Contacts of the helix formed by residues 18 - 35 (chain K) 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 THR 18 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PRO* 6.1 0.2 - - - +
16K THR 3.4 4.6 - - - +
17K ASP* 1.3 82.6 - - - +
19K ALA* 1.3 60.6 + - - +
20K GLU* 4.3 4.9 - - - -
21K GLU* 3.1 22.1 + - - +
22K ARG* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ASP 3.7 2.0 + - - -
18K THR* 1.3 68.7 - - - +
20K GLU* 1.3 62.3 + - - +
22K ARG* 3.1 9.4 + - - +
23K LYS* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K THR* 3.4 4.8 - - - -
19K ALA* 1.3 78.0 - - - +
21K GLU* 1.3 57.8 + - - +
23K LYS* 3.8 7.8 - - - +
24K ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K MET* 5.9 2.6 - - + +
15K PRO 3.1 28.6 - - - +
16K THR* 4.4 2.4 - - - -
18K THR* 3.1 27.9 + - - +
19K ALA 3.1 0.8 - - - -
20K GLU* 1.3 77.0 - - - +
22K ARG* 1.3 61.2 + - - +
24K ALA* 3.4 6.1 + - - +
25K TYR* 2.9 29.0 + - - +
68K LYS 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K THR* 4.6 13.8 + - - +
18K THR 3.0 11.3 + - - +
19K ALA* 3.1 11.0 + - - +
21K GLU* 1.3 73.7 - - - +
23K LYS* 1.3 64.3 + - - +
25K TYR* 3.1 8.1 + - - +
26K ARG* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K ALA 2.9 15.3 + - - +
20K GLU* 3.8 8.5 - - - +
22K ARG* 1.3 75.8 - - - +
24K ALA* 1.3 57.9 + - - +
26K ARG* 3.3 8.1 + - - +
27K LYS* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K GLU 2.9 19.4 + - - +
21K GLU* 3.8 7.0 - - - +
23K LYS* 1.3 75.9 - - - +
25K TYR* 1.3 57.8 + - - +
27K LYS* 3.4 7.0 + - - +
28K PHE* 2.9 30.8 + - - +
67K PRO* 3.8 25.2 - - + +
68K LYS 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K MET* 5.8 7.4 - - + -
16K THR* 6.3 2.9 - - - -
21K GLU 2.9 17.8 + - - +
22K ARG* 3.1 9.4 + - - +
24K ALA* 1.3 74.3 - - - +
26K ARG* 1.3 59.7 + - - +
28K PHE* 3.4 4.9 + - - +
29K ARG* 2.9 30.8 + - - +
67K PRO* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ARG 2.9 11.8 + - - +
23K LYS* 3.6 10.5 - - - +
25K TYR* 1.3 76.4 - - - +
27K LYS* 1.3 57.1 + - - +
29K ARG* 3.4 5.5 + - - +
30K LYS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K LYS 2.9 16.7 + - - +
24K ALA* 3.7 8.5 - - - +
26K ARG* 1.3 75.9 - - - +
28K PHE* 1.3 58.2 + - - +
30K LYS* 3.3 6.5 + - - +
31K PHE* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K ALA 2.9 18.1 + - - +
25K TYR* 3.9 4.9 - - - +
27K LYS* 1.3 76.0 - - - +
29K ARG* 1.3 58.6 + - - +
31K PHE* 3.2 8.6 + - - +
32K LEU* 2.9 27.4 + - - +
65K ASN* 4.7 15.3 - - - +
66K ASN* 6.0 0.7 - - - -
67K PRO* 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TYR 2.9 17.8 + - - +
26K ARG* 3.7 6.1 - - - +
28K PHE* 1.3 77.4 - - - +
30K LYS* 1.3 56.9 + - - +
32K LEU* 3.1 8.6 + - - +
33K LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ARG 2.9 17.8 + - - +
27K LYS* 3.7 6.5 - - - +
29K ARG* 1.3 76.3 - - - +
31K PHE* 1.3 57.6 + - - +
33K LEU* 3.3 7.1 + - - +
34K SER* 2.9 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K LYS 2.9 17.4 + - - +
28K PHE* 3.5 9.0 - - - +
29K ARG 3.2 0.2 - - - -
30K LYS* 1.3 78.3 - - - +
32K LEU* 1.3 61.1 + - - +
34K SER* 3.3 7.3 + - - -
35K GLU* 3.1 23.4 + - - +
65K ASN* 5.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K PHE 2.9 12.9 + - - +
29K ARG* 3.5 10.8 - - - +
31K PHE* 1.3 77.2 - - - +
33K LEU* 1.3 60.2 + - - +
35K GLU* 3.3 10.6 + - - +
36K GLY 3.5 0.2 + - - -
37K PHE* 3.0 39.7 + - + +
45K TYR* 5.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K ARG 2.9 15.8 + - - +
30K LYS* 3.8 7.4 - - - +
32K LEU* 1.3 77.1 - - - +
34K SER* 1.3 61.1 + - - +
36K GLY* 3.3 12.5 + - - -
37K PHE 3.7 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K LYS 2.9 18.1 + - - -
31K PHE* 3.8 7.6 - - - -
32K LEU 3.3 0.2 - - - -
33K LEU* 1.3 77.4 - - - +
35K GLU* 1.3 59.3 + - - +
36K GLY 3.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K PHE 3.1 16.3 + - - +
32K LEU* 3.8 7.4 - - - +
33K LEU 3.2 1.2 - - - -
34K SER* 1.3 76.6 - - - +
36K GLY* 1.3 58.7 + - - +
37K PHE* 3.6 2.0 - - + +
----------------------------------------------------------
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