Contacts of the helix formed by residues 393 - 404 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E GLY 3.1 9.5 + - - +
336E LEU* 3.9 11.1 - - + +
341E PHE* 4.0 14.0 - - + -
344E ILE* 5.4 1.8 - - + -
391E ILE 3.5 0.2 + - - -
392E GLY* 1.3 67.4 - - - -
394E ARG* 1.3 67.8 + - - +
395E ARG 2.9 2.2 - - - -
396E LEU* 2.9 27.6 + - + +
397E HIS* 3.9 5.9 - - - -
454E ATP 3.4 45.1 - - + +
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Residues in contact with ARG 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLY* 4.9 2.2 + - - -
391E ILE* 3.4 29.1 + - + +
392E GLY 3.2 0.6 - - - -
393E ALA* 1.3 77.5 - - - +
395E ARG* 1.3 53.9 + - - +
396E LEU 2.7 1.0 + - - -
397E HIS* 2.7 65.6 + - - +
398E THR* 3.1 9.4 + - - -
454E ATP 4.4 31.8 + - - -
49F THR* 5.4 3.4 + - - -
287F GLU* 5.0 5.3 - - - +
321F PRO 5.8 1.1 - - - +
322F GLU* 5.4 4.7 + - - +
325F GLY* 4.0 25.2 + - - +
326F ARG* 3.4 44.9 - - - +
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Residues in contact with ARG 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E PHE* 5.0 0.2 - - + -
381E ALA* 3.5 30.7 - - + +
384E VAL* 3.5 26.9 - - - +
385E ASN* 2.6 31.1 + - - +
388E THR* 3.9 10.7 + - - -
389E GLU* 2.7 36.6 + - - +
391E ILE* 3.6 25.4 - - + +
392E GLY 3.3 11.1 + - - +
393E ALA 2.9 0.4 - - - -
394E ARG* 1.3 77.5 - - - +
396E LEU* 1.3 57.7 + - - +
398E THR* 3.7 25.2 + - - +
399E VAL* 3.0 26.8 + - - +
402E ARG* 6.0 0.4 - - - +
324F GLN* 4.7 8.5 + - - +
330F ARG* 5.8 3.4 - - - +
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Residues in contact with LEU 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341E PHE* 3.8 39.0 - - + +
344E ILE* 4.1 23.1 - - + -
345E LEU* 4.1 27.8 - - + +
352E LEU* 3.5 17.9 - - + -
377E ILE* 4.9 3.4 - - + +
378E ALA* 4.4 1.8 - - - -
381E ALA* 3.1 28.9 - - + -
393E ALA* 2.9 19.1 + - + +
394E ARG 2.7 4.9 + - - -
395E ARG* 1.3 72.5 - - - +
397E HIS* 1.3 67.8 + - + +
398E THR 2.9 1.6 - - - -
399E VAL* 4.6 1.3 - - - -
400E MET* 2.8 29.0 + - + +
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Residues in contact with HIS 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E LEU* 4.0 35.2 - - + +
355E GLN* 5.2 5.8 - - - -
356E TYR* 4.7 1.4 + - - -
393E ALA 3.9 14.6 - - - -
394E ARG* 2.7 47.7 + - - +
396E LEU* 1.3 72.6 - - + +
398E THR* 1.3 61.9 + - - +
400E MET* 4.0 1.1 - - - +
401E GLU* 3.2 23.7 + - - +
454E ATP 4.3 20.6 + - - -
49F THR* 5.4 5.4 + - - -
51F LYS* 4.1 19.0 + - + +
325F GLY 5.1 4.9 - - - +
328F PRO* 4.6 9.0 - - + +
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Residues in contact with THR 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391E ILE* 4.5 9.9 - - - +
394E ARG 3.1 9.3 + - - -
395E ARG* 3.5 34.7 + - - +
396E LEU 2.9 0.6 - - - -
397E HIS* 1.3 76.4 - - - +
399E VAL* 1.3 74.8 + - + +
401E GLU* 3.2 5.5 + - - +
402E ARG* 3.0 32.3 + - + +
324F GLN 4.9 2.1 + - - -
325F GLY* 4.7 9.5 + - - -
328F PRO* 4.5 24.2 + - - +
