Contacts of the helix formed by residues 393 - 404 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY 3.1 9.0 + - - +
336A LEU* 3.9 9.1 - - + +
341A PHE* 3.7 17.8 - - + -
344A ILE* 5.3 2.5 - - + -
391A ILE 3.4 0.2 + - - -
392A GLY* 1.3 68.1 - - - -
394A ARG* 1.3 67.2 + - - +
395A ARG 2.9 2.2 - - - -
396A LEU* 2.8 24.9 + - + +
397A HIS* 3.9 5.2 + - - -
450A ATP 3.4 42.4 - - + +
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Residues in contact with ARG 394 (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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60A GLY* 6.2 1.8 - - - -
391A ILE* 3.3 28.1 + - + +
392A GLY 3.2 0.8 - - - -
393A ALA* 1.3 76.7 - - - +
395A ARG* 1.3 53.6 + - - +
396A LEU 2.6 1.2 + - - -
397A HIS* 2.6 68.2 + - - +
398A THR* 3.2 8.0 + - - -
450A ATP 3.7 34.6 + - - +
49B THR* 5.3 4.2 + - - -
287B GLU* 5.0 6.1 + - - +
321B PRO 5.6 1.3 - - - +
322B GLU* 5.3 4.9 - - - +
325B GLY* 3.9 23.9 + - - +
326B ARG* 3.6 44.2 - - - +
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PHE* 5.1 0.2 - - + -
381A ALA* 3.5 31.4 - - + +
384A VAL* 3.6 30.0 - - + +
385A ASN* 2.6 27.7 + - - +
388A THR* 4.0 3.8 + - - -
389A GLU* 2.7 35.0 + - - +
391A ILE* 3.6 26.2 - - + +
392A GLY 3.3 11.7 + - - +
394A ARG* 1.3 78.1 - - - +
396A LEU* 1.3 60.7 + - - +
398A THR* 3.3 24.8 + - - +
399A VAL* 3.0 24.4 + - + +
402A ARG* 6.0 0.4 - - - +
324B GLN* 4.6 8.1 + - - +
330B ARG* 5.4 7.7 - - - +
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Residues in contact with LEU 396 (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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341A PHE* 3.5 48.5 - - + +
344A ILE* 4.2 13.5 - - + -
345A LEU* 4.2 24.9 - - + -
352A LEU* 3.5 17.9 - - + -
377A ILE* 4.8 4.7 - - + +
378A ALA* 4.4 2.9 - - - -
381A ALA* 3.2 28.5 - - + -
393A ALA* 2.8 18.1 + - + +
394A ARG 2.6 4.6 + - - -
395A ARG* 1.3 68.5 - - - +
397A HIS* 1.3 67.8 + - + +
398A THR 2.9 1.6 - - - -
399A VAL* 4.1 0.8 - - - +
400A MET* 2.8 28.5 + - + +
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.0 31.2 - - + +
355A GLN* 5.2 6.1 - - - -
356A TYR* 4.8 1.6 + - - -
393A ALA 4.0 10.1 - - - -
394A ARG* 2.6 53.8 + - - +
396A LEU* 1.3 74.3 - - + +
398A THR* 1.3 62.6 + - - +
400A MET* 3.9 1.8 - - - +
401A GLU* 3.2 20.8 + - - +
450A ATP 4.2 21.3 + - - -
49B THR* 5.2 6.0 + - - -
51B LYS* 3.9 25.0 + - - +
325B GLY 5.2 4.7 - - - +
328B PRO* 4.5 8.6 - - + +
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Residues in contact with THR 398 (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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391A ILE* 4.6 6.1 - - - +
394A ARG 3.2 6.2 + - - -
395A ARG* 3.3 40.7 + - - +
396A LEU 2.9 1.0 - - - -
397A HIS* 1.3 75.1 - - - +
399A VAL* 1.3 74.1 + - + +
401A GLU* 3.0 6.6 + - - +
402A ARG* 2.9 33.8 + - + +
324B GLN 5.0 1.6 + - - -
325B GLY* 4.7 7.8 + - - -
327B LEU 5.4 0.2 + - - -
328B PRO* 4.2 30.4 - - - +
