Contacts of the helix formed by residues 334 - 343 (chain A) in PDB entry 2H31
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 334 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.6 8.8 - - - +
303A HIS* 3.6 11.4 + - - -
329A ALA* 4.9 0.6 - - - +
332A SER 3.4 4.6 + - - -
333A ASN* 1.3 74.3 - - - +
335A LEU* 1.3 65.6 + - - +
336A GLY 3.5 0.7 - - - -
337A PRO* 3.6 4.8 - - - +
338A VAL* 3.1 27.4 + - - +
426A CO2 3.0 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.6 36.6 - - + +
273A GLY* 4.0 17.3 - - - +
300A THR* 4.1 17.0 - - + +
301A SER* 6.1 0.2 - - - -
302A ALA* 3.7 18.8 - - + +
303A HIS* 4.8 1.6 + - + -
309A THR* 3.8 28.0 - - + -
327A ALA* 4.0 7.0 - - + -
328A VAL 4.2 10.1 - - - +
329A ALA* 3.9 16.1 - - + +
333A ASN* 3.2 0.2 + - - -
334A GLY* 1.3 75.6 - - - +
336A GLY* 1.3 68.7 + - - +
338A VAL* 3.1 4.2 - - - +
339A MSE 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 3.5 16.7 - - - +
333A ASN* 2.8 14.8 + - - -
335A LEU* 1.3 75.0 - - - +
337A PRO* 1.3 66.4 - - - +
339A MSE 3.6 1.8 - - - +
340A SER* 3.0 25.1 + - - -
347A VAL* 3.9 3.9 - - - +
349A SER* 3.5 18.4 - - - -
374A CYS* 4.0 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASN* 3.2 33.7 - - - +
334A GLY 3.6 6.7 - - - +
336A GLY* 1.3 87.7 - - - +
338A VAL* 1.3 61.3 + - - +
340A SER* 3.7 3.6 + - - -
341A GLY* 3.2 18.0 + - - -
349A SER* 4.5 2.5 - - - +
364A SER 4.2 11.4 - - - +
365A SER* 5.4 1.1 - - - -
368A LEU* 4.3 19.5 - - + -
369A PRO* 5.6 3.6 - - + -
372A LEU* 4.0 24.0 - - + +
374A CYS* 4.4 0.6 - - - -
426A CO2 4.2 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.6 21.8 - - + -
306A PRO* 6.1 3.8 - - + +
309A THR* 4.6 8.1 - - + -
310A LEU* 4.6 11.4 - - + -
334A GLY 3.1 19.2 + - - +
335A LEU* 3.1 19.7 - - + +
337A PRO* 1.3 73.0 - - - +
339A MSE 1.3 72.8 + - - +
341A GLY* 3.1 6.5 + - - -
342A ASN* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 5.0 14.1 - - + -
309A THR* 3.8 22.9 - - + +
310A LEU* 5.7 2.5 - - - -
313A LYS* 3.7 38.8 - - + -
325A PHE* 3.6 41.7 - - + -
327A ALA* 5.4 2.5 - - + -
335A LEU* 3.0 31.7 + - + +
336A GLY* 3.6 3.6 - - - +
338A VAL* 1.3 80.4 - - - +
340A SER* 1.3 65.0 + - - +
342A ASN* 2.8 16.6 + - - +
343A THR* 2.9 22.2 + - + +
347A VAL* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLY 3.0 13.4 + - - -
337A PRO 3.9 3.8 - - - -
339A MSE 1.3 79.5 - - - +
341A GLY* 1.3 59.6 + - - +
342A ASN 3.3 0.9 + - - -
343A THR* 3.3 17.8 - - - +
345A TYR 5.5 0.4 - - - -
347A VAL* 3.7 20.2 + - - +
372A LEU* 4.2 6.1 - - - +
373A GLY 3.6 9.0 + - - -
374A CYS* 3.1 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PRO 3.2 6.8 + - - -
338A VAL* 3.1 7.0 + - - -
339A MSE 3.0 2.0 + - - -
340A SER* 1.3 79.1 - - - +
342A ASN* 1.3 67.3 + - - +
343A THR 3.7 0.4 - - - -
371A GLY 5.4 0.7 - - - -
372A LEU* 3.5 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.9 18.0 - - + +
313A LYS* 3.1 38.0 + - + +
317A GLU* 3.5 1.2 - - - +
338A VAL* 2.8 40.9 + - - +
339A MSE 2.8 4.3 + - - +
341A GLY* 1.3 83.8 - - - +
343A THR* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS* 3.9 3.4 - - - -
317A GLU* 3.0 23.5 + - - -
325A PHE* 3.7 7.9 - - + -
339A MSE 2.9 35.4 - - + +
340A SER* 3.3 12.5 + - - +
341A GLY 3.7 0.6 - - - -
342A ASN* 1.3 78.1 - - - +
344A ALA* 1.3 62.4 + - - +
345A TYR* 3.0 26.5 + - - +
347A VAL* 3.9 19.3 - - + -
----------------------------------------------------------
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