Contacts of the helix formed by residues 370 - 388 (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 THR 370 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368E ALA 4.5 2.5 - - - +
369E PHE* 1.3 76.0 - - - +
371E THR* 1.3 56.8 + - - +
372E ASP* 3.5 8.8 + - - +
373E ALA* 2.6 44.0 + - - +
374E VAL* 2.9 5.9 + - - +
420E ASN* 4.2 16.6 - - - +
421E ILE 3.0 18.8 + - - +
422E ASP* 3.6 22.6 - - + +
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Residues in contact with THR 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E PHE 4.2 1.0 + - - -
370E THR* 1.3 69.2 - - - +
372E ASP* 1.3 70.6 + - - +
374E VAL* 2.8 12.7 + - + +
375E LYS* 2.7 27.2 + - + +
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Residues in contact with ASP 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370E THR* 3.3 7.3 + - - +
371E THR* 1.3 82.6 - - - +
373E ALA* 1.3 56.2 + - - +
375E LYS* 3.5 17.8 - - - +
376E LYS* 2.8 29.5 + - - +
423E ALA* 4.2 18.3 - - + +
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Residues in contact with ALA 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E PHE* 4.5 4.7 - - + -
370E THR* 2.6 29.7 + - - +
372E ASP* 1.3 68.9 - - - +
374E VAL* 1.3 59.0 + - - +
376E LYS* 3.0 4.9 + - - +
377E ILE* 2.7 34.6 + - - +
421E ILE* 3.1 30.5 - - + +
422E ASP 3.7 10.8 - - - +
423E ALA 4.0 7.5 - - - +
426E VAL* 4.0 8.7 - - + -
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Residues in contact with VAL 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E GLU* 3.6 31.2 - - + +
345E LEU* 4.0 15.9 - - + -
346E THR* 3.8 22.4 - - + -
353E THR* 4.6 8.7 - - + -
369E PHE* 4.2 19.7 - - + -
370E THR 2.9 11.4 + - - +
371E THR* 2.8 14.9 + - + +
373E ALA* 1.3 73.3 - - - +
375E LYS* 1.3 65.1 + - - +
377E ILE* 3.7 7.4 - - + +
378E ALA* 3.0 23.6 + - - +
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Residues in contact with LYS 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E GLU* 3.7 38.6 - - - +
371E THR* 2.7 21.6 + - + +
372E ASP* 3.5 21.8 - - - +
374E VAL* 1.3 72.4 - - - +
376E LYS* 1.3 57.4 + - - +
378E ALA* 3.9 1.4 - - - +
379E GLU* 2.9 55.5 + - - +
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Residues in contact with LYS 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E ASP 2.8 18.6 + - - +
373E ALA* 3.0 8.0 + - - +
375E LYS* 1.3 73.8 - - - +
377E ILE* 1.3 68.5 + - - +
379E GLU* 3.0 11.2 + - + +
380E ALA* 2.8 28.4 + - + +
423E ALA* 4.3 11.4 - - + +
426E VAL* 3.9 21.1 - - + -
427E ALA* 3.8 30.0 - - + +
430E LEU* 6.1 1.8 - - + -
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Residues in contact with ILE 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E LEU* 3.6 20.0 - - + -
353E THR* 5.5 1.1 - - + -
369E PHE* 4.2 17.9 - - + -
373E ALA 2.7 24.5 + - - +
374E VAL* 3.7 8.1 - - + +
376E LYS* 1.3 71.0 - - - +
378E ALA* 1.3 65.2 + - - +
380E ALA* 3.0 8.6 - - - +
381E ALA* 2.9 20.3 + - - +
396E LEU* 5.0 3.8 - - + -
399E VAL* 4.1 18.5 - - + +
400E MET* 3.7 29.2 - - + -
403E LEU* 3.2 24.2 - - + -
426E VAL* 3.4 26.0 - - + -
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Residues in contact with ALA 378 (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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338E ALA 3.9 1.6 - - - +
341E PHE* 3.6 29.1 - - + -
342E GLU* 3.6 22.9 - - + +
345E LEU* 3.8 11.4 - - + -
374E VAL 3.0 16.0 + - - +
377E ILE* 1.3 73.8 - - - +
379E GLU* 1.3 70.0 + - - +
380E ALA 2.5 3.3 + - - -
381E ALA* 2.8 17.1 + - - +
382E PHE* 3.0 12.2 + - - +
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Residues in contact with GLU 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E ALA* 4.3 18.8 + - + +
342E GLU* 4.0 12.2 - - - +
375E LYS* 2.9 55.0 + - - +
376E LYS* 3.5 10.5 - - + +
378E ALA* 1.3 72.9 - - - +
380E ALA* 1.3 50.5 + - - +
382E PHE* 3.6 7.4 - - - +
383E ARG* 2.8 33.5 + - - +
