Contacts of the helix formed by residues 347 - 361 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASP* 2.9 17.4 + - - -
283A GLN* 4.3 19.6 - - - -
334A VAL 4.9 1.6 - - - -
335A PRO 4.9 12.3 - - - -
336A GLY* 5.7 4.3 - - - -
346A GLY* 1.3 73.0 - - - -
348A TRP* 1.3 65.3 + - - +
349A PHE* 3.9 3.9 + - - +
350A VAL* 3.2 32.1 + - - +
351A GLN* 2.9 26.2 + - - +
1403A SO4 5.7 4.3 - - - -
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Residues in contact with TRP 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A VAL* 3.9 21.7 - - + +
335A PRO 5.2 6.8 + - - -
338A TYR* 3.4 35.1 + + - -
346A GLY 4.0 0.4 + - - -
347A SER* 1.3 72.6 - - - +
349A PHE* 1.3 58.6 - - - +
351A GLN* 3.7 6.2 - - + +
352A ALA* 2.8 32.9 + - - +
377A VAL* 4.1 10.5 - - + -
379A HIS* 3.3 72.8 - - + +
380A PHE* 3.7 29.4 - + - -
381A SER* 5.6 7.2 - - + -
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Residues in contact with PHE 349 (chain A).
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* 5.2 2.5 - - + -
282A ILE 4.1 9.0 - - - -
283A GLN* 3.7 13.5 - - + +
330A ALA* 3.5 36.8 - - + -
331A TYR 4.7 0.2 - - - -
332A SER* 3.5 29.4 - - - +
334A VAL* 5.3 4.7 - - + +
347A SER* 3.3 2.4 + - - +
348A TRP* 1.3 77.9 - - - +
350A VAL* 1.3 63.2 + - + +
352A ALA* 2.9 4.0 + - - +
353A LEU* 2.7 59.5 + - + +
370A LEU* 5.5 3.4 - - + -
373A VAL* 3.7 22.0 - - + -
374A ASN* 5.2 0.9 - - - -
377A VAL* 3.6 11.5 - - + +
387A PRO* 3.6 33.4 - - + -
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Residues in contact with VAL 350 (chain A).
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* 3.7 39.9 - - + +
188A ALA* 4.6 0.2 - - + -
189A LEU* 3.9 22.7 - - + -
235A LEU* 4.6 10.1 - - + -
283A GLN* 4.7 4.3 - - + -
347A SER* 3.2 18.6 + - - +
349A PHE* 1.3 90.8 - - + +
351A GLN* 1.3 74.0 + - - +
353A LEU* 3.0 4.8 + - + -
354A CYS* 2.7 41.1 + - - +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LYS* 4.8 2.6 - - - +
185A ASP* 2.9 33.3 + - - +
188A ALA* 4.5 12.4 - - - +
345A ARG 4.2 8.7 - - - +
346A GLY* 3.5 15.3 - - - +
347A SER 2.9 25.3 + - - +
348A TRP* 3.7 6.7 - - + +
350A VAL* 1.3 81.6 - - - +
352A ALA* 1.3 57.9 + - - +
354A CYS* 3.7 4.4 - - - +
355A SER* 2.8 34.3 + - - -
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A TRP 2.8 21.6 + - - +
349A PHE 3.4 2.9 - - - +
351A GLN* 1.3 69.1 - - - +
353A LEU* 1.3 66.5 + - - +
355A SER* 4.5 0.9 - - - -
356A ILE* 2.9 31.4 + - - +
373A VAL* 3.8 20.6 - - + +
376A ARG* 3.6 39.0 - - + +
377A VAL* 4.2 3.1 - - + -
379A HIS* 6.2 0.2 - - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.6 16.8 - - + -
193A PHE* 4.7 4.3 - - + -
281A PHE* 3.5 40.6 - - + -
349A PHE* 2.7 42.7 + - + +
350A VAL* 3.6 4.9 - - + +
352A ALA* 1.3 73.6 - - - +
354A CYS* 1.3 57.8 + - - +
357A LEU* 2.8 56.1 + - + +
366A ILE* 6.4 0.2 - - + -
369A ILE* 4.8 1.8 - - + -
370A LEU* 4.3 14.8 - - + -
373A VAL* 3.5 19.4 - - + +
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Residues in contact with CYS 354 (chain A).
