Contacts of the helix formed by residues 393 - 404 (chain X) in PDB entry 1G3I
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 ALA 393 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60X GLY 3.5 11.4 + - - +
336X LEU* 3.5 10.6 - - + +
341X PHE* 4.0 11.2 - - - -
344X ILE* 5.0 1.1 - - + -
391X ILE 3.8 0.2 + - - -
392X GLY* 1.3 68.4 - - - -
394X ARG* 1.3 52.7 + - - +
395X ARG 2.6 0.3 + - - -
396X LEU* 2.5 47.6 + - + +
397X HIS* 3.8 4.5 + - - +
461X ATP 3.2 47.8 - - + +
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Residues in contact with ARG 394 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287W GLU* 2.7 36.4 + - - +
321W PRO 4.9 0.2 - - - -
322W GLU* 3.1 47.9 + - - +
325W GLY* 3.9 16.1 - - - +
326W ARG* 3.5 31.1 - - - +
59X THR* 5.1 3.2 - - - +
60X GLY* 5.8 0.7 - - - -
391X ILE* 4.0 20.4 - - + +
392X GLY 3.1 0.6 + - - -
393X ALA* 1.3 75.4 - - - +
395X ARG* 1.3 60.6 + - - +
396X LEU 3.2 0.2 - - - -
397X HIS* 3.4 28.5 + - - +
398X THR* 3.5 11.6 - - - +
461X ATP 3.4 59.9 + - - +
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Residues in contact with ARG 395 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324W GLN* 5.3 3.6 + - - +
330W ARG* 5.9 2.8 - - - +
341X PHE* 4.7 2.0 - - + -
381X ALA* 3.1 28.9 - - + +
384X VAL* 3.2 31.7 - - - +
385X ASN* 2.8 19.0 - - - +
388X THR* 4.7 5.1 + - - -
389X GLU* 3.1 31.1 + - - +
391X ILE* 3.3 28.3 - - + +
392X GLY 2.8 17.7 + - - +
393X ALA 2.6 5.5 + - - -
394X ARG* 1.3 71.9 - - - +
396X LEU* 1.3 64.4 + - - +
398X THR* 2.5 35.2 + - - +
399X VAL* 2.9 16.9 - - + +
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Residues in contact with LEU 396 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341X PHE* 3.3 42.6 - - + +
344X ILE* 4.0 26.5 - - + -
345X LEU* 3.7 28.0 - - + -
352X LEU* 3.5 17.5 - - + -
377X ILE* 3.9 12.1 - - + +
381X ALA* 3.8 13.5 - - + -
393X ALA* 2.5 24.5 + - + +
395X ARG* 1.3 73.1 - - - +
397X HIS* 1.3 64.5 + - + +
399X VAL* 2.8 18.2 + - + +
400X MET* 2.8 16.6 + - + +
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Residues in contact with HIS 397 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W THR* 6.4 1.8 - - - -
51W LYS* 5.1 17.4 - - - +
325W GLY 4.5 6.4 + - - +
326W ARG* 5.3 9.4 + - - -
328W PRO* 4.2 16.3 - - + +
352X LEU* 3.6 33.9 - - + +
355X GLN* 5.9 0.4 + - - -
356X TYR* 6.4 0.2 - - - -
393X ALA* 4.5 7.7 + - - +
394X ARG* 3.5 18.6 + - + +
395X ARG 3.3 0.6 - - - -
396X LEU* 1.3 77.1 - - + +
398X THR* 1.3 62.9 + - - +
400X MET* 3.3 3.5 + - - +
401X GLU* 3.0 24.1 + - - +
461X ATP 3.4 33.3 + - - -
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Residues in contact with THR 398 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324W GLN 4.0 15.7 - - - +
325W GLY* 4.2 3.4 - - - -
328W PRO* 3.4 45.0 - - + +
330W ARG* 5.3 3.6 - - - +
391X ILE* 4.9 2.9 - - + -
394X ARG 3.5 13.7 - - - +
395X ARG* 2.5 38.2 + - - +
397X HIS* 1.3 75.3 - - - +
399X VAL* 1.3 62.0 + - - +
401X GLU* 3.9 3.3 + - - +
