Contacts of the helix formed by residues 17 - 35 (chain K) in PDB entry 2CHS
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 GLU 17 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K THR* 1.3 73.0 + - - +
18K GLU* 1.3 60.8 + - - +
20K ILE* 3.4 1.0 + - - +
21K LEU* 2.9 46.2 + - + +
55K ALA* 3.4 14.0 - - + +
56K VAL* 3.9 28.5 - - + +
60K LYS* 2.8 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ARG* 5.3 3.6 - - - +
16K THR* 3.3 8.6 - - + +
17K GLU* 1.3 82.2 - - - +
19K GLU* 1.3 58.6 + - - +
21K LEU* 3.9 10.4 - - - +
22K GLN* 3.0 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K VAL* 3.8 4.9 - - + -
13K GLU* 3.1 25.9 + - - +
14K ARG* 3.3 54.3 + - - +
16K THR* 3.5 17.7 - - + +
17K GLU 3.3 0.4 - - - -
18K GLU* 1.3 75.3 - - - +
20K ILE* 1.3 67.7 + - - +
22K GLN* 4.5 9.9 - - - +
23K LYS* 2.8 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K VAL* 3.8 24.5 - - + -
15K ASP* 3.6 24.2 - - - +
16K THR 3.1 21.9 + - - +
19K GLU* 1.3 77.7 - - - +
21K LEU* 1.3 61.7 + - - +
23K LYS* 3.8 0.5 - - - +
24K THR* 2.9 28.8 + - - +
53K LEU* 4.4 13.5 - - + -
55K ALA* 3.9 11.2 - - + +
56K VAL* 3.5 30.5 - - + +
58K PRO* 3.9 30.5 - - + -
89K ILE* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K GLU* 2.9 28.8 + - + +
18K GLU* 3.9 11.9 - - - +
20K ILE* 1.3 76.5 - - + +
22K GLN* 1.3 55.9 + - - +
24K THR* 4.8 0.2 - - - -
25K LYS* 2.9 32.4 + - - +
56K VAL* 3.7 17.5 - - + -
57K PHE 4.2 3.1 - - - +
58K PRO 4.4 2.7 - - - +
60K LYS* 3.7 54.5 - - + +
61K ALA* 3.6 19.8 - - + +
64K GLU* 6.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLU* 3.0 39.4 + - - +
19K GLU* 4.1 10.3 - - - +
21K LEU* 1.3 76.2 - - - +
23K LYS* 1.3 73.8 + - - +
25K LYS* 3.5 9.1 - - - +
26K GLN* 3.0 48.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
10K THR* 3.9 19.4 + - + +
11K THR 4.1 12.6 + - - +
12K VAL* 3.7 21.5 - - + +
13K GLU* 4.8 3.2 - - - +
19K GLU* 2.8 50.0 + - - +
22K GLN* 1.3 88.0 - - - +
24K THR* 1.3 64.7 + - - +
26K GLN* 3.8 17.2 - - + +
27K LEU* 3.0 24.4 + - - +
109K LEU* 5.6 0.3 - - - +
110K GLU* 4.3 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K THR* 4.8 2.9 - - - -
20K ILE 2.9 22.3 + - - -
23K LYS* 1.3 71.3 - - - +
25K LYS* 1.3 63.6 + - - +
27K LEU* 3.2 9.5 + - + +
28K LEU* 2.9 37.7 + - + +
47K LEU* 3.6 31.6 - - + -
58K PRO* 3.7 30.1 - - + +
61K ALA* 3.9 12.8 - - + -
89K ILE* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU 2.9 19.3 + - - +
22K GLN* 3.5 8.7 - - - +
24K THR* 1.3 75.6 - - - +
26K GLN* 1.3 62.5 + - + +
28K LEU* 3.3 7.1 + - - +
29K GLU* 2.9 61.2 + - - +
61K ALA* 3.8 12.9 - - + +
64K GLU* 4.0 44.8 + - + +
65K LEU* 4.6 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K GLN* 3.0 33.6 + - + +
23K LYS* 3.8 18.1 - - + +
25K LYS* 1.3 82.3 - - + +
27K LEU* 1.3 63.2 + - - +
