Contacts of the helix formed by residues 391 - 402 (chain A) in PDB entry 2P2M
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 ASN 391 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ARG* 6.0 1.4 - - - +
365A MET* 5.2 2.1 - - - +
389A PRO* 4.1 2.2 + - - +
390A ILE* 1.3 75.3 - - - +
392A PRO* 1.4 75.6 - - + +
393A GLU* 3.1 39.5 + - - +
394A ALA* 3.1 33.8 + - - +
395A TRP* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE 3.6 3.6 - - - +
391A ASN* 1.4 92.5 - - + +
393A GLU* 1.3 54.5 + - + +
395A TRP* 3.2 7.7 - - + +
396A GLU* 2.8 41.6 + - + +
434A ALA* 3.6 31.1 - - + +
435A GLY* 4.7 2.0 - - - -
511A TRP* 5.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET* 4.1 3.8 - - + +
391A ASN* 3.1 19.2 + - - +
392A PRO* 1.3 75.4 - - + +
394A ALA* 1.3 61.2 + - - +
396A GLU* 3.4 7.6 + - - +
397A TRP* 3.0 28.1 + - - +
573B PRO* 3.4 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PRO* 6.2 0.2 - - + -
361A ILE* 3.9 11.2 - - + +
362A ARG* 4.6 11.9 - - + -
365A MET* 3.7 28.9 - - + -
390A ILE* 4.1 15.7 - - + -
391A ASN* 3.1 23.0 + - - +
393A GLU* 1.3 73.7 - - - +
395A TRP* 1.3 61.1 + - - +
397A TRP* 3.2 2.4 + - - +
398A TYR* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 3.5 38.4 - + - -
390A ILE* 3.8 28.8 - - + +
391A ASN 3.1 11.8 + - - +
392A PRO* 3.2 13.9 - - + +
394A ALA* 1.3 78.2 - - - +
396A GLU* 1.3 65.6 + - - +
398A TYR* 3.4 4.9 + - - +
399A TRP* 2.9 53.7 + + + +
409A VAL* 3.5 40.9 + - + +
411A ASP* 4.8 8.0 - - + +
432A LEU* 3.8 26.2 - - + -
433A LYS 4.5 3.0 + - - -
434A ALA* 3.5 21.9 - - + +
435A GLY 3.6 16.7 - - - +
436A SER 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 3.0 27.2 + - - -
392A PRO* 2.8 26.1 + - + +
393A GLU* 3.8 7.2 - - - +
394A ALA 3.3 0.2 - - - -
395A TRP* 1.3 79.9 - - + +
397A TRP* 1.3 57.2 + - - +
399A TRP* 3.6 24.0 - - - +
400A LYS* 2.8 33.4 + - - +
434A ALA* 3.8 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ILE* 4.2 14.4 - - + -
364A LEU* 3.8 20.6 - - + -
365A MET* 3.5 52.6 + - + +
368A GLY* 3.7 26.8 - - - -
371A ALA* 3.9 13.2 - - + -
372A ILE* 5.2 1.6 - - + -
393A GLU 3.0 18.3 + - - +
394A ALA 3.2 3.8 + - - +
396A GLU* 1.3 76.2 - - - +
398A TYR* 1.3 62.4 + + - +
400A LYS* 4.6 4.3 - - - -
401A LYS* 2.7 70.1 + - + +
402A ILE* 4.0 27.4 - - + -
574B GLU* 4.6 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A MET* 5.0 2.7 - - + -
354A LEU* 3.5 12.2 + - + +
356A THR* 3.5 25.5 - - + +
361A ILE* 3.6 31.6 - - + -
383A LEU* 3.5 30.2 - - + +
384A GLY 2.7 39.2 + - - -
385A SER* 4.5 0.7 - - - -
390A ILE* 4.9 4.7 - - + -
394A ALA 2.9 17.4 + - - +
395A TRP* 3.6 4.3 - - - +
397A TRP* 1.3 84.8 - + - +
399A TRP* 1.3 60.0 + - - +
402A ILE* 3.1 45.4 + - + +
403A GLY 3.1 7.3 + - - -
409A VAL* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 3.5 35.6 + + - +
383A LEU* 4.3 2.9 - - - -
395A TRP* 2.9 43.9 + + + +
396A GLU* 3.6 20.6 - - - +
398A TYR* 1.3 75.3 - - - +
400A LYS* 1.3 74.3 + - + +
403A GLY* 3.4 6.2 - - - -
404A LYS 3.4 5.9 + - - -
405A GLU* 3.0 71.2 + - + -
406A LYS 5.3 0.2 - - - -
407A CYS 3.1 30.4 + - - -
408A PRO* 5.0 2.0 - - + +
409A VAL* 4.0 12.1 - - + -
432A LEU* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU 2.8 21.6 + - - +
397A TRP* 4.0 4.3 - - - +
399A TRP* 1.3 79.7 - - + +
401A LYS* 1.3 74.7 + - + +
404A LYS* 3.0 25.3 - - - +
405A GLU* 3.5 34.7 + - + +
574B GLU* 2.8 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP* 2.9 35.5 + - - +
372A ILE* 3.7 21.5 - - + +
377A ARG* 2.8 31.3 + - - +
397A TRP* 2.7 59.8 + - + +
400A LYS* 1.3 90.0 - - + +
402A ILE* 1.3 61.9 + - - +
404A LYS* 4.2 0.2 - - - +
574B GLU* 3.3 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A MET* 4.2 13.7 - - + -
343A CYS* 3.7 27.6 - - - -
354A LEU* 4.0 21.1 - - + -
364A LEU* 4.9 3.8 - - + -
371A ALA 5.1 1.1 - - - +
372A ILE* 3.9 13.2 - - + -
377A ARG* 3.8 16.4 - - - +
380A LEU* 3.4 31.5 - - + +
383A LEU* 4.0 5.2 - - + -
397A TRP* 4.0 26.0 - - + -
398A TYR* 3.1 30.9 + - + +
401A LYS* 1.3 76.6 - - - +
403A GLY* 1.3 62.1 + - - +
404A LYS* 3.3 0.9 + - - +
----------------------------------------------------------
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