Contacts of the helix formed by residues 370 - 388 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F ALA 4.5 2.5 - - - +
369F PHE* 1.3 73.9 - - - +
371F THR* 1.3 56.9 + - - +
372F ASP* 3.3 10.3 + - - +
373F ALA* 2.4 43.3 + - - +
374F VAL* 3.0 5.0 + - - -
420F ASN* 4.1 16.6 - - - +
421F ILE 2.9 20.0 + - - +
422F ASP* 3.5 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 371 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369F PHE 4.0 1.4 + - - -
370F THR* 1.3 68.7 - - - +
372F ASP* 1.3 60.9 + - - +
374F VAL* 2.7 33.1 + - + +
375F LYS* 2.8 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 372 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F THR* 3.2 8.6 + - - +
371F THR* 1.3 82.5 - - - +
373F ALA* 1.3 57.2 + - - +
375F LYS* 3.8 18.1 - - - +
376F LYS* 2.9 29.3 + - - +
423F ALA* 4.1 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369F PHE* 4.4 6.7 - - + -
370F THR* 2.4 31.9 + - - +
372F ASP* 1.3 68.8 - - - +
374F VAL* 1.3 52.4 + - - +
376F LYS* 3.1 4.4 + - - +
377F ILE* 2.7 41.0 + - - +
421F ILE* 3.0 31.4 - - + +
422F ASP 3.7 10.1 - - - -
423F ALA 4.0 7.3 - - - +
426F VAL* 4.0 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F GLU* 3.7 31.2 - - + +
345F LEU* 3.9 17.3 - - + -
346F THR* 3.9 22.4 - - + -
353F THR* 4.8 7.6 - - + -
369F PHE* 4.3 17.9 - - + +
370F THR 3.0 9.9 + - - +
371F THR* 2.7 18.1 + - + +
373F ALA* 1.3 69.0 - - - +
375F LYS* 1.3 69.7 + - - +
376F LYS 2.9 1.0 + - - -
377F ILE* 2.9 9.2 + - + +
378F ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F GLU* 3.5 39.1 + - - +
371F THR* 2.8 19.2 + - + +
372F ASP* 3.8 21.3 - - - +
374F VAL* 1.3 76.9 - - - +
376F LYS* 1.3 57.3 + - - +
378F ALA* 4.0 0.7 - - - +
379F GLU* 2.9 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F ASP 2.9 19.9 + - - +
373F ALA* 3.3 7.2 - - - +
374F VAL 2.9 0.4 + - - -
375F LYS* 1.3 75.2 - - - +
377F ILE* 1.3 66.8 + - - +
379F GLU* 3.3 9.3 + - + +
380F ALA* 2.9 27.1 + - + +
423F ALA* 4.4 11.7 - - + +
426F VAL* 3.9 21.1 - - + -
427F ALA* 4.0 26.0 - - - +
430F LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F LEU* 3.7 15.5 - - + -
353F THR* 5.4 1.3 - - + -
369F PHE* 4.2 18.6 - - + -
373F ALA 2.7 25.9 + - - +
374F VAL* 3.5 8.1 - - + +
376F LYS* 1.3 71.4 - - - +
378F ALA* 1.3 58.8 + - - +
380F ALA* 2.9 25.8 - - - +
381F ALA* 3.0 9.2 + - - +
396F LEU* 5.0 3.4 - - + -
399F VAL* 4.0 19.2 - - + +
400F MET* 3.7 31.6 - - + -
403F LEU* 3.4 24.2 - - + -
426F VAL* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F ALA 3.9 6.3 - - - +
341F PHE* 3.5 29.0 - - + -
342F GLU* 3.6 21.5 - - + +
345F LEU* 3.9 10.7 - - + +
374F VAL 2.9 14.5 + - - +
377F ILE* 1.3 73.0 - - - +
379F GLU* 1.3 65.8 + - - +
380F ALA 2.6 5.4 + - - -
381F ALA* 2.8 12.1 + - - +
382F PHE* 3.1 13.8 + - - +
396F LEU* 4.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F ALA* 4.2 19.1 - - + +
342F GLU* 3.8 16.1 - - - +
375F LYS* 2.9 50.6 + - - +
376F LYS* 3.8 10.3 - - + +
378F ALA* 1.3 71.8 - - - +
380F ALA* 1.3 56.1 + - - +
382F PHE* 3.6 6.7 - - - +
