Contacts of the helix formed by residues 18 - 33 (chain N) in PDB entry 6C6U
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 PHE 18 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B G 5.3 8.3 - - - -
27B C 4.5 20.2 - - - -
15N PHE* 3.1 34.4 + + + +
16N SER 5.1 3.1 - - - -
17N GLY* 1.3 79.1 - - - +
19N GLU* 1.3 57.4 + - - +
20N GLY 3.5 2.2 - - - -
21N ARG* 3.3 30.9 + - + +
22N VAL* 2.9 31.1 + - + +
88N ARG* 3.2 42.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N ALA* 4.9 3.6 - - + -
15N PHE 4.8 3.1 - - - +
17N GLY 3.3 11.3 + - - +
18N PHE* 1.3 75.3 - - - +
20N GLY* 1.3 62.3 + - - +
22N VAL* 3.2 8.5 + - - +
23N ALA* 2.9 27.9 + - - +
44N VAL* 3.3 31.5 - - + +
45N PRO* 5.6 0.2 - - - +
63N LYS* 3.4 24.1 + - - +
65N PHE 4.0 5.0 - - - +
66N PRO* 5.3 0.2 - - - +
67N GLY* 3.9 17.7 + - - -
68N TYR 2.9 33.4 + - - +
69N VAL* 3.7 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N GLU* 1.3 78.8 - - - +
21N ARG* 1.3 63.4 + - - +
23N ALA* 3.2 8.0 + - - +
24N THR* 2.9 32.0 + - - -
44N VAL* 5.4 3.8 - - - +
63N LYS* 5.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B C 4.8 7.7 - - - -
28B C 3.6 36.5 + - - -
29B C 5.8 1.7 + - - -
477I GLU* 5.4 1.6 - - - +
481I LEU* 5.2 2.5 - - + +
17N GLY 3.5 15.0 + - - -
18N PHE* 3.3 39.4 + - - +
19N GLU 3.3 0.8 - - - -
20N GLY* 1.3 75.7 - - - +
22N VAL* 1.3 59.7 + - - +
24N THR* 3.9 6.0 - - - -
25N SER* 2.9 34.8 + - - +
88N ARG* 3.7 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N VAL* 5.7 1.6 - - + -
14N ALA* 3.8 20.0 - - + -
18N PHE* 2.9 20.9 + - + +
19N GLU 3.2 8.7 + - - +
21N ARG* 1.3 76.2 - - - +
23N ALA* 1.3 57.9 + - - +
25N SER* 3.4 5.3 + - - -
26N LEU* 2.9 32.3 + - + +
69N VAL* 4.4 13.7 - - + -
86N VAL* 4.3 2.3 - - + +
87N PRO 4.0 5.6 - - - +
88N ARG* 3.3 38.6 - - + +
89N VAL* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N GLU 2.9 13.8 + - - +
20N GLY* 3.2 11.0 + - - +
22N VAL* 1.3 77.7 - - - +
24N THR* 1.3 56.9 + - - +
26N LEU* 3.3 6.7 + - - +
27N ARG* 3.0 35.7 + - - +
42N VAL* 4.0 27.0 - - + +
44N VAL* 4.6 12.1 - - + -
69N VAL* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481I LEU* 4.7 12.3 - - + -
20N GLY 2.9 16.4 + - - -
21N ARG* 3.9 7.8 - - - -
23N ALA* 1.3 78.0 - - - +
25N SER* 1.3 57.9 + - - +
27N ARG* 3.3 10.9 + - + +
28N GLU* 3.0 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477I GLU* 3.2 23.6 + - - -
481I LEU* 3.3 15.8 - - - +
21N ARG 2.9 19.1 + - - -
22N VAL* 3.9 5.6 - - - -
24N THR* 1.3 76.3 - - - +
26N LEU* 1.3 57.6 + - - +
28N GLU* 3.4 6.3 + - - +
29N HIS* 2.9 39.3 + - - -
