Contacts of the helix formed by residues 25 - 33 (chain D) in PDB entry 1T5A
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 THR 25 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 5.5 3.4 - - - +
397B GLU* 3.4 41.3 - - + +
400B ARG* 5.1 16.4 - - + +
401B LEU* 4.1 14.2 - - + +
23D ALA* 4.2 1.2 - - - +
24D ASP* 1.3 85.5 - - + +
26D PHE* 1.3 55.9 + - - +
27D LEU* 4.1 2.5 - - - -
28D GLU* 3.0 22.5 + - - +
29D HIS* 2.8 31.9 + - - +
390D TYR* 3.5 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.6 30.7 - + - -
393B GLN* 3.4 17.5 - - - +
397B GLU* 3.0 14.4 + - - +
25D THR* 1.3 69.7 - - - +
27D LEU* 1.3 59.2 + - - +
29D HIS* 2.9 20.6 + + + +
30D MET* 2.9 59.2 + - + +
390D TYR* 3.9 19.2 + + + -
393D GLN* 3.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLY* 3.7 22.9 - - - +
318B ASN* 4.4 10.5 - - + +
319B ARG* 4.6 10.5 - - + +
394B LEU* 5.1 9.0 - - + -
397B GLU* 2.8 20.0 + - + +
398B LEU* 3.8 39.0 - - + +
401B LEU* 3.7 25.1 - - + -
25D THR* 3.2 0.4 - - - -
26D PHE* 1.3 75.4 - - - +
28D GLU* 1.3 60.0 + - - +
30D MET* 3.5 26.8 + - + +
31D CYS* 3.0 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ARG* 4.0 24.2 + - - -
401B LEU* 3.5 24.2 - - + +
23D ALA* 3.7 12.1 - - + -
24D ASP* 5.1 1.8 - - + +
25D THR* 3.0 27.1 + - - +
27D LEU* 1.3 76.3 - - - +
29D HIS* 1.3 69.0 + - - +
31D CYS* 3.2 5.2 + - - +
32D ARG* 3.1 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN 5.1 0.7 - - - -
20D ALA* 2.6 54.0 + - + +
21D ALA* 3.8 4.7 - - + -
23D ALA* 4.0 2.6 - - - +
25D THR 2.8 11.9 + - - +
26D PHE* 2.9 26.0 - + - +
28D GLU* 1.3 76.4 - - - +
30D MET* 1.3 65.8 + - + +
32D ARG* 2.9 15.1 + - - +
33D LEU* 3.4 18.6 + - + +
387D ALA 5.3 0.7 - - - -
388D ALA* 2.8 29.7 + - - -
389D ILE 3.9 10.1 - - - -
390D TYR* 3.4 37.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LYS* 3.9 30.3 - - + +
312B MET* 3.2 18.8 - - - -
315B GLY* 4.6 7.2 - - - -
318B ASN* 5.7 1.1 - - - +
353B LEU 6.0 0.2 - - - +
354B ASP* 4.2 27.1 - - - +
394B LEU* 6.3 2.0 - - + -
26D PHE* 2.9 40.7 + - + +
27D LEU* 3.6 37.5 - - + +
29D HIS* 1.3 78.5 - - + +
31D CYS* 1.3 61.5 + - - +
32D ARG 2.9 1.2 + - - -
33D LEU* 3.2 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B MET* 3.6 6.2 - - - +
315B GLY 3.5 29.2 - - - -
316B ARG* 2.8 41.8 + - + -
319B ARG* 3.0 45.9 + - - +
27D LEU* 3.0 29.2 + - - -
28D GLU* 3.2 11.4 + - - +
30D MET* 1.3 75.5 - - - +
32D ARG* 1.3 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 4.8 3.5 + - - +
14D GLN* 3.5 15.4 + - - +
17D GLN* 4.0 0.2 - - - +
19D HIS* 2.9 59.4 + - + +
20D ALA* 3.7 14.8 - - + +
22D MET* 3.6 9.1 + - - +
23D ALA* 3.1 29.7 - - - +
28D GLU* 3.2 40.9 + - - +
29D HIS 2.9 10.1 + - - +
31D CYS* 1.3 79.7 - - - +
33D LEU* 1.3 66.8 + - - +
34D ASP* 3.0 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.9 30.9 - - + +
309B ALA* 5.8 0.2 - - - -
311B LYS* 3.8 36.1 - - + -
312B MET* 3.4 22.0 - - - +
316B ARG* 5.0 1.7 + - - -
17D GLN* 3.5 9.2 - - + +
20D ALA* 4.1 12.8 - - + -
29D HIS* 3.4 23.2 + - + +
30D MET* 3.2 23.1 + - + +
32D ARG* 1.3 75.5 - - - +
34D ASP* 1.3 59.0 + - - +
35D ILE* 4.2 1.3 + - - +
388D ALA* 4.0 26.0 - - + +
----------------------------------------------------------
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