29K GLU* 3.5 16.2 + - - +
30K LYS* 3.2 23.0 + - - +
109K LEU* 4.5 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K GLY* 4.1 8.1 - - - -
9K ALA* 3.7 48.2 - - - +
10K THR* 3.9 16.2 - - + +
23K LYS 3.0 17.2 + - - +
24K THR* 3.2 8.5 + - + +
26K GLN* 1.3 72.8 - - - +
28K LEU* 1.3 67.4 + - + +
30K LYS* 3.2 4.3 + - - +
31K ILE* 3.0 33.3 + - + +
47K LEU* 6.0 0.2 - - + -
89K ILE* 4.3 11.7 - - + +
91K VAL* 4.4 11.4 - - + -
107K VAL* 3.8 23.3 - - + +
109K LEU* 4.2 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K THR* 2.9 33.6 + - + +
25K LYS* 3.6 5.2 - - - +
27K LEU* 1.3 76.2 - - + +
29K GLU* 1.3 62.8 + - - +
31K ILE* 3.2 7.6 + - + +
32K ILE* 3.0 30.8 + - + +
45K MET* 3.7 27.1 - - + -
47K LEU* 4.9 4.5 - - + -
61K ALA 4.7 1.3 - - - -
62K VAL* 3.8 29.6 - - + +
65K LEU* 3.8 29.4 - - + -
91K VAL* 4.3 16.8 - - + -
93K MET* 4.2 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LYS* 2.9 50.6 + - - +
26K GLN* 3.5 18.6 - - - +
28K LEU* 1.3 76.6 - - - +
30K LYS* 1.3 57.5 + - - +
32K ILE* 3.3 9.9 + - + +
33K GLU* 3.0 29.4 + - - +
64K GLU 5.6 0.2 - - - +
65K LEU* 3.8 17.6 - - + +
----------------------------------------------------------
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 GLN 3.2 11.0 + - - +
27K LEU* 3.2 9.8 + - - +
29K GLU* 1.3 77.7 - - - +
31K ILE* 1.3 65.9 + - - +
33K GLU* 3.0 28.2 + - - +
34K GLU* 3.0 53.7 + - - +
107K VAL* 3.6 25.8 - - + -
109K LEU* 4.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K ILE* 3.8 27.4 - - + +
7K ARG 4.2 4.7 - - - +
8K GLY* 3.9 15.3 - - - +
27K LEU* 3.0 20.5 + - + +
28K LEU* 3.2 10.3 + - + +
30K LYS* 1.3 75.4 - - - +
32K ILE* 1.3 57.7 + - - +
35K ASN* 2.8 40.5 + - - +
37K THR* 5.0 0.7 - - - +
91K VAL* 3.6 30.7 - - + -
93K MET* 4.2 27.1 - - + -
107K VAL* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K LEU* 3.0 23.7 + - + +
29K GLU* 3.6 8.1 - - + +
31K ILE* 1.3 77.1 - - - +
33K GLU* 1.3 54.6 + - - +
36K HIS* 2.8 33.8 + - - -
37K THR* 3.4 29.8 - - - +
65K LEU* 4.1 22.2 - - + -
68K TRP* 3.5 41.7 - - + +
93K MET* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K GLU 3.0 16.3 + - - +
30K LYS* 3.0 36.8 + - - +
32K ILE* 1.3 76.0 - - - +
34K GLU* 1.3 66.5 + - - +
36K HIS* 2.8 34.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K LYS* 3.0 46.6 + - + +
31K ILE 3.8 2.2 - - - +
33K GLU* 1.3 87.5 - - - +
35K ASN* 1.3 63.5 + - - +
36K HIS* 3.8 6.1 + - - -
105K ARG* 3.4 46.9 + - + +
107K VAL* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K ILE* 3.8 18.1 - - + +
31K ILE* 2.8 39.8 + - - +
34K GLU* 1.3 74.7 - - - +
36K HIS* 1.3 72.0 + - - +
37K THR* 3.4 14.2 + - - +
103K GLN 4.8 0.5 - - - +
104K ILE* 3.9 11.3 - - - +
105K ARG* 3.0 51.3 + - - +
----------------------------------------------------------
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