Contacts of the helix formed by residues 389 - 399 (chain A) in PDB entry 2A8B
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 SER 389 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASP 4.1 1.6 - - - -
386A VAL* 3.4 32.8 - - - +
387A VAL 3.1 3.2 - - - -
388A ALA* 1.3 79.5 - - - +
390A SER* 1.3 67.3 + - - +
391A HIS* 2.9 31.2 + - - -
392A LEU* 3.5 16.8 + - - +
393A LEU* 3.3 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL 4.4 3.0 + - - -
389A SER* 1.3 73.6 - - - +
391A HIS* 1.3 68.4 + - - +
393A LEU* 3.2 3.8 + - - +
394A GLN* 3.0 24.3 + - - +
638A GLU* 2.6 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ALA 4.9 1.8 - - - -
389A SER* 2.9 36.7 + - - -
390A SER* 1.3 80.5 + - - +
392A LEU* 1.3 72.1 + - + +
394A GLN* 3.4 12.7 + - - +
395A SER* 3.2 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 4.0 24.9 - - - +
386A VAL* 4.3 17.5 - - + -
389A SER* 3.5 21.7 + - - +
390A SER 3.2 0.2 - - - -
391A HIS* 1.3 86.6 + - + +
393A LEU* 1.3 62.6 + - - +
395A SER* 3.0 9.3 + - - +
396A GLU* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 6.1 0.2 - - + -
386A VAL* 3.6 35.9 - - + +
387A VAL* 5.1 3.1 - - - +
389A SER 3.3 10.5 + - - +
390A SER 3.2 8.8 + - - +
392A LEU* 1.3 76.0 - - - +
394A GLN* 1.3 58.4 + - - +
396A GLU* 4.1 13.5 - - - +
397A PHE* 2.8 31.7 + - - +
634A SER* 5.2 1.1 - - - -
637A TYR* 3.6 14.9 - - + -
638A GLU* 3.8 31.6 - - + +
641A HIS* 3.7 48.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.0 13.4 + - - +
391A HIS* 3.6 11.9 + - - +
392A LEU 3.3 0.2 - - - -
393A LEU* 1.3 76.7 - - - +
395A SER* 1.3 63.4 + - - +
397A PHE* 3.4 4.0 - - - +
398A MET* 2.8 40.0 + - - +
634A SER* 3.8 27.4 - - - +
638A GLU* 5.1 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS 3.2 11.0 + - - -
392A LEU* 3.0 18.9 + - - +
394A GLN* 1.3 80.5 - - - +
396A GLU* 1.3 62.3 + - - +
398A MET* 3.8 9.0 - - - +
399A GLU* 3.2 29.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
376A ARG* 3.7 30.3 + - - +
378A LEU* 5.9 1.4 - - - +
386A VAL* 5.5 1.0 - - - +
392A LEU* 2.9 37.4 + - + +
393A LEU* 3.7 15.6 - - - +
395A SER* 1.3 75.6 - - - +
397A PHE* 1.3 66.9 + - - +
399A GLU* 3.2 19.9 + - - +
400A ILE* 3.6 9.9 - - - +
617A LEU* 3.9 22.3 + - + +
637A TYR* 2.5 31.4 + - - +
641A HIS* 4.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU 2.8 19.6 + - - +
394A GLN* 3.4 4.5 - - - +
396A GLU* 1.3 77.0 - - - +
398A MET* 1.3 60.6 + - + +
400A ILE* 3.0 37.5 + - + +
402A MET* 4.1 8.5 - - + -
620A VAL* 5.1 0.7 - - + -
624A ARG* 3.1 31.6 - - - -
631A VAL* 3.4 16.6 - - + -
632A GLN 3.4 11.0 - - - -
633A THR* 3.4 20.0 - - - -
634A SER* 3.4 32.1 - - - -
637A TYR* 3.6 31.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLN* 2.8 33.5 + - - +
395A SER* 3.8 8.7 - - - +
396A GLU 3.3 0.4 - - - -
397A PHE* 1.3 77.7 - - + +
399A GLU* 1.3 59.8 + - + +
400A ILE 3.2 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A PRO* 6.0 1.6 - - - +
395A SER* 3.2 16.4 + - - +
396A GLU* 3.5 11.7 - - - +
397A PHE 3.1 1.4 - - - -
398A MET* 1.3 77.9 - - + +
400A ILE* 1.3 58.4 + - - +
401A PRO* 3.6 9.5 - - - +
617A LEU* 5.9 1.6 - - + -
----------------------------------------------------------
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