Contacts of the helix formed by residues 393 - 404 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60V GLY 3.4 7.6 + - - +
336V LEU* 3.5 13.4 - - + +
341V PHE* 4.1 8.1 - - - -
344V ILE* 5.0 2.2 - - + -
391V ILE 3.8 0.6 + - - -
392V GLY* 1.3 69.6 - - - -
394V ARG* 1.3 52.5 + - - +
395V ARG 2.6 0.3 + - - -
396V LEU* 2.6 47.8 + - + +
397V HIS* 3.9 3.5 + - - +
459V ATP 3.1 50.5 - - + +
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Residues in contact with ARG 394 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287U GLU* 2.8 34.1 + - - +
321U PRO 5.0 0.4 - - - -
322U GLU* 3.3 44.8 + - - +
325U GLY* 4.0 16.3 - - - +
326U ARG* 3.5 31.7 - - - +
59V THR* 5.1 3.2 - - - +
60V GLY* 5.8 0.7 - - - -
391V ILE* 4.1 22.0 + - + +
392V GLY 3.1 0.4 + - - -
393V ALA* 1.3 76.7 - - - +
395V ARG* 1.3 61.6 + - - +
396V LEU 3.2 0.2 - - - -
397V HIS* 3.4 28.6 + - - +
398V THR* 3.5 12.0 - - - +
459V ATP 2.9 61.1 + - - +
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Residues in contact with ARG 395 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324U GLN* 5.4 4.2 + - - +
330U ARG* 6.0 1.4 - - - +
341V PHE* 4.7 2.2 - - + -
381V ALA* 3.2 28.7 - - - +
384V VAL* 3.2 32.7 - - - +
385V ASN* 2.8 20.1 - - - +
388V THR* 4.6 5.5 + - - -
389V GLU* 3.1 31.1 + - - +
391V ILE* 3.3 28.1 - - + +
392V GLY 2.8 17.9 + - - +
393V ALA 2.6 4.6 + - - -
394V ARG* 1.3 72.8 - - - +
396V LEU* 1.3 64.2 + - - +
398V THR* 2.4 36.2 + - - +
399V VAL* 2.8 16.4 - - + +
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Residues in contact with LEU 396 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341V PHE* 3.3 44.4 - - + +
344V ILE* 4.1 26.7 - - + -
345V LEU* 3.7 27.1 - - + -
352V LEU* 3.5 17.3 - - + -
377V ILE* 3.9 12.3 - - + +
381V ALA* 3.8 13.0 - - + -
393V ALA* 2.6 23.4 + - + +
395V ARG* 1.3 71.9 - - - +
397V HIS* 1.3 65.7 + - + +
399V VAL* 2.7 17.8 + - + +
400V MET* 2.8 16.8 + - + +
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Residues in contact with HIS 397 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49U THR* 6.5 0.4 - - - -
51U LYS* 5.2 18.4 - - + +
325U GLY 4.7 6.4 + - - +
326U ARG* 5.5 7.8 + - - -
328U PRO* 4.3 15.2 - - + +
352V LEU* 3.6 35.0 - - + +
355V GLN* 5.8 0.6 + - - -
356V TYR* 6.4 0.2 - - - -
393V ALA* 4.5 7.4 + - - +
394V ARG* 3.4 19.0 + - + +
395V ARG 3.3 0.6 - - - -
396V LEU* 1.3 77.0 - - + +
398V THR* 1.3 63.5 + - - +
400V MET* 3.3 4.3 + - - +
401V GLU* 3.0 24.4 + - - +
459V ATP 3.1 37.0 + - - -
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Residues in contact with THR 398 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324U GLN 4.1 14.6 - - - +
325U GLY* 4.3 3.8 - - - -
328U PRO* 3.5 44.3 - - + +
330U ARG* 5.4 2.9 - - - +
391V ILE* 4.9 3.4 - - + -
394V ARG 3.5 14.1 - - - +
395V ARG* 2.4 41.5 + - - +
397V HIS* 1.3 75.7 - - - +
399V VAL* 1.3 61.7 + - - +
401V GLU* 4.0 3.3 - - - +
