Contacts of the helix formed by residues 299 - 316 (chain A) in PDB entry 4GQS
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 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLY* 4.2 10.1 - - - +
174A PRO* 4.1 5.1 - - - +
175A CYS* 3.7 36.2 - - + +
178A ILE* 4.8 1.4 - - - +
198A MET* 5.2 3.8 - - + -
201A LEU* 3.8 19.4 - - + +
295A LEU* 2.6 28.3 + - - +
296A GLY* 4.5 3.3 - - - -
297A ALA 3.7 1.0 - - - -
298A GLY* 1.3 75.9 - - - +
300A GLU* 1.3 61.8 + - - +
301A THR 3.3 0.2 + - - -
302A THR* 3.4 1.7 + - - -
303A SER* 2.7 39.7 + - - -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU 5.4 0.7 - - - +
202A ASN* 4.7 8.8 - - - +
205A ILE* 3.7 32.6 - - + +
296A GLY 4.8 4.0 + - - +
299A THR* 1.3 81.6 - - - +
301A THR* 1.3 57.2 + - - +
303A SER* 4.2 5.6 + - - -
304A THR* 2.8 52.2 + - - +
307A ARG* 5.4 2.8 + - - -
479A VAL* 5.9 3.3 - - - +
502A 0XV 3.4 33.9 - - + -
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA 2.8 28.4 + - - +
298A GLY* 3.5 5.5 - - - -
300A GLU* 1.3 78.4 - - - +
302A THR* 1.3 67.7 + - - -
305A THR* 3.0 22.2 + - - -
361A LEU* 3.1 16.0 - - + +
362A ILE* 5.1 0.9 - - + -
501A HEM 3.3 37.1 - - + +
502A 0XV 3.5 43.7 - - + +
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 3.8 14.1 - - + -
298A GLY 2.6 26.4 + - - -
299A THR 3.4 1.2 + - - -
301A THR* 1.3 81.2 + - - +
303A SER* 1.3 63.6 + - - +
305A THR* 3.3 3.5 + - - -
306A LEU* 3.0 26.1 + - + +
441A ALA* 4.5 6.7 - - - +
444A GLU* 3.7 34.3 + - + +
445A LEU* 4.4 13.5 - - + -
501A HEM 3.5 25.7 - - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR 4.4 2.1 + - - -
170A LEU* 3.5 21.1 + - - +
171A GLY* 3.4 23.2 + - - -
174A PRO* 3.9 5.5 - - - +
299A THR* 2.7 27.8 + - - -
300A GLU* 3.7 7.1 + - - -
302A THR* 1.3 73.1 - - - +
304A THR* 1.3 62.8 + - - +
306A LEU* 3.4 2.6 + - - +
307A ARG* 3.2 34.9 + - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 2.8 45.7 + - - +
301A THR 3.9 0.9 - - - -
303A SER* 1.3 73.8 - - - +
305A THR* 1.3 58.4 + - - +
307A ARG* 3.5 19.1 + - - +
308A TYR* 3.0 29.2 + - + +
361A LEU* 3.4 28.9 - - + -
478A SER 3.6 13.7 - - - +
479A VAL* 4.7 2.0 - - + +
480A PRO* 3.7 19.0 - - + +
502A 0XV 5.9 0.2 - - - -
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A THR 3.0 12.7 + - - -
302A THR 3.3 8.6 + - - -
304A THR* 1.3 75.4 - - - +
306A LEU* 1.3 60.9 + - - +
308A TYR* 3.3 1.6 + - - +
309A ALA* 2.8 28.0 + - + +
355A VAL* 4.3 12.0 - - + +
356A GLN* 4.4 8.4 + - + +
359A ILE* 3.9 23.3 - - + +
361A LEU* 3.2 15.6 - - - +
445A LEU* 3.7 31.9 - - + -
501A HEM 3.7 10.1 - - + +
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Residues in contact with LEU 306 (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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152A LEU* 5.3 1.6 - - + -
170A LEU* 3.9 27.1 - - + +
173A ALA* 5.2 1.6 - - + -
174A PRO* 3.9 24.2 - - + -
302A THR* 3.0 16.1 + - + +
303A SER 3.7 4.5 - - - +
305A THR* 1.3 77.6 - - - +
307A ARG* 1.3 62.3 + - - +
309A ALA* 3.1 5.3 + - - +
310A LEU* 3.1 26.9 + - - +
445A LEU* 3.7 24.5 - - + -
448A PHE* 3.7 39.0 - - + -
449A LEU* 3.9 28.3 - - + +
452A ILE* 6.0 1.3 - - + -
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Residues in contact with ARG 307 (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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165A ASP* 4.9 2.5 - - - -
166A PRO* 4.4 2.9 - - + -
167A THR* 3.0 46.9 + - - +
170A LEU* 3.3 21.5 - - + +
300A GLU* 5.4 3.0 + - - -
303A SER* 3.2 24.6 + - - +
304A THR* 3.9 20.3 + - - +
306A LEU* 1.3 79.4 - - - +
308A TYR* 1.3 61.2 + - - +
311A LEU 3.3 7.1 + - - -
479A VAL* 3.9 13.9 - - - +
480A PRO* 3.5 33.6 + - + +
483A TYR* 2.7 46.0 + - + +
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Residues in contact with TYR 308 (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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304A THR* 3.0 21.5 + - + +
305A THR* 3.7 6.3 - - - +
307A ARG* 1.3 75.3 - - - +
309A ALA* 1.3 65.4 + - - +
311A LEU* 3.3 12.3 + - + +
312A LEU* 3.0 33.8 + - + +
358A TYR* 4.6 4.4 - + - -
359A ILE* 3.4 44.6 - - + -
361A LEU* 5.5 0.7 - - + -
469A THR* 2.6 32.0 + - - -
471A PRO* 2.8 32.4 - - + +
478A SER* 5.0 3.1 - - - -