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Residues in contact with ALA 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E LYS* 2.8 15.4 + - + +
377E ILE 3.0 14.1 - - - +
378E ALA 2.5 4.0 + - - -
379E GLU* 1.3 70.8 - - - +
381E ALA* 1.3 67.3 + - - +
383E ARG* 2.9 23.3 + - - +
384E VAL* 3.1 9.3 + - - +
399E VAL* 4.7 2.7 - - + -
430E LEU* 3.6 30.1 - - + -
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Residues in contact with ALA 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E PHE* 3.7 8.3 - - + -
377E ILE 2.9 8.7 + - - +
378E ALA 2.8 9.2 + - - +
380E ALA* 1.3 72.7 - - - +
382E PHE* 1.3 66.5 + - - +
384E VAL* 2.8 16.5 - - - +
385E ASN* 3.1 4.7 + - - +
395E ARG* 3.5 27.5 - - + +
396E LEU* 3.1 35.4 - - + -
399E VAL* 3.8 10.2 - - + +
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Residues in contact with PHE 382 (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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336E LEU 4.3 6.5 - - - -
337E SER* 3.6 15.3 - - - -
338E ALA* 2.9 43.1 - - + -
341E PHE* 3.2 17.5 - + + -
378E ALA 3.0 6.3 + - - +
379E GLU 3.6 8.3 - - - +
381E ALA* 1.3 80.6 - - - +
383E ARG* 1.3 72.8 + - - +
385E ASN* 3.0 6.9 + - + +
386E GLU* 3.0 49.5 + - + -
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Residues in contact with ARG 383 (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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379E GLU 2.8 20.6 + - - +
380E ALA* 2.9 20.8 + - - +
382E PHE* 1.3 77.8 - - - +
384E VAL* 1.3 60.5 + - - +
386E GLU* 3.2 7.4 + - - +
387E LYS* 3.0 58.1 + - + +
433E VAL 5.8 3.6 - - - +
434E VAL* 4.4 15.8 - - - +
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Residues in contact with VAL 384 (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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380E ALA 3.3 8.3 - - - +
381E ALA* 2.8 20.6 - - - +
383E ARG* 1.3 72.8 - - + +
385E ASN* 1.3 69.2 + - - +
386E GLU 2.9 1.8 - - - -
387E LYS* 2.6 20.5 + - - +
388E THR* 2.7 33.7 + - + +
395E ARG* 3.5 35.4 - - + +
399E VAL* 4.8 5.6 - - + -
402E ARG* 5.5 7.0 - - - +
433E VAL* 5.7 11.2 - - + +
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Residues in contact with ASN 385 (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* 4.0 10.1 - - - -
381E ALA 3.1 5.4 + - - +
382E PHE* 3.0 12.9 + - + +
384E VAL* 1.3 81.9 - - - +
386E GLU* 1.3 62.3 + - - +
388E THR 3.2 17.7 - - - +
390E ASN* 3.3 38.4 + - - +
391E ILE 3.6 3.9 + - - -
392E GLY* 2.7 40.2 + - - +
395E ARG* 2.6 46.3 + - - +
68K GLN* 3.5 3.8 + - - +
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Residues in contact with GLU 386 (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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382E PHE* 3.0 35.9 + - + +
383E ARG* 3.3 11.5 + - - +
384E VAL 2.8 1.4 + - - -
385E ASN* 1.3 78.4 - - - +
387E LYS* 1.3 87.3 + - + +
390E ASN* 4.7 2.2 - - - +
68K GLN* 3.9 8.4 + - - +
70K HIS* 3.1 31.7 + - + -
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Residues in contact with LYS 387 (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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383E ARG* 3.0 54.1 + - + +
384E VAL* 2.6 14.6 + - - +
386E GLU* 1.3 98.3 + - + +
388E THR* 1.3 68.1 + - + +
433E VAL 5.4 7.2 - - - +
434E VAL* 5.1 6.6 - - + +
435E GLU* 3.6 50.1 + - + +
70K HIS* 4.5 9.2 + - - -
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Residues in contact with THR 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E VAL* 2.7 37.2 + - + +
385E ASN 3.2 2.1 - - - +
387E LYS* 1.3 87.8 - - + +
389E GLU* 1.3 61.1 + - - -
390E ASN 3.5 0.7 - - - -
395E ARG* 3.9 5.0 + - - -
435E GLU* 5.1 7.6 - - + -
68K GLN* 2.7 29.8 - - - +
70K HIS* 4.1 6.6 + - - -
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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