Contacts of the helix formed by residues 303 - 319 (chain D) in PDB entry 6M17
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 ASP 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301D ALA 3.5 5.0 + - - +
302D TRP* 1.3 77.8 - - - +
304D ALA* 1.3 62.0 + - - +
305D GLN* 3.3 26.6 - - + +
306D ARG* 2.7 35.9 + - - +
307D ILE* 4.1 15.9 - - - +
364D VAL* 4.7 5.2 - - - +
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Residues in contact with ALA 304 (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 ASP* 1.3 77.5 - - - +
305D GLN* 1.3 73.0 + - + +
306D ARG 3.4 0.6 + - - -
307D ILE* 3.9 13.2 + - - +
308D PHE* 4.0 15.8 - - - -
333D LEU* 4.8 2.3 - - + +
334D THR* 3.8 29.2 - - + -
362D THR* 4.5 15.7 - - + +
364D VAL* 5.4 2.2 - - - +
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Residues in contact with GLN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ASP* 3.2 18.8 + - - +
304D ALA* 1.3 87.4 - - + +
306D ARG* 1.3 62.9 + - - +
307D ILE 3.3 1.3 - - - -
308D PHE* 3.5 4.5 + - - +
309D LYS* 3.1 26.4 + - + +
328D TRP* 3.9 25.0 + - + -
333D LEU* 3.4 32.5 - - - +
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Residues in contact with ARG 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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302D TRP* 3.2 63.8 - - + +
303D ASP* 2.7 21.8 + - - +
304D ALA 3.4 0.6 - - - -
305D GLN* 1.3 74.3 - - - +
307D ILE* 1.3 59.1 + - - +
309D LYS* 4.4 8.0 - - - +
310D GLU* 2.7 68.3 + - + +
421D ILE 5.9 0.4 + - - -
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Residues in contact with ILE 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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297D MET* 4.2 26.2 - - + -
302D TRP* 5.3 5.6 - - + -
303D ASP 4.1 15.3 - - - +
304D ALA* 3.9 11.4 + - - +
305D GLN 3.3 0.6 - - - -
306D ARG* 1.3 78.8 - - + +
308D PHE* 1.3 63.2 + - + +
310D GLU* 4.3 3.3 - - - +
311D ALA* 3.4 19.4 + - - +
362D THR* 4.1 18.8 - - + +
363D LYS 4.2 13.5 - - - +
364D VAL* 4.3 9.9 - - + -
365D THR 4.9 2.7 - - - +
368D ASP 3.7 22.0 - - - +
369D PHE* 3.8 25.6 - - + -
372D ALA* 3.8 11.5 - - + +
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Residues in contact with PHE 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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304D ALA 4.0 9.2 - - - -
305D GLN 3.5 4.1 + - - +
306D ARG 3.3 0.4 - - - -
307D ILE* 1.3 83.2 - - + +
309D LYS* 1.3 54.3 + - - +
310D GLU 3.3 0.4 - - - -
311D ALA* 3.0 3.8 + - - +
312D GLU* 2.7 35.0 + - - +
327D PHE* 4.6 6.5 - + - -
328D TRP* 4.0 21.9 - + + -
333D LEU* 3.6 42.4 - - + -
358D ILE* 4.1 24.7 - - + -
360D MET* 3.6 31.2 - - + -
362D THR* 4.5 11.9 - - + -
372D ALA* 4.2 22.2 - - + -
375D GLU* 5.8 0.4 - - + -
376D MET* 3.6 22.4 - - + +
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Residues in contact with LYS 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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305D GLN* 3.1 21.7 + - + +
306D ARG* 4.0 11.4 - - - +
308D PHE* 1.3 73.9 - - - +
310D GLU* 1.3 63.4 + - + +
312D GLU* 2.7 29.7 + - + +
313D LYS* 3.2 24.9 + - - +
328D TRP* 4.1 22.3 - - + +
901D NAG 3.7 22.0 + - - -
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Residues in contact with GLU 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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302D TRP* 5.2 10.5 - - + -
306D ARG* 2.7 65.4 + - + +
307D ILE* 4.4 3.4 - - - +
309D LYS* 1.3 78.1 - - - +
311D ALA* 1.3 62.7 + - - +
313D LYS* 3.5 17.5 + - - +
314D PHE* 3.2 19.6 + - - +
369D PHE* 4.8 12.8 - - + -
373D HIS* 4.3 3.8 + - - -
417D HIS* 5.8 1.4 + - - -
421D ILE* 2.9 45.7 - - + +
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Residues in contact with ALA 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 ILE 3.4 15.8 + - - +
308D PHE* 3.0 12.4 + - - +
310D GLU* 1.3 77.9 - - - +
312D GLU* 1.3 64.1 + - - +
314D PHE* 3.3 9.2 + - - +
315D PHE* 3.2 23.6 + - + -
