Contacts of the helix formed by residues 387 - 393 (chain A) in PDB entry 3T79
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 GLN 387 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLN 3.6 21.0 + - - -
193A SER* 4.1 7.9 + - - +
194A PRO* 3.9 18.6 - - - +
195A PHE* 4.0 24.8 - - + -
351A LEU* 4.3 14.4 - - + +
355A VAL* 5.8 2.2 - - + -
382A LEU* 4.1 4.1 - - - +
383A ASP 4.7 1.0 - - - +
384A ILE* 2.4 36.4 + - + +
386A SER* 1.3 101.6 + - - +
388A GLU* 1.3 65.9 + - - +
389A HIS 3.4 1.8 - - - -
390A LEU* 2.7 30.5 + - + +
391A LEU* 3.1 17.4 + - + +
105D ASN* 4.2 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 3.6 4.7 + - + +
385A GLU* 2.6 24.3 - - - +
386A SER* 2.6 20.6 - - - +
387A GLN* 1.3 67.1 - - - +
389A HIS* 1.3 82.3 + - + +
391A LEU* 2.6 38.0 - - + +
392A ALA* 3.0 4.6 + - - +
402A SER 5.9 2.2 - - - -
101D PHE* 4.4 10.9 - - - -
102D ASP 5.3 0.5 - - - +
105D ASN* 4.7 5.9 - - - +
106D VAL* 4.8 4.8 - - + +
267D HIS* 6.4 0.2 - - - +
274D GLU* 3.3 19.2 - - - +
275D TRP* 4.4 15.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 2.6 39.7 + - + +
387A GLN 3.4 0.6 - - - -
388A GLU* 1.3 85.5 - - + +
390A LEU* 1.3 90.3 + - + +
392A ALA* 2.4 37.3 + - - +
393A GLN* 3.4 17.2 + - - +
105D ASN* 2.1 74.8 + - + +
106D VAL* 3.2 12.6 - - + +
108D ALA* 4.7 0.8 - - - +
109D ILE* 3.7 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 4.6 11.9 - - + +
115A ILE* 2.6 57.2 - - + +
193A SER* 4.1 17.5 - - - +
195A PHE* 3.7 37.7 - - + -
196A THR* 4.8 6.1 - - + -
387A GLN* 2.7 27.1 + - + +
389A HIS* 1.3 103.2 - - + +
391A LEU* 1.3 56.1 + - - +
393A GLN* 3.3 11.1 + - - +
105D ASN* 4.6 2.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
115A ILE* 3.2 11.2 - - + +
355A VAL* 5.8 11.4 - - + -
384A ILE* 4.2 20.4 - - + -
387A GLN* 3.1 25.8 + - + +
388A GLU* 2.6 36.3 - - + +
390A LEU* 1.3 74.5 - - - +
392A ALA* 1.3 58.4 + - + +
393A GLN 2.7 17.9 + - - -
394A LEU* 2.9 29.9 + - + +
402A SER* 3.6 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU 3.0 8.3 + - - +
389A HIS* 2.4 35.3 + - - +
391A LEU* 1.3 72.1 - - + +
393A GLN* 1.3 56.6 + - - -
394A LEU* 3.4 8.1 + - - +
109D ILE* 4.5 17.3 - - + -
260D GLN 4.7 0.7 - - - +
261D LEU* 3.8 9.3 - - + +
262D PRO* 3.3 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.1 28.3 + - - +
111A GLN* 3.3 19.6 - - - +
112A LYS* 3.2 46.6 - - + +
115A ILE* 4.3 4.7 - - + -
116A ASN* 3.1 11.6 + - - -
389A HIS* 3.5 15.9 + - - +
390A LEU 3.3 13.6 - - - +
391A LEU 2.7 6.7 + - - -
392A ALA* 1.3 73.1 - - - +
394A LEU* 1.3 57.6 + - - -
108D ALA* 3.6 21.5 - - - +
109D ILE* 5.5 2.3 - - + +
112D LYS* 6.3 0.8 - - - +
260D GLN 6.0 0.2 - - - -
261D LEU* 4.8 10.5 - - + -
393D GLN* 5.1 2.4 - - - +
----------------------------------------------------------
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