86N VAL* 4.4 10.5 - - - -
87N PRO* 4.5 15.2 - - - +
88N ARG* 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N VAL* 5.6 2.2 - - + -
22N VAL* 2.9 22.3 + - + +
23N ALA* 3.6 4.9 - - - +
25N SER* 1.3 73.2 - - - +
27N ARG* 1.3 64.6 + - - +
29N HIS* 3.3 2.2 + - + -
30N ILE* 3.0 44.2 + - + +
39N PHE* 4.8 2.5 - - + -
42N VAL* 4.2 19.7 - - + -
69N VAL* 4.8 5.8 - - + -
71N VAL* 3.7 31.4 - - + -
82N LEU* 5.9 1.1 - - + -
83N VAL* 4.3 25.8 - - + -
86N VAL* 3.7 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N ALA* 3.0 19.0 + - - +
24N THR* 3.3 10.7 + - - +
26N LEU* 1.3 76.1 - - - +
28N GLU* 1.3 61.4 + - + +
30N ILE* 3.3 14.8 + - + +
31N LYS* 3.0 43.7 + - + +
40N GLY 5.9 0.4 + - - -
41N GLU* 5.2 5.7 - - - +
42N VAL* 3.3 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480I SER 4.8 7.8 - - - +
481I LEU* 4.6 22.0 - - + -
24N THR* 3.0 32.9 + - + +
25N SER* 3.8 6.3 - - - +
27N ARG* 1.3 78.4 - - - +
29N HIS* 1.3 60.6 + - + +
31N LYS* 3.3 13.8 + - - +
32N LEU* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I TYR* 3.8 34.8 - + - -
25N SER* 2.9 30.2 + - - +
26N LEU* 3.3 4.2 + - + +
28N GLU* 1.3 73.5 - - + +
30N ILE* 1.3 61.3 + - - +
32N LEU* 3.7 12.4 - - + +
33N HIS* 3.0 51.6 + - - +
82N LEU* 4.2 13.2 - - + +
85N SER* 4.5 14.8 + - - -
86N VAL* 3.8 25.5 - - + +
87N PRO* 3.5 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N LEU* 3.0 36.4 + - + +
27N ARG* 3.5 15.3 - - + +
28N GLU 3.2 0.2 - - - -
29N HIS* 1.3 76.6 - - + +
31N LYS* 1.3 64.3 + - + +
33N HIS 3.8 0.5 - - - -
34N ASN* 2.9 29.5 + - - -
35N MET 3.8 11.9 + - - +
36N GLU* 4.5 12.0 + - + -
39N PHE* 3.5 60.3 - - + -
41N GLU 5.8 2.9 - - - +
42N VAL* 6.2 2.0 - - + -
82N LEU* 4.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ARG* 3.0 29.7 + - + +
28N GLU* 3.3 15.2 + - - +
30N ILE* 1.3 80.1 - - + +
32N LEU* 1.3 60.8 + - - +
34N ASN* 4.2 7.6 + - - +
36N GLU* 5.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I TYR* 3.2 45.3 - - + +
63I SER* 4.2 21.9 + - - +
64I GLY* 4.8 1.8 - - - +
480I SER* 4.9 7.2 - - - +
481I LEU* 6.6 0.2 - - + -
28N GLU* 2.8 28.5 + - + +
29N HIS* 3.7 23.1 - - + +
30N ILE 3.2 0.2 - - - -
31N LYS* 1.3 79.7 - - - +
33N HIS* 1.3 68.9 + - + +
34N ASN* 3.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N HIS* 3.0 29.0 + - - +
30N ILE 3.8 0.7 - - - -
32N LEU* 1.3 82.9 - - + +
34N ASN* 1.3 66.4 + - - +
35N MET* 2.9 28.2 + - + +
82N LEU* 3.5 35.9 - - + -
85N SER* 5.7 1.4 + - - -
----------------------------------------------------------
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