Contacts of the helix formed by residues 20 - 34 (chain A) in PDB entry 2CSF
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 ALA 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 1.3 72.3 - - - +
21A ALA* 1.3 63.7 + - - +
23A TYR* 2.9 35.4 + - + +
24A ASP* 4.2 0.9 + - - +
59A LYS 5.3 3.4 - - - +
61A ASN* 5.3 3.4 - - + +
62A PRO* 3.2 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 2.9 14.9 + - - +
20A ALA* 1.3 77.6 - - - +
22A ILE* 1.3 55.0 + - - +
24A ASP* 2.6 36.3 + - + +
25A GLU* 3.1 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.8 16.6 - - + -
19A THR* 2.7 31.1 + - - +
20A ALA 3.7 3.4 - - - +
21A ALA* 1.3 71.9 - - - +
23A TYR* 1.3 77.2 + - + +
25A GLU* 3.5 14.3 + - - +
26A ILE* 3.0 38.1 + - + +
62A PRO* 4.8 0.2 - - + -
73A LEU* 3.2 55.4 - - + +
76A ILE* 4.6 1.6 - - + -
77A ARG* 3.8 25.8 - - + +
80A LEU* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 2.9 27.1 + - + +
21A ALA 2.8 3.6 + - - -
22A ILE* 1.3 81.2 - - + +
24A ASP* 1.3 62.7 + - - +
26A ILE* 3.1 21.6 + - + +
27A GLN* 3.2 17.2 + - - +
55A LEU* 3.4 44.2 - - + +
56A LEU* 3.8 6.9 - - + +
59A LYS* 3.4 45.1 - - + -
60A GLU* 2.6 39.0 + - - +
62A PRO* 4.1 9.9 - - + -
69A LEU* 4.2 9.0 - - - +
73A LEU* 3.9 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 5.2 0.5 - - - +
21A ALA* 2.6 21.3 + - + +
23A TYR* 1.3 74.9 - - - +
25A GLU* 1.3 64.6 + - + +
27A GLN* 2.8 35.4 + - - +
28A GLN* 3.1 23.0 + - + +
59A LYS* 3.9 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.1 20.9 + - + +
22A ILE* 3.7 8.7 + - - +
24A ASP* 1.3 75.5 - - + +
26A ILE* 1.3 57.2 + - - +
28A GLN* 4.0 10.6 - - - +
29A GLU* 2.8 33.4 + - - +
77A ARG* 4.7 12.3 + - - -
80A LEU* 3.5 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.0 34.5 - - + +
23A TYR* 3.1 19.9 + - + +
24A ASP 3.0 0.6 - - - -
25A GLU* 1.3 75.8 - - - +
27A GLN* 1.3 65.5 + - - +
29A GLU* 3.8 1.4 - - - +
30A MET* 3.1 38.3 + - + +
40A PHE* 3.4 43.9 - - + -
52A LEU* 4.0 17.7 - - + -
55A LEU* 5.6 1.6 - - + -
56A LEU* 4.1 8.1 - - + -
73A LEU* 5.0 3.4 - - + -
76A ILE* 4.1 16.4 - - + -
80A LEU* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR 3.2 12.1 + - - +
24A ASP* 2.8 30.2 + - - +
26A ILE* 1.3 78.5 - - - +
28A GLN* 1.3 64.5 + - + +
30A MET* 3.5 21.2 + - - +
31A LYS* 3.6 7.1 + - - +
56A LEU* 4.2 23.2 - - + +
59A LYS* 3.5 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.1 18.5 + - + +
25A GLU* 4.1 11.8 - - - +
27A GLN* 1.3 74.4 - - + +
29A GLU* 1.3 67.1 + - - +
30A MET 3.0 1.8 - - - -
31A LYS* 2.7 21.6 + - + +
32A ARG* 2.7 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU 2.8 23.9 + - - +
26A ILE 3.8 0.4 - - - +
28A GLN* 1.3 72.0 - - - +
30A MET* 1.3 53.0 + - - +
32A ARG* 4.1 7.8 - - - +
33A ALA* 2.7 40.6 + - - +
40A PHE* 3.6 23.8 - - + -
80A LEU* 3.8 9.5 - - + +
84A GLN* 3.8 8.4 + - - +
87A ARG* 3.1 48.1 + - - +
91A TYR* 3.3 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.1 41.1 + - + +
27A GLN* 3.5 11.2 - - - +
28A GLN 2.8 1.6 + - - -
29A GLU* 1.3 78.9 - - - +
31A LYS* 1.3 53.0 + - - +
34A LYS* 2.6 32.2 + - - -
35A VAL* 2.9 42.1 + - + +
36A SER* 3.4 2.2 - - - -
37A GLN* 3.1 42.4 - - + -
40A PHE* 3.9 10.8 - - + -
52A LEU* 4.4 0.4 - - + -
56A LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 3.6 5.9 + - - +
28A GLN* 2.7 28.9 + - + +
30A MET* 1.3 75.2 - - - +
32A ARG* 1.3 80.8 + - + +
34A LYS* 2.7 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 5.3 11.7 + - - -
3A SER 5.9 0.8 + - - -
28A GLN* 2.7 33.0 + - - +
29A GLU* 3.6 12.6 - - - +
31A LYS* 1.3 91.6 - - - +
33A ALA* 1.3 60.1 + - - +
34A LYS* 3.7 7.4 + - - +
84A GLN* 3.4 32.3 + - - +
88A ASP* 4.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 2.7 23.8 + - - +
30A MET 4.2 0.4 - - - +
32A ARG* 1.3 69.8 - - - +
34A LYS* 1.3 76.0 + - - +
35A VAL* 3.6 13.1 - - + +
84A GLN* 5.1 0.9 - - - +
88A ASP* 3.9 15.2 - - - +
91A TYR* 3.2 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET 2.6 13.2 + - - -
31A LYS* 2.7 36.5 + - - +
32A ARG 3.3 8.4 - - - +
33A ALA* 1.3 82.3 - - - +
35A VAL* 1.3 58.6 + - - +
99A SER* 5.7 7.9 - - - +
----------------------------------------------------------
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