372D ALA* 4.6 9.4 - - + +
373D HIS* 3.7 29.4 - - + +
376D MET* 3.8 16.2 - - + -
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Residues in contact with GLU 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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308D PHE 2.7 18.3 + - - +
309D LYS* 2.7 41.2 + - - +
311D ALA* 1.3 73.3 - - - +
313D LYS* 1.3 57.2 + - - +
315D PHE* 3.4 3.9 + - + +
316D VAL* 3.1 27.3 + - - +
321D PRO 5.5 1.3 - - - +
322D ASN* 3.4 22.9 - - - +
323D MET* 2.6 53.9 + - + +
328D TRP* 3.6 8.1 + - + -
376D MET* 3.9 10.0 - - + -
380D GLN* 5.7 1.1 - - - +
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Residues in contact with LYS 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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309D LYS 3.2 17.4 + - - +
310D GLU* 3.9 14.6 + - - +
311D ALA 3.2 0.2 - - - -
312D GLU* 1.3 74.9 - - - +
314D PHE* 1.3 63.2 + - - +
316D VAL* 3.6 14.4 - - + +
317D SER* 3.2 22.2 + - - -
420D SER 5.8 1.0 + - - -
421D ILE* 3.9 26.7 - - - +
1T NAG 4.1 17.7 - - - -
2T NAG 3.4 34.5 + - + +
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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 GLU 3.2 13.2 + - - +
311D ALA 3.5 8.3 - - - +
312D GLU 3.2 0.4 - - - -
313D LYS* 1.3 77.6 - - - +
315D PHE* 1.3 87.5 + + - +
317D SER* 3.3 17.6 + - - -
318D VAL* 3.6 10.0 + - + +
373D HIS* 3.9 23.1 - + - +
408D MET* 4.5 21.3 - - - -
411D SER* 3.7 22.7 - - - -
412D ALA 5.4 0.7 - - - -
417D HIS* 3.8 19.3 - + + -
543D ASP* 3.8 11.9 - - - -
544D ILE* 3.9 18.6 - - + -
545D SER* 3.2 31.8 - - - -
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Residues in contact with PHE 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 ALA 3.2 22.3 + - - -
312D GLU* 3.4 6.8 + - - +
313D LYS 3.4 0.2 - - - -
314D PHE* 1.3 88.4 - + - +
316D VAL* 1.3 64.8 + - - +
317D SER 3.1 1.8 - - - -
318D VAL* 3.4 12.6 - - + +
320D LEU* 3.2 45.7 + - + +
321D PRO 5.0 1.1 - - - +
373D HIS* 4.3 9.2 - + - -
376D MET* 3.8 33.2 - - + -
377D GLY* 4.1 13.2 - - - -
380D GLN* 3.7 29.8 - - + +
408D MET* 3.6 52.5 - - + -
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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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312D GLU 3.1 21.1 + - - +
313D LYS* 3.6 20.4 - - + +
315D PHE* 1.3 75.4 - - - +
317D SER* 1.3 64.4 + - - +
318D VAL 3.3 0.8 + - - -
319D GLY* 3.6 8.9 + - - -
320D LEU 3.6 17.0 + - - +
321D PRO 5.3 1.9 + - - +
322D ASN* 4.1 20.9 - - - +
901D NAG 4.4 24.0 - - + +
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Residues in contact with SER 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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313D LYS* 3.2 19.9 + - - -
314D PHE* 3.3 11.7 - - - -
315D PHE 3.1 0.8 - - - -
316D VAL* 1.3 79.2 - - - +
318D VAL* 1.3 55.9 + - - +
319D GLY 3.5 0.4 + - - -
545D SER* 3.5 9.4 - - - -
546D ASN* 2.5 48.3 + - - -
547D SER 2.9 13.9 - - - +
548D THR* 5.0 0.2 + - - -
1T NAG 5.2 2.9 + - - -
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Residues in contact with VAL 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* 3.6 7.3 + - + +
315D PHE* 3.4 20.8 + - + +
317D SER* 1.3 77.1 - - - +
319D GLY* 1.3 57.3 + - - +
320D LEU* 3.8 25.6 - - + -
544D ILE* 3.5 45.1 - - + +
545D SER* 5.7 0.2 - - - -
547D SER* 3.3 19.1 - - - +
548D THR* 3.6 11.8 - - - +
550D ALA* 4.7 1.1 - - + -
551D GLY* 3.6 32.8 - - - +
554D LEU* 6.2 2.5 - - + -
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Residues in contact with GLY 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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315D PHE 3.5 0.8 + - - -
316D VAL 3.6 7.1 + - - -
317D SER 3.5 2.4 - - - -
318D VAL* 1.3 80.4 - - - +
320D LEU* 1.3 70.2 + - - +
321D PRO* 4.7 0.7 - - - +
548D THR* 4.9 11.4 - - - -
551D GLY* 5.3 4.6 - - - -
555D PHE* 5.6 2.6 - - - +
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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