Contacts of the strand formed by residues 24 - 31 (chain A) in PDB entry 2DHI
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 TRP 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 32.4 - - + +
16A ARG 4.0 1.1 - - - -
17A GLN* 3.4 27.4 - - + +
23A ARG* 1.3 95.2 + - - +
25A LYS* 1.3 59.4 + - - +
26A LYS 4.3 0.6 + - - -
70A ILE* 3.9 9.6 - - + -
71A GLN* 2.9 30.3 + - - +
72A PRO 3.9 0.4 + - - -
73A PRO* 3.7 37.6 - - + -
81A LEU* 3.9 15.0 - - + -
93A SER* 3.2 39.7 - - - -
94A LEU 3.3 28.3 - - - -
95A CYS* 3.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 2.9 - - - -
16A ARG* 3.0 32.4 + - + +
18A SER* 4.9 5.2 - - - -
21A LEU* 3.4 34.2 - - + +
23A ARG* 4.7 6.5 - - + +
24A TRP* 1.3 75.2 - - - +
26A LYS* 1.3 65.1 + - - +
27A ASN* 3.0 31.7 + - - +
41A ASP* 5.6 4.8 + - - -
49A GLU* 4.3 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 3.5 60.1 + - + +
14A LEU* 4.0 2.1 - - - +
15A LEU* 3.5 30.9 - - + +
25A LYS* 1.3 71.5 - - - +
27A ASN* 1.3 66.8 + - - +
41A ASP 4.2 4.2 - - - +
42A ASP* 5.4 0.3 - - - +
97A GLU* 5.1 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 2.9 22.3 - - - -
14A LEU 2.7 33.8 + - - +
16A ARG* 3.2 18.2 - - - +
25A LYS* 3.0 38.5 - - - +
26A LYS* 1.3 78.9 + - - +
28A TRP* 1.3 60.7 + - - +
29A PHE* 3.9 11.9 - - + -
39A TYR* 5.2 0.2 - - + -
40A TYR 4.0 4.0 + - - -
41A ASP* 4.2 8.2 + - - +
49A GLU* 3.0 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.5 26.9 - - - -
12A GLY* 2.9 48.2 - - - -
13A TRP* 3.1 39.9 - + + -
27A ASN* 1.3 76.5 - - - +
29A PHE* 1.3 61.7 + - - +
30A ASP* 2.5 29.1 + - - -
39A TYR* 2.9 4.7 - - - -
40A TYR* 2.7 53.8 + + - +
41A ASP 4.9 0.2 + - - -
42A ASP 4.2 21.8 - - - +
43A GLN* 4.9 6.7 - - + +
45A ARG* 4.0 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 3.1 25.9 + - - +
14A LEU* 3.6 56.3 - - + -
15A LEU 4.5 0.9 - - - -
16A ARG* 4.1 14.1 - - + -
27A ASN* 3.9 11.9 - - + -
28A TRP* 1.3 75.3 - - - +
30A ASP* 1.3 78.4 + - - +
37A LEU* 4.1 19.1 - - + -
39A TYR* 3.8 34.3 - + + -
92A ILE* 5.5 1.3 - - + -
94A LEU* 3.2 43.1 - - + -
105A TRP* 4.1 12.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.6 31.5 - - + -
10A LYS 3.9 5.8 - - - -
11A SER* 2.7 27.7 - - - -
28A TRP* 2.5 37.4 + - - +
29A PHE* 1.3 89.5 - - - +
31A LEU* 1.3 63.3 + - - +
32A TRP* 3.5 7.4 - - - +
37A LEU* 3.5 4.7 - - - +
38A ILE 3.1 34.9 + - - +
40A TYR* 4.2 8.0 - - + -
45A ARG* 5.4 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.0 8.3 - - - +
9A VAL* 2.7 49.1 + - + -
10A LYS 3.4 10.7 + - - +
30A ASP* 1.3 72.4 - - - +
32A TRP* 1.3 63.0 + - - +
35A GLY 3.2 22.0 - - - +
36A HIS 3.8 0.4 - - - -
37A LEU* 3.6 24.3 - - + +
54A MET* 4.2 14.8 - - + -
105A TRP* 4.2 12.3 - - + -
108A THR* 3.7 28.7 - - + -
109A LEU* 4.3 9.4 - - + -
112A SER* 4.2 20.0 - - - +
----------------------------------------------------------
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