Contacts of the helix formed by residues 374 - 389 (chain O) in PDB entry 3H1I
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 374 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370N ASP* 3.4 32.8 - - - +
371N GLY* 5.0 0.4 - - - -
374N PRO* 6.1 0.4 - - + -
370O MET 5.4 2.0 - - - +
371O SER* 4.0 5.3 + - - +
373O GLU* 1.3 81.9 - - + +
375O ALA* 1.3 55.2 + - - +
376O GLN* 2.7 19.3 + - - +
377O GLY* 2.7 32.2 + - - -
378O LEU* 2.9 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370N ASP* 3.4 23.5 + - - +
44O ALA* 5.6 6.3 - - + +
46O ARG* 3.8 20.4 - - + -
110O GLU* 4.9 5.8 - - - +
209O ILE* 3.7 12.6 - - + +
373O GLU 3.6 3.6 + - - -
374O THR* 1.3 69.4 - - - +
376O GLN* 1.3 56.6 + - - +
378O LEU* 4.0 8.1 - - - -
379O LEU* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370N ASP* 4.7 1.9 + - - +
46O ARG* 3.0 35.7 + - - +
99O TYR* 3.9 25.9 + - - -
110O GLU* 6.0 0.2 - - - +
374O THR* 2.7 11.0 + - - +
375O ALA* 1.3 73.2 - - - +
377O GLY* 1.3 62.3 + - - +
378O LEU 3.1 1.6 - - - -
379O LEU* 4.1 0.7 - - - +
380O ASN* 2.9 37.0 + - + +
77V ARG* 3.2 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371O SER* 3.3 26.0 - - - +
372O VAL* 4.3 3.2 - - - +
374O THR* 2.7 18.5 + - - -
376O GLN* 1.3 76.0 - - - +
378O LEU* 1.3 53.3 + - - -
380O ASN* 3.4 9.1 + - - +
381O GLU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O LEU* 4.7 13.2 - - + -
40O ASN* 5.3 8.1 - - + +
209O ILE* 3.3 30.3 - - + -
372O VAL* 3.6 29.9 - - + +
373O GLU 5.3 1.6 - - - +
374O THR 2.9 10.9 + - - +
375O ALA* 4.0 4.5 - - - +
377O GLY* 1.3 73.4 - - - +
379O LEU* 1.3 57.9 + - - +
380O ASN 2.7 14.4 + - - -
381O GLU* 2.8 17.2 + - + +
382O ILE* 3.0 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O ARG* 3.1 42.2 - - + +
47O ILE 3.8 13.9 - - - +
48O GLY* 4.2 3.6 - - - +
50O PHE* 3.0 26.1 - - + -
108O CYS* 4.4 5.6 - - + -
207O VAL* 3.4 13.7 - - + -
208O GLY* 3.3 43.5 - - - +
209O ILE* 3.3 14.4 - - + +
375O ALA 3.1 17.8 + - - +
376O GLN 4.5 1.1 - - - +
378O LEU* 1.3 77.7 - - - +
380O ASN* 1.3 59.3 + - - +
382O ILE* 4.0 3.6 - - - -
383O GLY 3.4 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 380 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O PHE* 4.1 8.1 - - - -
104O LYS* 3.6 23.4 + - - -
106O THR* 5.6 0.3 - - - +
376O GLN* 2.9 27.9 + - + +
377O GLY* 3.4 10.0 + - - +
378O LEU 2.7 1.4 + - - -
379O LEU* 1.3 75.5 - - - +
381O GLU* 1.3 65.9 + - - +
382O ILE 3.1 1.6 - - - -
383O GLY* 4.1 0.2 - - - -
384O SER* 2.9 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368O TYR* 4.2 33.6 - - + +
372O VAL* 4.6 14.2 - - + +
377O GLY 3.1 15.0 + - - +
378O LEU* 2.8 12.1 + - + +
380O ASN* 1.3 76.0 + - - +
382O ILE* 1.3 66.4 + - + +
384O SER* 4.3 10.3 - - - -
385O GLU* 4.0 24.1 + - - +