383F ARG* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F LYS* 2.9 16.2 + - + +
377F ILE 2.9 15.5 - - - +
378F ALA 2.6 1.4 + - - -
379F GLU* 1.3 76.3 - - - +
381F ALA* 1.3 67.2 + - - +
383F ARG* 3.1 16.7 - - - +
384F VAL* 3.1 13.8 - - - +
399F VAL* 4.7 4.0 - - + -
430F LEU* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341F PHE* 3.7 10.1 - - + -
377F ILE 3.0 7.1 + - - +
378F ALA 2.8 5.0 + - - +
380F ALA* 1.3 69.7 - - - +
382F PHE* 1.3 68.2 + - - +
384F VAL* 2.7 22.3 - - - +
385F ASN* 3.0 5.2 + - - -
395F ARG* 3.5 30.9 - - + +
396F LEU* 3.2 35.0 - - + -
399F VAL* 4.1 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 382 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F LEU 4.4 6.7 - - - -
337F SER* 3.7 13.5 - - - -
338F ALA* 2.9 45.1 - - + -
341F PHE* 3.4 15.5 - + + -
378F ALA 3.1 7.6 + - - +
379F GLU 3.6 8.5 - - - +
381F ALA* 1.3 78.2 - - - +
383F ARG* 1.3 71.6 - - - +
385F ASN* 2.7 18.9 + - + +
386F GLU* 2.9 38.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F GLU 2.8 20.1 + - - +
380F ALA* 3.1 15.3 - - - +
382F PHE* 1.3 78.2 - - - +
384F VAL* 1.3 62.4 + - - +
386F GLU* 3.3 7.1 + - - +
387F LYS* 3.1 49.9 + - + +
433F VAL* 5.1 13.4 - - + +
435F GLU* 3.5 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F ALA 3.1 10.8 - - - +
381F ALA* 2.7 25.4 - - - +
382F PHE 2.8 1.6 + - - -
383F ARG* 1.3 72.1 - - + +
385F ASN* 1.3 68.8 + - - +
386F GLU 3.0 1.6 - - - -
387F LYS* 2.8 8.7 + - - +
388F THR* 2.7 43.3 + - + +
395F ARG* 3.3 35.2 - - + +
399F VAL* 4.7 6.7 - - + -
402F ARG* 5.6 6.1 - - - +
433F VAL* 5.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 385 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341F PHE* 4.3 6.8 - - + -
381F ALA 3.0 7.6 + - - +
382F PHE* 2.7 17.4 + - + +
384F VAL* 1.3 77.9 - - - +
386F GLU* 1.3 62.3 + - - +
388F THR 3.3 15.9 - - - +
389F GLU 4.5 0.4 - - - -
390F ASN* 3.0 34.9 + - - +
391F ILE 3.5 9.0 + - - -
392F GLY* 2.9 42.6 + - - +
395F ARG* 2.5 47.3 + - - +
68L GLN* 3.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F PHE* 2.9 35.7 + - + +
383F ARG* 3.5 11.1 + - - +
385F ASN* 1.3 78.9 - - - +
387F LYS* 1.3 88.9 + - + +
388F THR 3.3 0.3 + - - -
390F ASN* 4.7 2.0 - - - +
68L GLN* 3.8 9.9 + - - +
70L HIS* 3.1 33.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 387 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ARG* 3.1 43.7 + - + +
384F VAL* 2.8 14.0 + - - +
386F GLU* 1.3 96.2 + - + +
388F THR* 1.3 65.7 + - + +
433F VAL* 5.7 4.3 - - + -
435F GLU* 3.5 48.4 + - + +
437F GLU* 5.7 0.7 - - - +
70L HIS* 4.3 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 388 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F VAL* 2.7 37.6 + - + +
385F ASN 3.3 1.3 - - - +
386F GLU 4.1 0.5 - - - +
387F LYS* 1.3 86.1 - - + +
389F GLU* 1.3 67.8 + - - -
390F ASN 3.2 0.6 + - - -
395F ARG* 3.7 4.3 + - - -
433F VAL* 6.0 3.6 - - + -
434F VAL 4.5 16.4 - - - +
435F GLU* 5.6 0.9 - - - -
437F GLU* 5.7 5.6 - - - +
68L GLN* 2.8 23.9 - - - +
70L HIS* 4.1 6.8 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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