479A VAL* 4.3 5.4 - - - -
480A PRO* 3.5 43.9 - - + +
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Residues in contact with ALA 309 (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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305A THR* 2.8 19.7 + - + +
306A LEU* 3.4 7.2 - - - +
308A TYR* 1.3 76.1 - - - +
310A LEU* 1.3 62.6 + - - +
312A LEU* 3.2 5.8 + - - +
313A LEU* 3.0 28.3 + - + +
355A VAL* 4.0 27.0 - - + +
445A LEU* 6.0 0.2 - - + -
449A LEU* 4.0 30.5 - - + -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PRO* 4.6 1.6 - - + -
170A LEU* 4.0 26.2 - - + -
306A LEU 3.1 10.8 + - - +
307A ARG 4.6 0.2 - - - -
309A ALA* 1.3 77.7 - - - +
311A LEU* 1.3 64.1 - - - +
313A LEU* 2.9 24.1 + - + +
314A LEU* 3.0 17.6 + - - +
449A LEU* 4.7 12.1 - - + -
452A ILE* 4.7 16.6 - - + -
453A LEU* 5.5 2.0 - - + -
458A LEU* 3.5 31.7 - - + +
483A TYR* 3.7 14.4 - - - +
485A LEU* 4.2 9.2 - - + -
487A PHE* 4.0 28.7 - - + -
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Residues in contact with LEU 311 (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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307A ARG 3.3 4.6 + - - +
308A TYR* 3.5 19.1 - - + +
310A LEU* 1.3 78.2 - - - +
312A LEU* 1.3 61.6 + - - +
314A LEU* 3.2 15.4 + - + +
315A LYS* 3.2 11.3 + - - +
467A LEU* 4.0 25.4 - - + -
468A ASP 5.1 2.2 - - - +
469A THR* 4.3 13.0 - - + -
480A PRO* 4.0 14.6 - - + -
481A PRO* 3.8 33.9 - - + +
483A TYR* 3.5 50.1 + - + -
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Residues in contact with LEU 312 (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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308A TYR* 3.0 24.2 + - + +
309A ALA 3.5 6.3 - - - +
311A LEU* 1.3 78.2 - - - +
313A LEU* 1.3 59.4 + - + +
315A LYS 3.3 1.0 + - - -
316A HIS* 3.0 37.3 + - + +
355A VAL* 3.8 21.1 - - + -
358A TYR* 3.7 32.8 - - + -
359A ILE* 4.2 6.5 - - + -
407A PHE* 3.6 49.7 - - + -
469A THR* 3.8 24.0 - - + +
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Residues in contact with LEU 313 (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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309A ALA* 3.0 20.3 + - + +
310A LEU* 2.9 20.3 + - + +
312A LEU* 1.3 79.0 - - + +
314A LEU* 1.3 61.7 + - - +
316A HIS* 3.4 10.6 - - + +
317A PRO* 3.7 2.4 - - - +
319A VAL* 4.4 15.9 - - + -
320A THR* 2.7 41.3 + - - +
323A VAL* 5.4 1.8 - - + -
351A VAL* 4.4 15.9 - - + -
355A VAL* 6.0 0.7 - - + -
407A PHE* 5.7 2.0 - - + -
449A LEU* 4.9 11.4 - - + -
453A LEU* 4.1 25.1 - - + -
458A LEU* 3.5 25.9 - - + +
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Residues in contact with LEU 314 (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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310A LEU 3.0 13.1 + - - +
311A LEU* 3.2 9.8 + - + +
313A LEU* 1.3 76.3 - - - +
315A LYS* 1.3 62.8 + - - +
316A HIS 3.4 0.7 + - - -
317A PRO* 3.5 8.9 - - - +
458A LEU* 3.5 41.5 - - + +
459A LYS 3.8 1.3 - - - +
460A SER* 3.4 38.4 - - - +
464A PRO* 3.3 22.9 - - - +
467A LEU* 4.4 10.5 - - + -
483A TYR* 4.3 18.2 - - + -
484A GLN 4.4 0.7 - - - +
485A LEU* 3.4 29.8 - - + -
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Residues in contact with LYS 315 (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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311A LEU 3.2 3.0 + - - +
312A LEU 3.3 3.8 + - - +
314A LEU* 1.3 78.8 - - - +
316A HIS* 1.3 87.7 + - + +
317A PRO* 3.4 7.3 - - - +
318A GLU* 4.3 1.4 - - - +
464A PRO* 3.4 28.0 - - - +
465A LYS* 4.2 15.3 - - - +
467A LEU* 3.1 35.0 - - + +
468A ASP* 5.6 0.7 - - - +
469A THR* 3.8 25.2 + - + +
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Residues in contact with HIS 316 (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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312A LEU* 3.0 25.3 + - + +
313A LEU* 3.4 5.1 - - - +
315A LYS* 1.3 108.9 + - + +
317A PRO* 1.3 63.4 - - - +
318A GLU* 2.9 29.8 - - - +
319A VAL* 3.1 25.7 + - + +
320A THR* 3.1 14.6 + - - -
407A PHE* 3.9 45.2 + + + +
469A THR* 5.2 1.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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