392O HIS* 5.6 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 4.3 23.3 - - + -
36O ALA* 3.6 19.5 - - + +
38O LEU* 3.9 25.6 - - + -
207O VAL* 3.4 21.8 - - + -
208O GLY 4.9 2.2 - - - +
209O ILE* 4.5 12.8 - - + -
378O LEU* 3.0 40.1 + - + +
379O LEU* 4.1 1.8 - - - +
381O GLU* 1.3 78.4 - - - +
383O GLY* 1.3 62.2 + - - +
385O GLU* 3.3 5.1 + - - +
386O ALA* 2.8 27.8 + - + +
391O THR 4.9 0.7 - - - +
392O HIS* 5.1 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 383 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O PHE* 4.0 15.5 - - - -
207O VAL* 3.3 30.3 - - - +
379O LEU 3.4 7.9 + - - -
382O ILE* 1.3 78.6 - - - +
384O SER* 1.3 65.6 + - - +
386O ALA* 2.7 15.0 + - - -
387O LEU* 2.9 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O PHE* 4.3 3.8 - - - -
104O LYS* 4.3 17.8 - - - +
380O ASN* 2.9 36.2 + - - -
381O GLU* 4.3 13.7 - - - -
383O GLY* 1.3 73.5 - - - +
385O GLU* 1.3 58.4 + - - +
387O LEU* 3.8 4.5 + - - +
388O LEU* 3.5 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381O GLU* 4.0 18.2 - - - +
382O ILE* 3.3 6.8 + - - +
383O GLY 2.8 3.2 + - - -
384O SER* 1.3 75.6 - - - +
386O ALA* 1.3 53.8 + - - +
387O LEU 2.5 17.2 + - - -
388O LEU* 3.1 2.3 + - - -
389O SER* 3.0 40.3 + - - +
390O GLY 3.3 0.7 + - - -
391O THR* 3.3 22.4 + - - +
392O HIS* 4.0 5.2 - - + -
393O THR* 2.8 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O ILE* 4.3 6.3 - - + -
34O ILE* 3.0 38.1 - - + +
36O ALA* 3.7 28.3 - - + -
205O ALA* 3.7 4.3 - - + +
207O VAL* 4.6 3.4 - - + -
382O ILE* 2.8 17.9 + - + +
383O GLY* 2.7 13.9 + - - +
385O GLU* 1.3 69.6 - - - +
387O LEU* 1.3 56.3 + - - +
390O GLY* 4.0 7.6 - - - +
391O THR 3.8 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O ILE* 4.2 9.9 - - + +
50O PHE* 3.8 13.7 - - + +
51O ILE 4.3 14.8 - - - +
52O LYS* 3.6 40.7 + - + -
104O LYS* 5.0 13.2 - - + -
202O ALA 5.4 1.3 - - - +
203O ARG 3.1 26.5 - - - +
204O MET 3.8 2.7 - - - +
205O ALA* 3.3 28.9 - - + +
383O GLY 2.9 13.2 + - - +
384O SER* 4.0 5.4 - - - +
385O GLU 2.5 7.1 + - - -
386O ALA* 1.3 75.6 - - - +
388O LEU* 1.3 65.3 + - + +
389O SER 3.3 1.4 + - - -
390O GLY 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O LYS* 4.3 22.9 - - + +
103O GLU* 5.7 4.9 - - - +
264O VAL* 3.9 32.1 - - + -
317O SER* 5.5 12.6 - - - -
384O SER* 3.5 18.3 + - - +
385O GLU* 3.1 3.6 + - - +
387O LEU* 1.3 85.6 - - + +
389O SER* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 389 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O ILE* 5.4 0.4 - - - -
385O GLU* 3.0 22.8 + - - +
387O LEU 3.3 1.0 + - - -
388O LEU* 1.3 83.1 - - - +
390O GLY* 1.3 61.5 + - - +
391O THR* 2.6 35.3 + - - +
----------------------------------------------------------
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