Contacts of the helix formed by residues 378 - 393 (chain A) in PDB entry 1H13
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 TYR 378 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE 5.5 0.7 - - - -
69A PRO* 4.3 22.6 - - + +
375A THR 4.6 2.4 + - - +
376A GLY 3.2 0.8 - - - -
377A ASP* 1.3 88.8 - - + +
379A ARG* 1.3 63.3 + - - +
380A TYR 3.3 3.8 + - - -
381A TYR* 3.7 3.0 + - - +
382A ASN* 3.2 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN 3.9 17.7 + - - -
46A THR 3.2 26.5 + - - -
47A GLN 3.6 11.9 - - - +
48A GLN 2.8 19.2 + - - -
49A LEU* 3.6 10.9 - - + +
51A TYR* 3.0 27.7 + - - -
67A ILE* 3.3 25.7 - - + +
374A PRO* 4.0 16.8 - - + -
375A THR* 3.8 15.9 + - - +
376A GLY* 3.0 36.3 + - - +
377A ASP* 3.4 1.4 + - - -
378A TYR* 1.3 76.2 - - - +
380A TYR* 1.3 62.5 + - - +
381A TYR 3.4 0.2 - - - -
382A ASN* 4.5 0.2 - - - -
383A GLY* 2.7 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.7 9.8 - - + +
64A ILE* 4.0 14.8 - - + -
65A LYS 3.6 10.3 - - - +
66A ALA* 3.4 46.2 - - + -
67A ILE* 3.8 13.1 - - - +
76A ARG* 3.6 27.3 - - + +
78A GLU* 4.0 7.6 + - - +
79A GLY* 3.0 40.6 + - - -
82A TRP* 4.2 4.4 - + - -
280A PHE* 5.0 3.6 - + - -
377A ASP 5.1 0.8 + - - -
378A TYR 3.3 1.8 - - - -
379A ARG* 1.3 79.5 - - - +
381A TYR* 1.3 92.9 + + + +
384A SER* 2.7 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 3.6 24.2 - + - -
280A PHE* 0.8 220.7 + + + -
283A TRP* 3.2 27.9 - + - -
284A ARG* 2.8 28.7 + - - +
378A TYR 3.7 4.1 + - - +
380A TYR* 1.3 90.1 - + + +
382A ASN* 1.3 65.4 + - - +
385A LEU* 3.1 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 4.3 15.0 - - - -
327A GLN* 5.4 3.8 + - - +
341A GLY* 3.8 8.0 - - - -
342A GLU* 3.4 30.1 - - - +
343A GLY* 2.8 36.6 - - - +
374A PRO* 3.7 11.2 - - + +
378A TYR* 3.2 31.7 + - - +
379A ARG* 4.5 0.2 - - - -
381A TYR* 1.3 77.4 - - - +
383A GLY* 1.3 56.6 + - - +
386A TYR* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.2 2.8 - - - +
47A GLN 6.2 0.2 - - - -
49A LEU* 4.0 10.3 - - - -
373A GLN* 5.6 3.5 + - - -
374A PRO* 3.7 20.6 - - - +
379A ARG* 2.7 23.5 + - - -
382A ASN* 1.3 72.2 - - - +
384A SER* 1.3 63.2 + - - +
386A TYR* 3.6 2.9 - - - +
387A MET* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.6 9.9 - - - +
49A LEU* 3.9 12.1 - - - +
64A ILE* 4.5 5.9 - - - +
79A GLY* 4.6 1.9 + - - -
82A TRP* 3.7 30.5 - - - +
379A ARG 3.9 0.2 + - - -
380A TYR* 2.7 37.4 + - - -
381A TYR 3.8 2.5 - - - -
383A GLY* 1.3 76.1 - - - +
385A LEU* 1.3 63.3 + - - +
387A MET* 3.4 2.9 + - - +
388A LEU* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 4.9 4.0 - - + -
283A TRP* 3.8 4.3 - - + -
284A ARG* 3.9 16.2 - - + -
287A MET* 3.8 32.3 - - + +
343A GLY* 3.5 35.9 - - - +
346A ALA* 3.7 3.5 - - + +
347A ALA* 4.8 5.2 - - + +
381A TYR* 3.1 53.8 + - + +
384A SER* 1.3 77.9 - - - +
386A TYR* 1.3 60.1 + - - +
388A LEU* 3.3 13.4 + - + +
389A ALA* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.6 26.2 - - - -
36A THR* 3.7 32.7 + - + -
342A GLU* 4.5 10.5 - - + -
346A ALA* 3.9 9.3 - - + +