402V ARG* 3.6 16.8 + - - +
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Residues in contact with VAL 399 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377V ILE* 4.2 26.7 - - + +
380V ALA* 4.6 13.5 - - + +
381V ALA* 3.8 21.8 - - + -
384V VAL* 5.6 1.8 - - + -
395V ARG* 2.8 35.4 - - + +
396V LEU* 2.7 9.9 + - + +
398V THR* 1.3 78.3 - - - +
400V MET* 1.3 67.7 + - + +
402V ARG* 3.1 17.4 + - - +
403V LEU* 3.1 13.1 + - + +
430V LEU* 5.7 10.9 - - + +
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Residues in contact with MET 400 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345V LEU* 4.7 5.8 - - + -
352V LEU* 3.8 34.8 - - + -
353V THR* 4.7 6.5 - - + +
356V TYR* 4.0 23.3 - - + -
369V PHE* 4.0 33.4 - - + -
377V ILE* 3.9 29.4 - - + -
396V LEU* 2.8 18.6 + - + +
397V HIS* 3.8 6.1 - - - +
399V VAL* 1.3 73.0 - - - +
401V GLU* 1.3 53.9 + - - +
403V LEU* 2.6 39.9 + - + +
404V MET* 2.7 24.0 + - + +
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Residues in contact with GLU 401 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ILE* 4.0 17.2 - - - +
33U ASN* 5.3 5.7 + - - -
51U LYS* 3.5 13.2 - - + +
328U PRO* 4.4 12.8 - - + +
329U ILE* 3.2 44.3 - - + +
356V TYR* 2.8 29.4 + - - +
397V HIS 3.0 17.4 + - - +
398V THR* 4.0 9.4 - - - +
399V VAL 3.3 0.2 - - - -
400V MET* 1.3 75.6 - - - +
402V ARG* 1.3 60.8 + - - +
404V MET* 4.0 2.8 - - - +
405V ASP* 3.4 21.3 + - - +
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Residues in contact with ARG 402 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398V THR 3.6 9.7 + - - +
399V VAL* 3.1 11.6 + - - +
400V MET 3.0 0.6 - - - -
401V GLU* 1.3 77.7 - - - +
403V LEU* 1.3 60.8 + - - +
405V ASP* 3.1 38.1 + - - +
406V LYS 4.7 0.3 + - - -
429V ALA 4.4 11.6 + - - +
430V LEU* 3.9 45.5 + - + +
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Residues in contact with LEU 403 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369V PHE* 5.3 0.9 - - + -
377V ILE* 3.5 34.3 - - + -
399V VAL* 3.1 12.5 + - + +
400V MET* 2.6 32.5 + - + +
402V ARG* 1.3 69.7 - - - +
404V MET* 1.3 70.8 + - - +
405V ASP 3.0 8.6 + - - -
406V LYS* 3.9 8.5 + - - +
407V ILE* 4.5 3.3 - - - +
421V ILE* 4.8 9.9 - - + -
425V TYR* 4.0 24.4 + - + -
426V VAL* 4.3 13.7 - - + -
429V ALA* 3.6 32.4 - - + +
430V LEU* 5.2 6.0 - - + +
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Residues in contact with MET 404 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U ILE* 6.0 0.2 - - - +
356V TYR* 3.5 53.6 - - + +
360V MET* 4.9 3.4 - - + -
367V ILE* 4.3 12.6 - - + -
369V PHE* 3.3 34.1 - - + -
400V MET* 2.7 24.9 + - + +
401V GLU* 4.0 5.6 - - - +
403V LEU* 1.3 86.5 - - - +
405V ASP* 1.3 58.0 + - - +
406V LYS 3.3 2.0 - - - -
407V ILE* 3.3 25.4 - - + -
408V SER* 3.0 33.0 + - - -
421V ILE* 4.3 8.5 - - + -
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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