Contacts of the helix formed by residues 310 - 320 (chain D) in PDB entry 1QMZ
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 THR 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D GLU* 2.5 38.6 + - - +
233D HIS* 3.6 34.1 - - + +
234D LEU* 3.7 13.5 - - + +
237D ASN* 5.4 2.2 - - + -
308D ALA* 3.7 7.9 - - + +
309D PRO* 1.3 79.9 - - - +
311D VAL* 1.3 68.6 + - - +
312D ASN 3.1 2.1 + - - -
313D GLN* 3.1 24.9 + - - +
314D PHE* 3.4 13.3 + - - -
352D PRO* 3.9 7.6 - - - -
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Residues in contact with VAL 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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233D HIS* 3.9 17.3 - - + +
310D THR* 1.3 73.2 - - - +
312D ASN* 1.4 57.9 + - - +
314D PHE* 3.0 3.8 + - - -
315D LEU* 2.9 33.6 + - + +
337D GLY* 4.1 24.7 - - - +
340D SER* 4.7 5.2 - - - +
341D LEU* 5.6 3.8 - - + -
352D PRO* 3.8 31.9 - - + +
355D ILE* 3.8 23.1 - - + -
356D ALA* 3.8 23.9 - - + +
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Residues in contact with ASN 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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157C ARG* 5.6 1.2 - - - +
229D ASN* 4.7 3.2 - - - +
230D GLU* 3.1 46.8 + - - +
233D HIS* 4.0 21.7 - - + +
310D THR* 3.6 1.6 - - - +
311D VAL* 1.4 77.6 - - - +
313D GLN* 1.3 62.1 + - - +
315D LEU* 3.4 9.7 + - - +
316D THR* 3.3 33.0 + - - +
334D MET* 3.1 29.2 - - + +
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Residues in contact with GLN 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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122C ARG* 4.7 7.8 + - - +
152C PHE 5.1 4.7 - - - +
153C GLY* 5.5 9.6 - - - -
154C VAL 5.5 1.3 + - - +
186D LEU* 3.7 36.7 - - + +
230D GLU* 2.6 31.3 + - - +
234D LEU* 4.6 0.6 - - - +
307D ALA 5.7 0.4 - - - -
308D ALA 3.0 23.3 + - - +
309D PRO* 4.1 1.5 - - + +
310D THR* 3.1 23.3 + - - +
312D ASN* 1.3 77.0 - - - +
314D PHE* 1.3 61.9 + - + +
316D THR* 3.7 12.6 - - - +
317D GLN* 2.9 25.3 - - - +
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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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183D HIS* 4.0 20.0 - + - -
186D LEU* 3.5 37.5 - - + -
187D ARG* 3.9 17.0 - - + -
190D GLU* 3.4 25.1 - - - -
309D PRO* 4.1 18.6 - - + -
310D THR 3.4 13.7 + - - -
311D VAL 3.0 3.4 + - - +
313D GLN* 1.3 77.6 - - + +
315D LEU* 1.4 65.1 + - - +
317D GLN* 3.2 14.8 + - - +
318D TYR* 2.9 36.4 + + + +
352D PRO* 4.1 2.0 - - + -
353D SER* 3.7 28.7 - - - -
356D ALA* 3.8 17.3 - - + -
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Residues in contact with LEU 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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233D HIS* 6.2 0.7 - - + +
311D VAL* 2.9 28.7 + - + +
312D ASN* 3.4 11.9 + - - +
314D PHE* 1.4 73.8 - - - +
316D THR* 1.3 50.8 + - - +
318D TYR* 2.8 8.6 + - + -
319D PHE* 2.6 65.4 + - + -
333D ALA* 3.6 36.1 - - + +
334D MET* 4.0 17.7 - - + +
337D GLY* 4.9 2.0 - - - -
356D ALA* 3.5 32.4 - - + +
359D ALA* 4.4 2.0 - - + -
360D PHE* 4.0 7.9 - - + +
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Residues in contact with THR 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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153C GLY* 5.2 2.0 - - - -
154C VAL 2.7 38.6 - - - +
155C PRO* 3.7 14.1 - - + +
312D ASN* 3.3 24.2 + - - +
313D GLN* 3.7 15.5 - - - +
315D LEU* 1.3 75.2 - - - +
317D GLN* 1.3 60.7 + - - +
319D PHE* 3.5 26.2 + - - +
320D LEU* 3.6 16.3 + - - +
334D MET* 5.4 1.2 - - - +
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Residues in contact with GLN 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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154C VAL* 3.6 32.7 - - + +
179D HIS* 4.5 4.0 + - - +
182D ILE* 4.9 1.0 - - - +
183D HIS* 3.4 41.9 + - - +
186D LEU* 3.5 21.4 - - - +
313D GLN 2.9 21.3 - - - +
314D PHE* 3.2 18.7 + - - +
315D LEU 3.2 0.2 - - - -
316D THR* 1.3 72.5 - - - +
318D TYR* 1.3 70.4 + - + +
320D LEU* 3.1 25.1 + - - +
321D HIS* 3.9 8.5 - - - -
379D LYS* 4.2 15.7 + - - +
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Residues in contact with TYR 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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183D HIS* 4.6 5.9 - + - -
314D PHE* 2.9 33.1 + + + -
315D LEU* 2.8 13.9 + - - +
317D GLN* 1.3 72.5 - - + +
319D PHE* 1.4 65.3 + - - +
321D HIS* 2.9 21.8 + - - +
322D GLN 4.1 1.7 + - - -
353D SER* 2.8 30.7 + - - -
356D ALA* 3.5 24.9 - - + -
357D GLY* 3.3 26.2 - - - -
360D PHE* 4.1 16.8 - - + -
372D TRP* 3.9 15.5 - + - -
376D LEU* 3.7 31.9 - - + +
379D LYS* 5.3 1.3 - - - -
380D THR* 3.8 25.6 - - + +
382D TYR* 4.2 3.3 - - - -
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Residues in contact with PHE 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 LEU* 2.6 40.7 + - + +
316D THR* 3.7 23.6 - - - +
317D GLN 3.2 0.2 - - - -
318D TYR* 1.4 71.1 - - - +
320D LEU* 1.3 63.6 + - + +
321D HIS 3.1 1.2 + - - -
322D GLN* 3.2 27.3 + - - +
330D GLU* 3.4 67.1 - - + +
333D ALA* 3.8 23.1 - - + -
334D MET* 3.9 18.4 - - + -
360D PHE* 3.9 18.4 - + - -
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Residues in contact with LEU 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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154C VAL* 4.0 16.4 - - + -
155C PRO* 4.3 21.8 - - + -
179D HIS* 4.0 29.4 - - + +
316D THR 3.7 13.2 - - - +
317D GLN 3.1 12.8 + - - +
319D PHE* 1.3 77.2 - - + +
321D HIS* 1.3 64.9 + - + +
322D GLN 3.3 3.0 + - - +
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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