Contacts of the helix formed by residues 347 - 361 (chain B) in PDB entry 1GQF
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 SER 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B ASP* 3.0 15.3 + - - -
283B GLN* 3.8 27.2 - - - -
334B VAL* 5.1 1.6 - - - -
335B PRO 4.6 12.6 - - - -
336B GLY* 5.6 4.5 - - - -
346B GLY* 1.3 75.0 - - - +
348B TRP* 1.3 63.4 + - - +
349B PHE 3.8 1.1 + - - -
350B VAL* 2.9 37.1 + - - +
351B GLN* 3.0 19.8 + - - +
1403B SO4 5.3 4.9 - - - -
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Residues in contact with TRP 348 (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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334B VAL* 4.0 21.1 - - + +
335B PRO 5.4 1.8 + - - -
337B TYR* 3.9 26.2 - + - -
338B TYR* 4.4 21.9 - + - -
346B GLY 4.9 4.3 - - - -
347B SER* 1.3 70.9 - - - +
349B PHE* 1.3 56.6 + - - +
351B GLN* 3.8 11.6 - - - +
352B ALA* 2.8 37.4 + - - +
377B VAL* 4.1 12.6 - - + -
379B HIS* 3.1 76.3 + - + +
380B PHE* 3.5 24.7 - + - -
382B GLU* 5.3 4.0 - - + -
1405B SO4 3.2 25.7 + - - -
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 5.0 4.0 - + + -
282B ILE 3.7 23.1 - - - -
283B GLN* 3.5 18.6 - - + +
330B ALA* 3.6 32.3 - - + -
332B SER* 3.4 28.5 - - - +
334B VAL* 5.6 3.2 - - + +
347B SER* 3.8 0.6 + - - -
348B TRP* 1.3 78.8 - - - +
350B VAL* 1.3 62.2 + - + +
352B ALA* 3.3 1.7 - - - +
353B LEU* 2.8 51.4 + - + +
370B LEU* 5.6 2.2 - - + -
373B VAL* 3.6 25.8 - - + -
374B ASN* 5.6 0.2 - - - -
377B VAL* 3.6 13.8 - - + +
387B PRO* 4.0 24.7 - - + -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASP* 3.6 42.8 - - + +
188B ALA* 4.8 2.5 - - + -
189B LEU* 3.7 25.4 - - + -
233B ILE* 6.1 0.2 - - + -
235B LEU* 4.4 9.2 - - + -
283B GLN* 4.3 20.0 - - + -
347B SER* 2.9 23.6 + - - +
349B PHE* 1.3 85.1 - - + +
351B GLN* 1.3 64.2 + - - +
353B LEU* 3.4 6.5 + - + +
354B CYS* 2.9 28.9 + - - -
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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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185B ASP* 4.9 1.5 + - - +
345B ARG* 4.6 13.3 + - - +
346B GLY* 5.3 3.4 - - - +
347B SER 3.0 17.2 + - - +
348B TRP* 3.8 14.1 - - - +
350B VAL* 1.3 77.8 - - - +
352B ALA* 1.3 54.7 + - - +
354B CYS* 3.8 3.6 - - - +
355B SER* 2.8 42.4 + - - -
379B HIS* 5.3 3.8 + - - -
1405B SO4 4.5 14.3 + - - -
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Residues in contact with ALA 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 2.8 23.0 + - - +
349B PHE 3.3 4.5 - - - +
351B GLN* 1.3 73.5 - - - +
353B LEU* 1.3 64.8 + - - +
355B SER* 3.5 0.6 - - - -
356B ILE* 2.9 28.5 + - - +
373B VAL* 3.8 19.7 - - + -
376B ARG* 3.5 37.7 - - + +
377B VAL* 4.1 5.2 - - + -
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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
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189B LEU* 4.2 21.5 - - + -
193B PHE* 4.4 9.0 - - + -
233B ILE* 6.2 0.2 - - + -
281B PHE* 3.9 33.2 - - + -
349B PHE* 2.8 31.8 + - + +
350B VAL* 3.6 5.2 - - + +
352B ALA* 1.3 72.5 - - - +
354B CYS* 1.3 58.0 + - - +
356B ILE* 3.7 1.6 - - - +
357B LEU* 2.8 48.0 + - + +
366B ILE* 6.2 0.4 - - + -
369B ILE* 4.8 5.6 - - + +
370B LEU* 3.9 28.0 - - + -
373B VAL* 3.5 19.1 - - + +