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Residues in contact with VAL 399 (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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377A ILE* 4.3 22.9 - - + +
380A ALA* 4.8 2.7 - - + -
381A ALA* 4.0 24.0 - - + +
384A VAL* 4.8 3.1 - - + -
395A ARG* 3.0 18.9 + - + +
396A LEU* 4.1 2.2 - - - +
398A THR* 1.3 84.8 - - + +
400A MET* 1.3 64.6 + - - +
402A ARG* 3.0 24.5 + - - +
403A LEU* 2.9 20.9 + - + +
430A LEU* 3.7 34.3 - - + -
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Residues in contact with MET 400 (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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345A LEU* 4.5 4.7 - - + -
352A LEU* 3.4 28.7 - - + -
353A THR* 4.0 22.4 - - + +
356A TYR* 3.2 42.2 - - + -
369A PHE* 3.9 22.9 - - + -
377A ILE* 3.7 33.0 - - + -
396A LEU 2.8 13.9 + - - +
397A HIS* 3.9 4.7 - - - +
399A VAL* 1.3 76.6 - - - +
401A GLU* 1.3 52.6 + - - +
403A LEU* 2.8 10.9 + - - +
404A MET* 2.7 37.0 + - + +
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Residues in contact with GLU 401 (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 TYR* 2.5 30.5 + - - +
397A HIS 3.2 10.6 + - - +
398A THR 3.0 8.9 + - - +
400A MET* 1.3 77.9 - - - +
402A ARG* 1.3 63.8 + - - +
403A LEU 3.1 0.9 + - - -
404A MET* 4.5 2.7 - - - +
405A ASP* 3.2 24.3 + - - +
408A SER* 4.3 15.2 + - - -
29B ILE* 4.2 17.7 - - + +
33B ASN* 4.6 5.6 + - - -
51B LYS* 3.2 31.5 - - + +
328B PRO* 4.7 10.1 - - + -
329B ILE* 3.8 26.9 - - + -
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Residues in contact with ARG 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 5.3 9.7 - - - +
395A ARG* 6.0 0.2 - - - +
398A THR* 2.9 25.5 + - + +
399A VAL* 3.0 33.7 + - - +
401A GLU* 1.3 76.0 - - - +
403A LEU* 1.3 58.5 + - - +
405A ASP* 3.5 18.6 - - - +
406A LYS* 3.7 10.1 + - - +
429A ALA 3.7 6.9 - - - +
430A LEU* 4.0 46.3 + - + +
431A GLY 5.3 1.0 + - - -
432A GLU 4.9 8.7 + - - -
433A VAL* 5.3 9.1 - - - +
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Residues in contact with LEU 403 (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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369A PHE* 4.5 2.7 - - + -
377A ILE* 3.4 26.7 - - + -
399A VAL* 2.9 11.1 + - + +
400A MET* 2.8 10.1 + - - +
402A ARG* 1.3 77.2 - - - +
404A MET* 1.3 105.4 + - + +
405A ASP* 2.7 13.9 + - - +
406A LYS* 4.3 5.2 + - - +
407A ILE* 5.4 1.4 + - + +
421A ILE* 4.4 14.4 - - + -
425A TYR* 5.3 9.1 + - + -
426A VAL* 3.4 37.9 - - + -
429A ALA* 4.0 25.0 - - + +
430A LEU* 4.1 10.8 - - + -
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Residues in contact with MET 404 (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 TYR* 3.7 54.1 - - + -
360A MET* 4.0 18.4 - - + -
367A ILE* 3.5 23.8 - - + -
369A PHE* 4.1 4.5 - - - -
400A MET* 2.7 20.6 + - + +
401A GLU* 3.9 4.9 - - - +
403A LEU* 1.3 99.3 - - + +
405A ASP* 1.3 66.0 + - - +
406A LYS 3.7 0.7 - - - -
407A ILE* 4.0 14.4 - - + +
408A SER* 3.0 24.1 + - - -
421A ILE* 3.8 15.7 - - - -
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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