330F ARG* 5.7 1.6 + - - -
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Residues in contact with VAL 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E ILE* 4.1 25.1 - - + +
380E ALA* 4.7 3.4 - - + -
381E ALA* 3.8 24.5 - - + +
384E VAL* 4.8 2.9 - - + -
395E ARG* 3.0 21.4 + - + +
396E LEU* 4.0 3.8 - - - +
398E THR* 1.3 80.4 - - + +
400E MET* 1.3 70.3 + - - +
402E ARG* 3.1 24.6 + - - +
403E LEU* 2.9 18.7 + - + +
430E LEU* 3.9 26.4 - - + +
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Residues in contact with MET 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E LEU* 4.7 2.5 - - + -
352E LEU* 3.5 22.0 - - + -
353E THR* 3.7 35.4 - - + +
356E TYR* 3.4 45.5 - - + +
369E PHE* 3.9 13.0 - - + -
377E ILE* 3.7 36.6 - - + -
396E LEU* 2.8 24.4 + - - +
397E HIS* 4.0 2.9 - - - +
399E VAL* 1.3 72.2 - - - +
401E GLU* 1.3 56.2 + - - +
403E LEU* 2.6 32.5 + - - -
404E MET* 2.8 13.5 + - + +
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Residues in contact with GLU 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR* 2.7 32.0 + - - +
397E HIS 3.2 16.3 + - - +
398E THR 3.8 3.4 - - - +
400E MET* 1.3 78.2 - - - +
402E ARG* 1.3 63.0 + - - +
404E MET* 4.7 3.0 - - - +
405E ASP* 3.4 21.1 + - - +
408E SER* 4.4 13.9 + - - -
29F ILE* 4.3 18.4 - - - +
33F ASN* 4.8 4.1 + - - -
51F LYS* 3.1 33.6 - - + +
328F PRO* 4.4 11.7 - - + -
329F ILE* 3.7 26.8 - - + +
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Residues in contact with ARG 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E VAL* 5.5 7.9 - - - +
395E ARG* 6.0 0.2 - - - +
398E THR* 3.0 23.7 + - - +
399E VAL* 3.3 32.6 - - - +
400E MET 2.8 0.8 + - - -
401E GLU* 1.3 79.3 - - - +
403E LEU* 1.3 56.3 + - - +
405E ASP* 3.1 27.1 - - - +
406E LYS* 3.8 7.6 + - - -
429E ALA 4.2 5.8 - - - +
430E LEU* 3.9 46.3 + - + +
433E VAL* 4.0 25.2 - - - +
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Residues in contact with LEU 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E PHE* 4.6 2.0 - - + -
377E ILE* 3.2 40.8 - - + -
399E VAL* 2.9 11.0 + - + +
400E MET* 2.6 14.5 + - - +
402E ARG* 1.3 69.8 - - - +
404E MET* 1.3 102.3 + - + +
405E ASP* 2.7 17.9 + - - +
406E LYS* 4.3 5.2 + - - +
407E ILE* 5.3 1.6 + - + +
421E ILE* 4.3 12.3 - - + -
425E TYR* 5.1 9.8 + - + -
426E VAL* 3.6 23.1 - - + -
429E ALA* 3.9 23.3 - - + +
430E LEU* 3.8 15.9 - - + +
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Residues in contact with MET 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR* 3.7 56.5 - - + +
360E MET* 4.0 18.6 - - + -
367E ILE* 3.5 24.0 - - + -
369E PHE* 4.0 6.1 - - - -
400E MET* 2.8 13.2 + - + +
401E GLU* 4.0 4.5 - - - +
403E LEU* 1.3 100.4 - - + +
405E ASP* 1.3 68.9 + - - +
406E LYS 3.7 0.4 - - - -
407E ILE* 4.3 14.8 - - + -
408E SER* 2.9 23.3 + - - -
421E ILE* 3.6 18.4 - - - -
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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