368A PHE* 3.6 27.5 + + - -
371A LEU* 3.7 28.5 + - + -
373A GLN* 4.0 23.2 + - + +
374A PRO* 3.5 24.9 - - + -
382A ASN 2.9 19.9 + - - +
383A GLY 3.6 5.6 - - - +
385A LEU* 1.3 75.0 - - - +
387A MET* 1.3 58.1 + - - +
389A ALA* 3.3 1.6 + - - +
390A MET* 2.9 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.2 7.6 - - + +
36A THR* 3.8 22.4 - - + -
37A PHE* 3.7 44.9 - - + +
40A MET* 3.6 27.8 - - + +
86A ALA* 3.7 20.2 - - + -
90A LEU* 4.3 2.7 - - + -
383A GLY 3.0 18.1 + - - +
384A SER 3.6 4.5 - - - +
385A LEU 3.2 0.2 - - - -
386A TYR* 1.3 77.6 - - - +
388A LEU* 1.3 64.8 + - + +
390A MET* 3.2 12.7 + - + -
391A LEU* 3.2 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 3.8 55.0 - - + +
85A THR* 4.5 17.5 - - + -
86A ALA* 4.7 2.9 - - + +
148A TYR* 4.5 12.1 - - + +
287A MET* 4.9 9.6 - - + -
384A SER 3.2 14.8 + - - +
385A LEU* 3.8 19.7 - - + +
387A MET* 1.3 77.6 - - + +
389A ALA* 1.3 64.1 + - - +
391A LEU* 3.1 16.0 + - + +
392A HIS* 3.0 34.9 + - + +
397A PHE* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 5.4 1.9 - - - -
346A ALA* 3.5 35.7 - - + +
349A ALA* 5.5 0.2 - - + -
350A VAL* 3.7 16.2 - - + -
368A PHE* 3.9 11.0 - - + -
385A LEU 2.8 18.4 + - - +
386A TYR 3.7 2.2 - - - +
388A LEU* 1.3 78.7 - - - +
390A MET* 1.3 62.2 + - - +
392A HIS* 3.1 1.1 + - - -
393A VAL* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.9 20.6 - - + -
33A VAL* 3.7 33.2 - - + +
36A THR* 3.9 7.0 - - + +
368A PHE* 3.7 18.8 - - + -
369A TRP* 3.7 29.6 - - + -
386A TYR* 2.9 48.1 + - + +
387A MET* 3.2 16.6 + - + +
389A ALA* 1.3 77.0 - - - +
391A LEU* 1.3 53.4 + - - +
393A VAL* 3.7 3.8 + - - +
394A SER* 2.7 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.1 7.2 - - + -
85A THR 4.8 0.2 - - - +
86A ALA* 3.6 35.2 - - + -
89A MET* 4.1 15.0 - - + -
90A LEU* 3.7 41.3 - - + -
387A MET* 3.5 18.4 - - + +
388A LEU* 3.1 13.8 + - + +
389A ALA 3.1 0.6 - - - -
390A MET* 1.3 75.0 - - - +
392A HIS* 1.3 64.6 + - - +
394A SER* 3.2 7.2 + - - -
396A ASN* 3.0 37.5 + - + -
397A PHE* 3.3 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 4.8 1.2 - - - +
20A LEU* 5.3 0.2 - - - +
148A TYR* 5.5 2.2 + - - -
287A MET* 4.7 8.4 - - - -
291A LEU* 3.5 36.3 - - + +
294A HIS* 4.6 12.9 + - - -
295A LEU* 5.5 1.8 - - + +
350A VAL* 3.7 35.2 - - + +
353A LEU* 3.9 20.5 - - + +
388A LEU* 3.0 33.6 + - + +
389A ALA 3.1 6.0 + - - +
391A LEU* 1.3 76.5 - - - +
393A VAL* 1.3 60.6 + - + +
394A SER 3.3 1.0 + - - -
395A GLY* 4.1 5.0 + - - -
397A PHE* 3.2 51.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 3.4 0.2 - - - +
20A LEU* 3.1 32.1 + - + -
21A ALA* 2.9 26.3 + - - +
349A ALA* 4.4 12.3 - - + +
350A VAL* 4.3 16.2 - - + -
353A LEU* 5.7 0.4 - - + -
365A PHE* 3.8 21.1 - - + -
368A PHE* 4.0 19.7 - - + -
369A TRP* 4.2 13.9 - - + -
389A ALA 2.9 23.5 + - - +
390A MET* 3.9 6.7 - - - +
392A HIS* 1.3 78.9 - - - +
394A SER* 1.3 57.8 + - - +
395A GLY 3.6 1.1 - - - -
----------------------------------------------------------
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