Contacts of the helix formed by residues 348 - 361 (chain B) in PDB entry 1QDU
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 TRP 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B TYR* 3.2 58.6 + + + +
342B ASN* 5.2 5.8 - - + +
346B GLY 5.2 1.1 - - - -
347B THR* 1.3 72.7 - - - +
349B TYR* 1.3 57.0 + - - +
351B GLN* 4.3 2.0 - - - +
352B SER* 2.9 31.4 + - - -
377B VAL* 4.0 18.4 - - + +
381B LYS* 3.7 81.5 + - + +
383B GLY 5.3 0.2 - - - -
384B LYS 4.6 0.7 - - - -
385B GLN* 3.7 28.0 - - + +
4100T PHQ 3.3 51.1 + + - -
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Residues in contact with TYR 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 3.6 12.8 - + + -
282A ILE 4.0 5.8 - - - -
283A GLN* 4.2 7.2 - - + +
330B GLY* 2.9 40.2 + - - -
331B MET 4.0 2.9 - - - -
332B ALA* 3.1 34.3 - - + -
347B THR* 3.2 1.4 + - - -
348B TRP* 1.3 76.6 - - - +
350B ILE* 1.3 74.9 + - + +
352B SER* 3.1 2.3 + - - -
353B LEU* 2.7 49.9 + - + +
370B LEU* 4.1 12.9 - - + +
373B VAL* 3.9 22.9 - - + -
377B VAL* 4.4 5.8 - - - -
385B GLN* 3.9 11.4 - - - +
387B PRO* 4.0 21.8 - - + -
389B PRO* 5.8 1.2 - - + +
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASP* 3.6 29.4 - - + +
189A LEU* 3.6 35.7 - - + -
235A LEU* 4.2 13.0 - - + -
281A PHE* 5.0 11.4 - - + -
283A GLN* 3.7 28.5 - - + -
347B THR* 3.3 18.1 + - - +
349B TYR* 1.3 91.3 - - + +
351B GLN* 1.3 67.5 + - - +
353B LEU* 2.9 8.0 + - + +
354B CYS* 2.9 27.4 + - - -
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Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.6 9.8 + - - +
185A ASP* 2.7 40.0 + - - +
188A ALA* 4.0 14.3 - - - +
345B GLU* 3.2 30.8 + - + +
346B GLY 4.1 0.9 - - - -
347B THR 3.0 25.4 + - - +
348B TRP* 4.3 1.8 - - - +
350B ILE* 1.3 79.7 - - - +
352B SER* 1.3 56.1 + - - +
354B CYS* 3.9 3.6 - - - +
355B GLN* 3.0 31.6 + - - +
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B TRP 2.9 20.0 + - - -
349B TYR 3.1 3.6 + - - -
351B GLN* 1.3 77.6 - - - +
353B LEU* 1.3 63.8 + - - +
355B GLN* 3.9 6.8 - - - +
356B SER* 3.0 29.8 + - - -
373B VAL* 3.7 11.2 - - - +
376B GLU* 3.6 28.9 - - - +
377B VAL* 3.8 11.8 - - - +
381B LYS* 5.3 5.8 - - - -
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 5.3 4.7 - - + -
193A PHE* 5.4 0.2 - - + -
281A PHE* 3.3 52.5 - - + -
349B TYR* 2.7 34.2 + - + +
350B ILE* 3.4 12.1 - - + +
352B SER* 1.3 75.5 - - - +
354B CYS* 1.3 60.2 + - - +
356B SER* 3.4 1.9 + - - -
357B LEU* 2.9 51.8 + - + +
366B ILE* 5.2 1.6 - - + -
369B ILE* 4.7 4.0 - - + -
370B LEU* 4.5 13.7 - - + -
373B VAL* 3.8 17.4 - - + +
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Residues in contact with CYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA* 3.9 14.8 - - + -
189A LEU* 3.1 44.0 - - - -
192A THR* 3.7 24.2 - - + -
350B ILE* 2.9 20.6 + - - +
351B GLN* 3.9 2.7 - - - +
353B LEU* 1.3 74.7 - - - +
355B GLN* 1.3 69.2 + - - +
357B LEU* 2.8 22.6 + - - +
358B ARG* 2.8 19.6 + - - +
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLN 3.0 20.0 + - - +
352B SER* 3.9 7.5 - - - +
354B CYS* 1.3 75.8 - - - +
356B SER* 1.3 65.5 + - - +
358B ARG* 3.3 15.6 + - - +
359B GLU* 3.2 44.8 + - - +
376B GLU* 5.7 6.5 + - - +
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B SER* 3.0 20.6 + - - -
353B LEU 3.7 1.6 - - - -
354B CYS 3.1 1.0 - - - -
355B GLN* 1.3 78.0 - - - +
357B LEU* 1.3 67.8 + - - +
358B ARG 3.1 0.2 + - - -
359B GLU* 3.2 5.9 + - - +
360B ARG* 2.8 28.4 + - - +
369B ILE* 3.6 20.0 - - - -
372B GLU* 3.2 29.9 + - - +
373B VAL* 3.9 10.7 + - - +
376B GLU* 4.8 3.3 - - - +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A THR* 4.8 7.9 - - - +
193A PHE* 4.0 29.8 - - + -
196A LEU* 4.7 5.8 - - + -
281A PHE* 5.7 0.7 - - + -
353B LEU* 2.9 56.6 + - + +
354B CYS* 2.8 17.0 + - + +
356B SER* 1.3 71.0 - - - +
358B ARG* 1.3 64.7 + - + +
361B CYS* 2.9 52.1 + - - +
366B ILE* 4.7 9.9 - - + -
369B ILE* 4.0 12.1 - - + +
400B PHE* 4.5 16.6 - - + -
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA* 6.2 0.4 - - - +
191A THR* 3.6 30.1 - - - +
192A THR* 3.3 26.0 - - + +
195A GLU* 3.3 25.0 + - - +
354B CYS* 2.8 19.3 + - - +
355B GLN* 3.3 16.6 - - - +
357B LEU* 1.3 75.2 - - - +
359B GLU* 1.3 61.7 + - + +
362B PRO* 2.8 30.8 - - - +
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN* 3.2 38.7 + - - +
356B SER* 3.2 5.7 + - - +
358B ARG* 1.3 81.8 - - + +
360B ARG* 1.3 65.1 + - + +
362B PRO* 3.4 40.4 + - - +
372B GLU* 5.0 6.1 - - - +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B SER* 2.8 24.4 + - - +
359B GLU* 1.3 81.4 - - + +
361B CYS* 1.3 67.6 + - - +
362B ARG* 3.0 25.5 + - - +
363B GLY 3.2 3.3 + - - -
364B ASP* 2.9 51.0 + - - +
368B THR* 3.9 10.5 + - - +
369B ILE* 3.5 24.0 - - + -
372B GLU* 2.8 49.8 + - - +
150C ASP* 3.0 43.2 + - - +
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Residues in contact with CYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.2 20.0 - - + -
357B LEU* 2.9 56.0 + - - +
360B ARG* 1.3 72.2 - - - +
362B PRO* 1.3 73.0 - - + +
363B GLY* 3.1 13.2 + - - +
364B ASP 4.9 7.6 - - - -
366B ILE* 6.3 0.2 - - - -
369B ILE* 4.8 9.4 - - - -
399B VAL* 4.8 1.8 - - - +
400B PHE* 3.8 38.1 - - - +
401B PRO* 5.2 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