Contacts of the strand formed by residues 21 - 25 (chain A) in PDB entry 3FJD
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 HIS 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU 3.6 0.3 - - - +
15A TYR* 3.5 2.3 - - - -
16A CYS* 2.7 38.2 + - + +
19A GLY* 3.3 21.9 + - - -
20A GLY* 1.3 78.0 - - - +
22A PHE* 1.3 62.8 + - - +
23A LEU 3.8 0.3 + - - -
33A GLY 3.7 16.2 - - - -
34A THR* 3.8 10.5 - - - +
35A ARG* 3.6 29.7 + - + +
111A LEU* 3.8 20.8 - - + +
112A LYS 4.2 3.2 + - - -
113A LYS 3.1 27.6 - - - -
114A ASN 3.8 4.6 + - - -
115A GLY* 3.3 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.9 27.4 - - + -
14A LEU 3.3 4.3 - - - +
15A TYR* 3.8 33.0 - + + -
20A GLY 5.4 1.3 - - - -
21A HIS* 1.3 74.1 - - - +
23A LEU* 1.3 65.0 + - - +
24A ARG 3.4 0.2 + - - -
33A GLY* 3.2 4.5 - - - -
34A THR* 2.9 46.7 + - - +
35A ARG* 3.9 11.9 - - - -
36A ASP 4.6 0.4 - - - -
37A ARG* 3.5 53.6 - - + -
42A ILE* 3.8 31.2 - - + -
111A LEU* 4.6 0.4 - - - -
135A LEU* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.9 37.1 + - + +
21A HIS 3.8 1.4 + - - -
22A PHE* 1.3 73.7 - - - +
24A ARG* 1.3 62.5 + - - +
25A ILE* 5.3 0.2 - - + -
31A VAL* 3.8 24.0 - - + -
32A ASP 3.8 6.5 - - - +
42A ILE* 3.3 14.0 - - - +
44A PHE* 3.2 34.5 - - + -
56A ILE* 4.8 1.3 - - + -
65A LEU* 4.0 28.0 - - + -
73A LEU* 5.0 1.6 - - + -
109A VAL* 4.8 8.3 - - + -
111A LEU* 4.4 10.8 - - + -
132A TRP* 3.7 31.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
22A PHE 4.1 3.1 - - - +
23A LEU* 1.3 78.4 - - - +
25A ILE* 1.3 67.4 + - - +
26A LEU* 3.8 30.6 - - + +
30A THR 3.8 0.5 - - - +
31A VAL* 3.2 8.4 - - - +
32A ASP* 2.8 74.0 + - - +
33A GLY 4.5 1.6 + - - -
34A THR* 3.8 25.6 + - + +
39A ASP* 2.8 45.7 + - - +
41A HIS* 3.6 18.6 - - + +
42A ILE* 3.9 5.8 - - + -
44A PHE* 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.3 0.2 - - + -
24A ARG* 1.3 79.1 - - - +
26A LEU* 1.3 65.3 + - - +
29A GLY* 4.5 0.7 - - - -
30A THR 3.4 7.4 - - - +
31A VAL* 4.3 8.5 - - + -
41A HIS* 3.4 24.1 + - - +
44A PHE* 3.6 28.2 - - + -
58A SER* 4.7 7.3 + - - -
61A THR* 4.5 3.8 + - - +
63A GLN* 3.6 33.7 + - + +
64A TYR 4.1 5.6 - - - +
65A LEU* 3.7 44.0 - - + +
75A GLY* 3.9 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