Contacts of the helix formed by residues 393 - 404 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60U GLY 3.5 16.6 + - - +
336U LEU* 3.5 15.5 - - + +
341U PHE* 4.0 11.0 - - - -
344U ILE* 5.0 0.9 - - + -
391U ILE 3.8 0.4 + - - -
392U GLY* 1.3 70.1 - - - -
394U ARG* 1.3 53.4 + - - +
395U ARG 2.6 0.2 + - - -
396U LEU* 2.5 47.5 + - + +
397U HIS* 3.9 5.4 + - - +
458U ATP 3.8 36.3 - - + +
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Residues in contact with ARG 394 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287T GLU* 2.9 33.7 + - - +
321T PRO 4.8 0.6 + - - -
322T GLU* 3.3 45.7 + - - +
325T GLY* 4.0 16.5 - - - +
326T ARG* 3.6 31.6 - - - +
59U THR* 5.0 4.9 - - - +
60U GLY* 5.5 1.1 - - - -
391U ILE* 4.0 21.9 + - + +
392U GLY 3.2 0.2 - - - -
393U ALA* 1.3 75.4 - - - +
395U ARG* 1.3 61.3 + - - +
396U LEU 3.2 0.4 - - - -
397U HIS* 3.3 31.0 + - - +
398U THR* 3.5 11.6 + - - +
458U ATP 3.5 57.7 + - - +
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Residues in contact with ARG 395 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324T GLN* 5.3 3.8 + - - -
330T ARG* 5.9 2.8 - - - +
341U PHE* 4.7 2.2 - - + -
381U ALA* 3.1 28.9 - - + +
384U VAL* 3.2 31.9 - - - +
385U ASN* 2.7 19.9 - - - +
388U THR* 4.6 5.5 + - - -
389U GLU* 3.1 30.5 + - - +
391U ILE* 3.3 28.3 - - + +
392U GLY 2.8 17.7 + - - +
393U ALA 2.6 5.7 + - - -
394U ARG* 1.3 72.1 - - - +
396U LEU* 1.3 64.3 + - - +
398U THR* 2.5 34.8 + - - +
399U VAL* 2.9 18.3 - - + +
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Residues in contact with LEU 396 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341U PHE* 3.3 44.4 - - + +
344U ILE* 4.0 26.9 - - + -
345U LEU* 3.8 26.2 - - + -
352U LEU* 3.5 17.7 - - + -
377U ILE* 3.9 12.6 - - + +
381U ALA* 3.7 13.2 - - + -
393U ALA* 2.5 22.5 + - + +
395U ARG* 1.3 72.3 - - - +
397U HIS* 1.3 65.4 + - + +
399U VAL* 2.7 18.3 + - + +
400U MET* 2.8 16.6 + - + +
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Residues in contact with HIS 397 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51T LYS* 5.3 15.3 - - + +
325T GLY 4.5 6.5 + - - -
326T ARG* 5.5 7.9 - - - -
328T PRO* 4.2 15.8 - - + +
352U LEU* 3.6 35.0 - - + +
355U GLN* 5.8 0.6 + - - -
356U TYR* 5.2 1.9 + - - -
393U ALA* 4.5 8.3 + - - +
394U ARG* 3.5 22.0 + - + +
395U ARG 3.3 0.4 - - - -
396U LEU* 1.3 77.6 - - + +
398U THR* 1.3 62.4 + - - +
400U MET* 3.2 4.2 + - - +
401U GLU* 3.0 24.4 + - - +
458U ATP 4.0 27.3 + - - -
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Residues in contact with THR 398 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324T GLN 4.0 14.8 - - - +
325T GLY* 4.4 2.7 - - - -
328T PRO* 3.5 44.9 - - + +
330T ARG* 5.2 4.0 - - - +
391U ILE* 4.9 4.3 - - + -
394U ARG 3.6 13.0 - - - +
395U ARG* 2.5 39.0 + - - +
397U HIS* 1.3 74.8 - - - +
399U VAL* 1.3 62.8 + - - +
401U GLU* 3.9 3.3 + - - +
