Contacts of the helix formed by residues 24 - 34 (chain A) in PDB entry 2NYM
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 ASP 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 2.9 23.5 + - - +
23A GLU* 1.3 77.9 - - - +
25A VAL* 1.3 47.1 - - - +
26A GLN* 2.4 32.9 + - - +
27A LEU* 2.5 31.1 + - - +
28A ARG* 4.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.4 4.1 - - - +
24A ASP* 1.3 70.7 - - - +
26A GLN* 1.3 61.6 + - - +
27A LEU 3.1 0.4 - - - -
28A ARG* 2.9 35.7 - - - +
29A LEU* 3.0 23.9 + - + +
62A GLU* 3.3 41.1 - - + +
64A GLU* 6.5 0.7 - - + -
65A VAL* 4.2 5.8 - - + -
285B LYS* 5.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 2.4 25.6 + - - +
25A VAL* 1.3 73.4 - - - +
27A LEU* 1.3 59.6 + - + +
29A LEU* 3.6 24.9 - - - +
30A ASN* 3.9 6.4 + - - +
64A GLU* 5.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.8 35.4 - - + +
22A ASN* 2.9 33.2 - - + +
24A ASP* 2.5 26.9 + - - +
26A GLN* 1.3 72.9 - - + +
28A ARG* 1.3 64.0 + - - +
29A LEU 2.7 6.6 + - - -
30A ASN* 2.9 21.3 + - + +
31A SER* 3.0 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 3.3 21.3 + - - +
20A LEU* 3.7 19.9 - - - +
21A ARG* 4.2 4.3 - - - +
22A ASN* 3.8 10.8 - - + +
23A GLU* 3.9 25.0 + - - +
24A ASP 3.6 2.0 + - - +
25A VAL* 2.9 48.0 - - - +
27A LEU* 1.3 78.2 - - - +
29A LEU* 1.3 65.4 + - - +
31A SER* 3.9 0.9 - - - -
32A ILE* 3.2 24.9 + - - +
60A TYR* 4.2 20.0 - - + +
61A ASP* 5.1 1.8 + - - +
62A GLU* 3.5 27.4 + - - +
65A VAL* 4.5 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.0 17.7 + - + +
26A GLN* 3.6 22.0 - - - +
27A LEU 2.7 1.2 + - - -
28A ARG* 1.3 74.1 - - - +
30A ASN* 1.3 59.2 + - + +
32A ILE* 2.7 8.9 + - - +
33A LYS* 2.6 64.5 + - + +
64A GLU* 3.7 34.3 - - + +
65A VAL* 3.4 36.8 - - + -
68A ALA* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.3 12.3 - - - +
19A GLU* 4.8 3.3 - - - +
26A GLN 3.9 7.3 + - - +
27A LEU* 2.9 18.3 + - + +
29A LEU* 1.3 79.2 - - + +
31A SER* 1.3 72.6 + - - +
33A LYS* 3.0 18.0 + - - +
34A LYS* 3.1 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.8 20.6 + - - +
19A GLU* 3.1 42.6 + - - +
20A LEU* 3.2 25.7 - - - +
27A LEU 3.0 6.7 + - - -
28A ARG 3.9 1.6 - - - -
29A LEU 2.9 0.6 + - - -
30A ASN* 1.3 84.9 + - - +
32A ILE* 1.3 62.5 + - - -
34A LYS* 2.9 11.4 + - - +
35A LEU* 3.0 9.9 + - - -
38A ILE* 4.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.5 19.7 - - + +
28A ARG 3.2 12.3 + - - +
29A LEU* 2.7 12.5 + - - +
31A SER* 1.3 76.1 - - - +
33A LYS* 1.3 57.2 + - - +
35A LEU* 2.8 38.7 + - + +
55A LEU* 3.7 30.1 - - + -
60A TYR* 4.0 24.7 - - + +
65A VAL* 4.4 9.0 - - + +
68A ALA* 4.2 8.1 - - + -
69A LEU* 3.7 37.2 - - + +
72A GLN* 3.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.6 48.6 + - + +
30A ASN* 3.0 14.3 + - - +
32A ILE* 1.3 74.5 - - - +
34A LYS* 1.3 59.9 + - + +
35A LEU 3.5 0.7 - - - -
64A GLU* 4.3 13.1 + - - +
68A ALA* 4.4 17.5 - - + -
72A GLN* 3.3 16.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
16A LEU* 3.9 22.1 - - + +
30A ASN* 3.1 30.2 + - - +
31A SER 2.9 10.5 + - - +
33A LYS* 1.3 78.6 - - + +
35A LEU* 1.3 53.4 + - - +
36A SER* 2.5 20.9 + - - -
37A THR* 2.7 33.7 + - + +
38A ILE* 3.3 12.2 - - + +
72A GLN* 4.9 1.1 - - - +
----------------------------------------------------------
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