Contacts of the helix formed by residues 24 - 37 (chain B) in PDB entry 6QXT
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 ASP 24 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.2 3.3 - - + +
23B GLU* 1.3 77.0 - - - +
25B VAL* 1.3 59.8 + - - +
26B SER* 4.4 3.4 - - - +
27B VAL* 3.9 21.1 - - + +
28B PHE* 3.0 31.2 + - - +
208B LEU 4.5 1.8 + - - -
209B ASP 5.2 2.2 - - - +
210B LYS* 4.6 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER 4.3 11.9 - - - +
172A TYR* 3.8 15.8 - - - +
173A PHE 4.8 7.2 - - - +
174A SER* 4.9 12.3 - - - +
23B GLU 3.9 3.0 + - - -
24B ASP* 1.3 69.5 - - - +
26B SER* 1.3 60.7 + - - +
28B PHE* 3.8 5.8 - - - +
29B ALA* 2.9 32.6 + - - +
197B PRO* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A SER* 6.3 0.2 - - - -
24B ASP* 3.3 3.7 - - - +
25B VAL* 1.3 79.1 - - - +
27B VAL* 1.3 57.4 + - - +
29B ALA* 4.0 3.3 - - - +
30B GLN* 2.9 31.5 + - - +
27J SER* 4.7 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 6.0 6.1 - - + -
22B ILE* 5.2 5.6 - - + -
24B ASP* 3.5 20.0 + - + +
26B SER* 1.3 78.5 - - - +
28B PHE* 1.3 57.9 + - - +
30B GLN* 4.0 5.7 - - - +
31B LEU* 2.9 30.3 + - - +
27J SER* 5.0 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER 5.9 1.6 - - - +
172A TYR* 6.3 1.6 - - - -
22B ILE* 3.9 24.3 - - + +
24B ASP 3.0 20.3 + - - +
25B VAL* 3.8 7.0 - - - +
27B VAL* 1.3 75.4 - - - +
29B ALA* 1.3 59.8 + - - +
31B LEU* 3.2 5.2 + - - +
32B VAL* 2.9 29.5 + - - +
196B GLU 6.2 0.4 - - - -
197B PRO* 5.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 5.7 7.2 - - + +
172A TYR* 3.8 30.4 - - + +
25B VAL 2.9 18.1 + - - +
26B SER* 4.1 3.1 - - - +
28B PHE* 1.3 76.7 - - - +
30B GLN* 1.3 57.8 + - - +
32B VAL* 3.4 6.3 + - - +
33B LYS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 2.9 19.8 + - - +
27B VAL* 4.0 5.8 - - - +
29B ALA* 1.3 76.0 - - - +
31B LEU* 1.3 57.6 + - - +
33B LYS* 3.5 6.4 + - - +
34B GLU* 2.9 29.0 + - - +
27J SER 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL 2.9 20.3 + - - +
28B PHE* 3.6 6.3 - - - +
30B GLN* 1.3 75.4 - - - +
32B VAL* 1.3 59.1 + - - +
34B GLU* 3.3 8.5 + - - +
35B PHE* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE 2.9 15.7 + - - +
29B ALA* 3.9 6.5 - - - +
31B LEU* 1.3 73.6 - - - +
33B LYS* 1.3 61.1 + - - +
35B PHE* 2.9 22.9 + - - +
36B TYR* 2.9 14.7 + - - +
167B VAL* 5.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A CYS 4.8 12.8 - - - +
143A THR* 5.5 6.1 - - - -
144A VAL 5.8 2.2 - - - +
29B ALA 2.9 17.0 + - - +
30B GLN* 3.8 7.9 - - - +
32B VAL* 1.3 76.4 - - - +
34B GLU* 1.3 57.0 + - - +
36B TYR* 3.4 5.5 + - - +
37B GLN* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN 2.9 18.1 + - - +
31B LEU* 3.5 8.5 - - - +
32B VAL 3.2 0.2 - - - -
33B LYS* 1.3 76.7 - - - +
35B PHE* 1.3 57.8 + - - +
37B GLN* 4.6 4.0 - - - +
38B TYR* 3.1 28.9 - - - +
41B GLN* 5.1 11.7 - - + +
43B ASN* 5.5 5.2 - - + -
44B LEU* 4.2 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 2.9 11.9 + - - +
32B VAL* 2.9 13.8 + - - +
34B GLU* 1.3 79.1 - - - +
36B TYR* 1.3 63.4 + - - +
38B TYR* 3.6 14.8 - - - +
44B LEU* 6.1 0.2 - - - -
61B LEU* 5.1 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.6 21.1 - - + -
32B VAL 2.9 12.9 + - - +
33B LYS* 4.0 6.3 - - - +
35B PHE* 1.3 79.6 - - - +
37B GLN* 1.3 58.0 + - + +
38B TYR 3.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS 2.9 17.8 + - - +
34B GLU* 4.0 3.4 - - - -
36B TYR* 1.3 75.6 - - + +
38B TYR* 1.3 52.6 + - - +
39B ASP* 3.1 3.1 - - - -
40B GLU* 2.6 40.0 + - + +
41B GLN* 3.2 13.3 + - + -
----------------------------------------------------------
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