402X ARG* 3.6 16.5 + - - +
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Residues in contact with VAL 399 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377X ILE* 4.3 26.2 - - + +
380X ALA* 4.7 11.9 - - + +
381X ALA* 3.7 22.4 - - + -
384X VAL* 5.6 2.2 - - + -
395X ARG* 2.9 35.9 - - + +
396X LEU* 2.8 9.2 + - + +
398X THR* 1.3 78.6 - - - +
400X MET* 1.3 68.5 + - + +
402X ARG* 3.1 15.9 + - - +
403X LEU* 3.1 13.3 + - + +
430X LEU* 5.7 11.5 - - + +
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Residues in contact with MET 400 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345X LEU* 4.7 5.8 - - + -
352X LEU* 3.8 36.3 - - + +
353X THR* 4.7 6.5 - - + +
356X TYR* 4.0 22.7 - - + -
369X PHE* 3.9 33.0 - - + -
377X ILE* 3.9 29.6 - - + -
396X LEU* 2.8 19.5 + - + +
397X HIS* 3.8 5.8 - - - +
399X VAL* 1.3 71.6 - - - +
401X GLU* 1.3 53.5 + - - +
403X LEU* 2.6 41.0 + - + +
404X MET* 2.7 23.9 + - + +
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Residues in contact with GLU 401 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ILE* 4.0 17.7 - - - +
33W ASN* 5.2 7.3 + - - -
51W LYS* 3.3 14.3 - - + +
328W PRO* 4.4 14.6 - - + +
329W ILE* 3.1 44.9 - - + +
356X TYR* 2.8 27.7 + - - +
397X HIS 3.0 16.0 + - - +
398X THR 4.0 7.0 - - - +
399X VAL 3.3 0.2 - - - -
400X MET* 1.3 76.3 - - - +
402X ARG* 1.3 58.9 + - - +
404X MET* 4.0 3.1 - - - +
405X ASP* 3.4 21.7 + - - +
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Residues in contact with ARG 402 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398X THR 3.6 9.3 + - - +
399X VAL* 3.1 11.6 + - - +
400X MET 3.0 1.0 - - - -
401X GLU* 1.3 77.0 - - - +
403X LEU* 1.3 65.2 + - - +
405X ASP* 3.2 34.1 + - - +
406X LYS* 4.8 0.5 + - - +
429X ALA 4.3 11.5 + - - +
430X LEU* 3.9 45.1 + - + +
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Residues in contact with LEU 403 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369X PHE* 5.3 0.9 - - + -
377X ILE* 3.5 33.7 - - + -
399X VAL* 3.1 13.4 + - + +
400X MET* 2.6 32.3 + - + +
402X ARG* 1.3 70.0 - - - +
404X MET* 1.3 72.8 + - - +
405X ASP 3.0 9.0 + - - -
406X LYS* 3.9 10.6 + - - +
407X ILE* 4.5 2.9 - - - +
421X ILE* 4.8 9.6 - - + -
425X TYR* 4.0 22.2 + - + -
426X VAL* 4.3 13.9 - - + -
429X ALA* 3.5 33.5 - - + +
430X LEU* 5.2 5.3 - - + +
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Residues in contact with MET 404 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356X TYR* 3.5 54.7 - - + +
360X MET* 4.9 3.4 - - + -
367X ILE* 4.2 12.3 - - + -
369X PHE* 3.3 35.2 - - + -
400X MET* 2.7 25.7 + - + +
401X GLU* 4.0 5.4 - - - +
403X LEU* 1.3 85.0 - - - +
405X ASP* 1.3 57.8 + - - +
406X LYS 3.3 2.0 - - - -
407X ILE* 3.3 25.8 - - + -
408X SER* 2.9 32.6 + - - -
421X ILE* 4.3 8.3 - - + -
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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
------------------------------------------------------------
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