402U ARG* 3.6 16.8 + - - +
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Residues in contact with VAL 399 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377U ILE* 4.3 26.7 - - + +
380U ALA* 4.7 11.7 - - + +
381U ALA* 3.7 21.5 - - + -
384U VAL* 5.6 2.2 - - + -
395U ARG* 2.9 36.1 - - + +
396U LEU* 2.7 9.8 + - + +
398U THR* 1.3 77.3 - - - +
400U MET* 1.3 66.6 + - + +
402U ARG* 3.1 15.7 + - - +
403U LEU* 3.1 12.9 + - + +
430U LEU* 5.7 10.7 - - + +
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Residues in contact with MET 400 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345U LEU* 4.7 5.4 - - + -
352U LEU* 3.8 35.2 - - + -
353U THR* 4.7 6.7 - - + +
356U TYR* 4.0 24.2 - - + -
369U PHE* 4.0 33.0 - - + -
377U ILE* 3.9 30.1 - - + -
396U LEU* 2.8 19.1 + - - +
397U HIS* 3.8 6.3 - - - +
399U VAL* 1.3 72.8 - - + +
401U GLU* 1.3 54.0 + - - +
403U LEU* 2.6 40.1 + - + +
404U MET* 2.7 23.0 + - + +
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Residues in contact with GLU 401 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T ILE* 3.9 18.4 - - - +
33T ASN* 5.3 5.8 + - - -
51T LYS* 3.5 13.1 - - + +
328T PRO* 4.4 11.9 - - + +
329T ILE* 3.1 45.5 - - + +
356U TYR* 2.8 29.2 + - - +
397U HIS 3.0 17.0 + - - +
398U THR* 3.9 9.2 - - - +
399U VAL 3.3 0.2 - - - -
400U MET* 1.3 76.3 - - - +
402U ARG* 1.3 59.8 + - - +
404U MET* 4.0 3.9 - - - +
405U ASP* 3.4 21.8 + - - +
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Residues in contact with ARG 402 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398U THR 3.6 9.9 + - - +
399U VAL* 3.1 11.3 + - - +
400U MET 3.0 0.8 - - - -
401U GLU* 1.3 78.1 - - - +
403U LEU* 1.3 64.3 + - - +
405U ASP* 3.1 34.1 + - - +
406U LYS 4.8 0.2 + - - -
429U ALA 4.3 11.3 + - - +
430U LEU* 4.0 45.1 + - + +
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Residues in contact with LEU 403 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369U PHE* 5.3 0.7 - - + -
377U ILE* 3.5 34.1 - - + -
399U VAL* 3.1 12.8 + - + +
400U MET* 2.6 33.0 + - + +
402U ARG* 1.3 69.8 - - - +
404U MET* 1.3 72.2 + - - +
405U ASP 3.0 9.2 + - - -
406U LYS* 3.9 8.5 + - - +
407U ILE* 4.5 2.4 - - - +
421U ILE* 4.8 8.7 - - + -
425U TYR* 3.9 25.6 + - + -
426U VAL* 4.2 13.0 - - + -
429U ALA* 3.5 33.5 - - + +
430U LEU* 5.2 5.6 - - + +
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Residues in contact with MET 404 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356U TYR* 3.5 54.3 - - + +
360U MET* 4.9 3.1 - - + -
367U ILE* 4.2 12.6 - - + -
369U PHE* 3.3 34.5 - - + -
400U MET* 2.7 25.1 + - + +
401U GLU* 4.0 5.2 - - - +
403U LEU* 1.3 87.1 - - - +
405U ASP* 1.3 56.9 + - - +
406U LYS 3.3 2.0 - - - -
407U ILE* 3.4 26.5 - - + -
408U SER* 3.0 32.0 + - - -
421U ILE* 4.3 7.9 - - + -
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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