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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
----------------------------------------------------------
188B ALA* 3.4 39.5 - - + +
189B LEU* 3.4 33.4 - - - -
192B CYS* 3.8 18.6 - - + -
350B VAL* 2.9 19.3 + - - +
351B GLN* 3.8 3.6 - - - +
353B LEU* 1.3 73.7 - - - +
355B SER* 1.3 65.1 + - - +
357B LEU* 3.0 2.6 + - - +
358B GLU* 2.8 34.9 + - - +
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Residues in contact with SER 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* 2.8 27.2 + - - -
352B ALA* 3.5 1.6 - - - -
354B CYS* 1.3 76.7 - - - +
356B ILE* 1.3 63.6 + - - +
358B GLU* 3.0 21.3 + - - +
359B GLU* 3.2 13.2 + - - +
376B ARG* 2.5 32.4 + - - -
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Residues in contact with ILE 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 ALA 2.9 18.9 + - - +
353B LEU 3.9 2.0 - - - +
355B SER* 1.3 71.6 - - - +
357B LEU* 1.3 57.1 + - - +
359B GLU* 4.8 4.9 - - - +
360B HIS* 3.0 35.3 + - + +
361B GLY 3.8 0.2 + - - -
369B ILE* 3.9 21.5 - - + +
372B ARG* 3.6 36.1 - - + +
373B VAL* 3.5 39.9 - - + +
376B ARG* 3.3 34.8 - - + +
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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
----------------------------------------------------------
192B CYS* 3.4 17.3 - - - -
193B PHE* 3.5 38.8 - - + -
196B LEU* 4.4 16.4 - - + +
281B PHE* 6.0 0.7 - - + -
353B LEU* 2.8 30.6 + - + +
354B CYS 3.3 5.6 - - - +
356B ILE* 1.3 76.3 - - - +
358B GLU* 1.3 63.0 + - - +
361B GLY* 2.6 34.0 + - - +
362B LYS* 5.0 1.4 - - - +
366B ILE* 5.5 2.5 - - + -
369B ILE* 3.7 39.3 - - + -
400B PHE* 4.5 13.0 - - + -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B CYS* 4.6 15.7 - - + -
195B SER* 5.9 4.5 - - - +
354B CYS* 2.8 25.7 + - - +
355B SER* 3.0 14.6 + - - +
357B LEU* 1.3 78.9 - - - +
359B GLU* 1.3 62.9 + - - +
361B GLY 4.2 1.2 + - - -
362B LYS* 4.2 13.7 + - - +
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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 SER 3.2 10.5 + - - +
356B ILE* 4.3 2.2 - - - +
358B GLU* 1.3 82.5 - - + +
360B HIS* 1.3 88.3 + - + +
362B LYS* 5.3 1.2 + - - -
363B ASP* 3.4 8.9 - - - +
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Residues in contact with HIS 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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151A TYR* 5.4 1.4 + - - -
356B ILE* 3.0 22.4 + - + +
359B GLU* 1.3 104.4 + - + +
361B GLY* 1.3 59.3 + - - +
362B LYS 2.8 13.0 + - - -
363B ASP* 2.7 36.8 + - - +
364B LEU* 3.0 37.6 + - + +
369B ILE* 4.0 4.3 - - + +
372B ARG* 3.2 29.2 + - - -
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Residues in contact with GLY 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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196B LEU* 4.0 10.8 - - - -
356B ILE 3.8 0.6 + - - -
357B LEU* 2.6 33.5 + - - -
358B GLU 4.2 1.4 + - - -
359B GLU 3.8 0.6 - - - -
360B HIS* 1.3 70.2 - - - +
362B LYS* 1.3 63.5 + - - +
363B ASP 3.6 0.4 + - - -
364B LEU 4.5 1.6 - - - +
369B ILE* 4.1 14.1 - - - +
400B PHE* 3.2 32.4 + - - +
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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