Contacts of the helix formed by residues 341 - 352 (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 GLY 341 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLN* 3.6 12.0 - - - +
339A CYS 3.3 4.1 + - - -
340A ALA* 1.3 74.8 - - - +
342A GLU* 1.3 70.9 + - - -
343A GLY 3.3 2.5 - - - -
344A GLN* 3.5 5.4 + - - +
345A LYS* 3.1 29.6 + - - +
382A ASN* 3.8 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY* 1.3 79.2 - - - -
343A GLY* 1.3 59.1 + - - +
345A LYS* 3.4 1.4 + - - +
346A ALA* 2.8 30.7 + - - +
368A PHE* 4.8 0.2 - - - -
371A LEU* 3.8 35.9 - - + +
372A SER 4.2 12.6 - - - +
374A PRO* 3.6 40.8 - - + +
375A THR 5.0 1.2 + - - +
382A ASN* 3.4 20.0 - - + +
386A TYR* 4.5 3.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 4.4 0.9 - - - -
342A GLU* 1.3 79.9 - - - +
344A GLN* 1.3 55.0 - - - +
346A ALA* 3.3 2.7 + - - +
347A ALA* 2.9 24.4 + - - +
382A ASN* 2.8 38.5 - - - +
385A LEU* 3.5 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.1 34.4 + - - +
283A TRP* 3.6 39.4 - - + +
313A LEU* 4.6 0.6 - - - +
325A TYR* 3.6 13.3 - - + -
326A GLU 3.0 20.0 + - - -
327A GLN* 3.3 14.7 - - - +
340A ALA* 3.1 29.2 - - + +
341A GLY 3.5 7.7 + - - +
342A GLU 3.3 0.2 - - - -
343A GLY* 1.3 73.6 - - - +
345A LYS* 1.3 65.9 + - - +
347A ALA* 3.3 5.0 + - - +
348A ASN* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 3.7 23.3 - - - +
340A ALA* 3.7 28.1 + - + -
341A GLY* 3.1 16.7 + - - +
342A GLU 3.7 3.8 - - - +
344A GLN* 1.3 75.9 - - - +
346A ALA* 1.3 57.6 + - - +
348A ASN* 3.4 3.0 + - - +
349A ALA* 3.0 27.2 + - - +
364A PHE* 4.8 3.4 - - - +
367A GLU* 4.3 21.1 + - + +
368A PHE* 4.0 11.3 - - + +
371A LEU* 4.1 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 5.7 0.2 - - - -
342A GLU 2.8 18.0 + - - +
343A GLY 3.4 5.6 - - - +
345A LYS* 1.3 74.2 - - - +
347A ALA* 1.3 65.5 + - - +
349A ALA* 3.1 10.7 + - - +
350A VAL* 3.1 18.2 + - - +
368A PHE* 3.5 22.6 - - + -
385A LEU 3.7 13.5 - - - +
386A TYR* 3.9 6.7 - - - -
389A ALA* 3.5 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 3.4 30.3 - - + +
284A ARG* 4.6 1.8 - - - -
287A MET* 3.6 36.4 + - + +
343A GLY 2.9 17.0 + - - +
344A GLN* 3.6 7.6 - - - +
346A ALA* 1.3 75.6 - - - +
348A ASN* 1.3 64.9 + - - +
350A VAL 3.2 2.1 + - - -
351A ALA* 3.1 18.4 + - - +
385A LEU* 4.8 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 4.3 5.9 + - - -
283A TRP 4.7 1.2 - - - +
286A ILE* 3.3 21.7 - - - +
310A LEU* 3.9 9.5 - - + +
313A LEU* 3.4 27.1 - - - +
325A TYR* 2.9 29.0 + - - +
344A GLN* 3.0 22.8 + - - +
345A LYS 3.8 4.5 - - - +
347A ALA* 1.3 78.4 - - - +
349A ALA* 1.3 65.0 + - - +
351A ALA* 3.4 18.9 - - - +
352A LEU* 3.6 10.6 + - - +
364A PHE* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.6 9.2 - - - +
345A LYS 3.0 13.8 + - - +
346A ALA 3.1 8.7 + - - +
348A ASN* 1.3 74.4 - - - +
350A VAL* 1.3 65.2 + - - +
352A LEU* 3.1 30.5 + - - +
364A PHE* 4.4 5.8 - - - +
365A PHE* 4.4 11.7 - - + -
368A PHE* 3.8 33.0 - - + -
393A VAL* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 3.6 41.3 - - + +
290A GLY* 3.6 2.4 - - - -
291A LEU 4.4 2.9 - - - +
346A ALA 3.1 14.3 + - - +
347A ALA 3.2 1.5 + - - +
349A ALA* 1.3 75.8 - - - +
351A ALA* 1.3 63.5 + - - +
352A LEU 3.0 1.0 + - - -
353A LEU* 3.1 29.0 + - + +
389A ALA* 3.7 28.5 - - + -
392A HIS* 3.7 31.2 - - + +
393A VAL* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE* 3.3 55.3 + - + +
290A GLY* 4.1 2.2 - - - -
306A VAL* 3.8 11.6 - - + +
310A LEU* 4.8 3.4 - - + -
347A ALA 3.1 7.5 + - - +
348A ASN 3.4 13.0 - - - +
349A ALA 3.2 0.2 - - - -
350A VAL* 1.3 75.9 - - - +
352A LEU* 1.3 56.7 + - - +
354A ALA* 2.9 25.3 + - - +
355A SER* 3.6 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 3.5 20.5 - - + -
18A ARG* 4.5 0.5 + - - -
20A LEU* 4.0 10.1 - - + -
24A MET* 4.6 0.4 - - + -
310A LEU* 3.6 27.1 - - + -
348A ASN 3.7 5.8 - - - +
349A ALA* 3.2 21.8 - - - +
350A VAL 3.0 1.2 - - - -
351A ALA* 1.3 72.8 - - - +
353A LEU* 1.3 55.5 + - - +
354A ALA 2.9 5.8 - - - -
355A SER* 3.0 31.0 + - - +
360A GLN 4.2 3.6 - - - +
361A ALA* 3.7 45.3 - - + +
364A PHE* 4.1 3.8 - - + -
365A PHE* 3.7 28.0 - - + +
----------------------------------------------------------
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