Contacts of the helix formed by residues 15 - 29 (chain A) in PDB entry 2CRA
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 SER 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 1.3 75.9 - - - +
16A LYS* 1.3 69.5 + - - +
17A GLY* 3.1 5.8 - - - -
18A GLN* 2.8 31.9 + - - -
19A LEU* 2.9 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 1.3 75.0 - - - +
17A GLY* 1.3 60.4 + - - +
19A LEU* 4.4 8.2 - - - +
20A ARG* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.1 4.3 - - - -
16A LYS* 1.3 85.6 - - - +
18A GLN* 1.3 61.9 + - - +
20A ARG* 3.6 18.5 - - - +
21A GLU* 4.0 12.5 - - - +
44A THR* 4.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.3 13.3 + - + -
15A SER* 2.8 39.2 + - - +
17A GLY* 1.3 76.0 - - - +
19A LEU* 1.3 65.8 + - - +
20A ARG 3.0 2.1 + - - -
21A GLU 3.2 6.1 + - - -
22A LEU* 3.4 8.8 + - - +
44A THR* 3.0 59.9 + - - +
45A SER* 4.9 2.2 + - - -
46A LEU* 3.3 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 5.5 6.1 - - + -
13A PRO 4.1 3.4 - - - +
14A TYR* 2.9 50.0 - - + +
15A SER 2.9 13.5 + - - +
16A LYS* 4.4 6.1 - - - +
18A GLN* 1.3 74.1 - - - +
20A ARG* 1.3 57.6 + - - +
22A LEU* 3.6 7.9 - - + -
23A GLU* 2.8 52.9 + - + +
54A TRP* 3.3 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 3.0 22.1 + - - +
17A GLY* 3.6 12.8 - - - +
18A GLN 3.0 0.6 - - - -
19A LEU* 1.3 78.4 - - - +
21A GLU* 1.3 75.7 + - - +
23A GLU* 4.4 6.6 - - - +
24A ARG* 3.3 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY 4.0 8.5 - - - +
18A GLN 3.2 1.2 + - - -
19A LEU 3.2 0.4 - - - -
20A ARG* 1.3 100.8 - - - +
22A LEU* 1.3 65.0 + - - +
24A ARG* 3.6 7.3 + - - +
25A GLU* 2.8 43.7 + - - +
40A ILE* 4.6 7.4 - - + -
43A ALA* 4.3 19.1 - - + +
44A THR* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 4.5 4.3 - - + -
18A GLN 3.5 15.5 - - - +
19A LEU* 3.2 27.5 + - + +
21A GLU* 1.3 76.1 - - - +
23A GLU* 1.3 60.1 + - - +
25A GLU* 3.2 1.6 + - - -
26A TYR* 2.8 30.7 + - - +
40A ILE* 3.8 14.8 - - + -
44A THR* 4.6 0.4 - - + -
46A LEU* 4.0 17.9 - - + -
51A ILE* 3.2 42.0 - - + -
54A TRP* 3.6 30.7 - - + -
55A PHE* 3.4 16.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 2.8 37.2 + - - +
20A ARG* 4.4 5.1 - - - +
22A LEU* 1.3 71.6 - - - +
24A ARG* 1.3 63.9 + - + +
26A TYR* 3.2 6.7 + - - +
27A ALA* 2.9 25.3 + - - +
54A TRP* 3.7 26.2 - - + -
58A ARG* 5.1 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.3 25.8 + - + +
21A GLU* 3.7 11.7 - - - +
22A LEU 3.2 0.6 - - - -
23A GLU* 1.3 81.5 - - + +
25A GLU* 1.3 72.5 + - - +
27A ALA* 3.2 13.9 + - - +
28A ALA* 3.3 12.1 + - - +
----------------------------------------------------------
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 GLU* 2.8 44.1 + - - +
22A LEU 3.7 3.4 - - - +
24A ARG* 1.3 83.5 - - - +
26A TYR* 1.3 62.7 + - - +
28A ALA* 3.2 8.9 + - - +
29A ASN* 3.0 29.5 + - - -
32A ILE* 4.7 2.9 - - + -
36A LYS* 3.3 49.0 + - + +
40A ILE* 3.7 13.7 - - + +
55A PHE* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 2.8 17.5 + - - +
23A GLU* 3.4 6.7 - - - +
25A GLU* 1.3 75.5 - - - +
27A ALA* 1.3 65.5 + - - +
29A ASN* 2.8 30.7 + - - +
30A LYS* 3.2 62.8 + - + +
54A TRP* 4.2 7.2 - + + -
55A PHE* 3.5 16.1 - + + -
58A ARG* 3.4 56.3 + - + -
59A ARG* 3.5 19.5 - - + +
62A GLU* 3.7 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 2.9 12.1 + - - +
24A ARG* 3.2 11.4 + - - +
26A TYR* 1.3 80.9 - - + +
28A ALA* 1.3 60.9 + - - +
30A LYS* 5.5 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG 3.3 8.3 + - - +
25A GLU* 3.2 14.7 + - - +
26A TYR 3.0 0.6 - - - -
27A ALA* 1.3 81.6 - - - +
29A ASN* 1.3 70.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.0 16.0 + - - +
26A TYR* 2.8 16.9 + - - +
28A ALA* 1.3 92.5 - - - +
30A LYS* 1.3 65.1 + - - +
31A PHE 3.6 14.4 + - - +
32A ILE* 3.3 28.2 - - - +
36A LYS* 5.3 8.7 - - - +
55A PHE* 3.6 2.1 - - - -
----------------------------------------------------------
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