYR* 3.7 59.0 - - + +
301D GLY 4.4 8.1 - - - +
302D SER* 4.5 5.4 - - - -
303D HIS* 3.5 28.5 - - + +
322D SER 3.4 17.0 + - - +
323D MET* 3.3 2.5 + - - +
324D VAL 3.1 0.2 - - - -
325D SER* 1.3 87.5 - - - +
327D LEU* 1.3 61.2 + - - +
329D TRP* 4.0 9.3 - - - +
330D PHE* 4.1 7.6 - - - -
378D ASN* 4.2 11.2 - - - +
385D MET* 4.7 4.0 - - + -
386D ALA* 5.2 3.4 - - + +
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Residues in contact with LEU 327 (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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300D LEU* 3.8 31.2 - - + +
301D GLY 3.7 16.6 - - - +
302D SER* 3.6 23.1 - - - -
323D MET* 2.6 20.7 + - + +
326D VAL* 1.3 73.6 - - - +
328D GLY* 1.3 58.9 + - - +
329D TRP 3.2 2.3 + - - -
330D PHE* 3.4 3.3 + - + +
331D ALA* 3.0 32.0 + - + +
370D PHE* 4.5 8.7 - - + -
372D PHE* 4.4 1.8 - - + -
402D TRP* 3.4 30.7 - - + -
403D ILE* 4.1 22.9 - - + -
407D TYR* 4.1 5.2 - - + +
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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