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* 3.6 38.1 - - + +
189A LEU* 3.8 23.6 - - - -
192A CYS* 3.9 16.3 - - + -
350A VAL* 2.7 29.1 + - - +
351A GLN* 3.7 5.8 - - - +
353A LEU* 1.3 72.9 - - - +
355A SER* 1.3 68.8 + - - +
357A LEU* 3.0 1.7 + - - +
358A GLU* 2.8 28.5 + - - +
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Residues in contact with SER 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLN 2.8 22.2 + - - -
352A ALA* 4.0 1.3 - - - -
354A CYS* 1.3 74.8 - - - +
356A ILE* 1.3 63.2 + - - +
358A GLU* 3.6 10.5 + - - +
359A GLU* 3.6 16.5 + - - +
376A ARG* 2.8 28.2 + - - -
141B ILE* 4.5 21.2 - - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ALA 2.9 21.2 + - - +
355A SER* 1.3 73.8 - - - +
357A LEU* 1.3 60.9 + - - +
359A GLU* 3.2 10.1 + - - +
360A HIS* 3.0 38.3 + - + +
369A ILE* 3.6 29.4 - - + +
372A ARG* 3.6 26.0 - - + +
373A VAL* 3.5 37.2 - - + +
376A ARG* 3.4 34.3 - - + +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A CYS* 3.6 12.8 - - - -
193A PHE* 3.7 27.4 - - + -
196A LEU* 3.8 22.4 - - + +
281A PHE* 5.4 1.6 - - + -
353A LEU* 2.8 36.2 + - + +
354A CYS 3.0 3.0 + - - +
356A ILE* 1.3 80.8 - - - +
358A GLU* 1.3 56.8 + - - +
359A GLU 3.0 0.5 + - - -
361A GLY* 2.8 34.8 + - - +
362A LYS* 5.5 2.3 + - - -
366A ILE* 5.2 2.9 - - + -
369A ILE* 3.5 38.4 - - + -
400A PHE* 4.3 13.5 - - + -
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 4.6 6.2 - - - +
192A CYS* 4.5 18.4 + - + -
195A SER* 3.7 26.7 + - - +
354A CYS 2.8 20.5 + - - +
355A SER* 3.7 5.3 - - - +
357A LEU* 1.3 71.5 - - - +
359A GLU* 1.3 60.5 + - - +
362A LYS* 5.9 7.2 - - - +
140B SER 5.3 6.6 + - - +
141B ILE* 5.2 5.5 - - - +
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A SER* 3.6 15.0 + - - +
356A ILE* 3.6 6.5 - - - +
357A LEU 3.0 1.2 + - - -
358A GLU* 1.3 78.2 - - - +
360A HIS* 1.3 90.8 + - + +
361A GLY 3.8 0.6 - - - +
362A LYS 5.4 0.2 - - - -
363A ASP* 3.5 7.3 - - - +
376A ARG* 5.1 6.4 + - - -
141B ILE* 3.3 27.3 - - + +
142B LYS* 4.2 16.8 + - - +
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Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ILE* 3.0 21.8 + - + +
359A GLU* 1.3 108.6 + - + +
361A GLY* 1.3 59.8 + - - +
362A LYS 2.9 7.0 + - - -
363A ASP* 2.6 33.7 + - - -
364A LEU* 2.8 60.1 + - + +
369A ILE* 3.8 3.9 - - + +
372A ARG* 3.3 28.3 + - - -
147B ARG* 5.7 9.2 - - - -
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Residues in contact with GLY 361 (chain A).
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* 3.4 12.7 - - - +
357A LEU* 2.8 24.6 + - - +
359A GLU 4.1 0.2 - - - +
360A HIS* 1.3 77.4 - - - +
362A LYS* 1.3 62.3 + - - +
364A LEU 4.7 2.9 - - - +
369A ILE* 3.9 14.6 - - - -
400A PHE* 3.2 34.8 + - - +
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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