Contacts of the strand formed by residues 20 - 26 (chain T) in PDB entry 4IBL
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 LYS 20 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L ILE* 3.8 14.6 - - + -
70L CYS 2.8 30.6 + - - +
72L CYS* 3.8 12.3 - - - -
78L GLY 2.9 28.2 + - - -
79L ARG* 4.0 17.8 + - - +
15T LYS 3.6 1.7 - - - +
16T SER* 3.0 4.5 - - - -
17T THR* 2.9 33.4 + - - +
18T ASN 3.1 3.8 + - - -
19T PHE* 1.3 74.2 - - - +
21T THR* 1.3 59.5 + - - +
22T ILE* 4.5 10.9 - - + +
58T ASP* 4.0 15.5 + - - -
60T THR* 3.5 9.6 - - - +
133T LEU* 3.6 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T TRP* 3.6 35.4 - - + -
15T LYS 3.4 3.4 - - - +
16T SER* 2.9 17.9 + - - +
19T PHE 2.8 20.3 + - - -
20T LYS* 1.3 72.9 - - - +
22T ILE* 1.3 62.9 + - - +
23T LEU 4.3 0.2 - - - -
58T ASP* 3.2 4.0 - - - +
59T LEU* 2.9 27.7 + - + +
60T THR* 2.9 12.3 + - - -
63T ILE* 3.6 25.3 - - + +
100T PHE* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L ARG* 3.5 67.8 - - + +
13T THR 3.8 0.2 - - - +
14T TRP* 4.9 0.7 - - - -
15T LYS* 2.8 51.0 + - + +
20T LYS* 4.5 12.8 - - + +
21T THR* 1.3 84.1 - - - +
23T LEU* 1.3 75.5 + - - +
24T GLU* 4.3 2.7 - - + -
56T GLU* 3.9 15.5 - - + +
57T CYS 3.5 9.4 - - - +
58T ASP* 4.0 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T LEU* 4.3 6.5 - - + -
13T THR 3.6 22.7 - - - +
14T TRP* 3.9 30.7 - - + +
21T THR 4.3 0.4 + - - -
22T ILE* 1.3 76.0 - - - +
24T GLU* 1.3 63.6 + - - +
25T TRP* 3.6 7.5 - - + -
36T VAL* 4.2 9.6 - - + -
56T GLU* 3.1 4.7 - - - -
57T CYS* 2.8 34.3 + - + +
59T LEU* 3.9 18.4 - - + +
73T ALA* 3.8 22.0 - - + -
75T VAL* 3.7 30.5 - - + -
97T SER* 4.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L ARG* 2.8 27.2 + - - -
11T ASN 3.5 1.5 - - - +
12T LEU* 3.2 4.7 - - - +
13T THR* 2.9 41.5 + - - +
15T LYS* 3.4 39.7 - - + +
22T ILE* 4.3 2.9 - - + -
23T LEU* 1.3 79.7 - - - +
25T TRP* 1.3 65.4 + - - +
55T THR 3.6 6.3 - - - +
56T GLU* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 25 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T ALA* 3.6 12.3 - - + -
10T TYR 3.7 12.6 - - - +
11T ASN 3.8 5.2 - - - -
12T LEU* 3.8 17.3 - - + -
23T LEU* 3.6 13.2 - - + -
24T GLU* 1.3 82.8 - - - +
26T GLU* 1.3 84.8 + - - +
34T TYR* 3.4 46.7 - + + -
36T VAL* 3.6 22.0 - - + -
52T THR* 4.4 4.5 - - + -
54T ASP 3.5 17.0 - - - -
55T THR* 3.2 34.1 + - + +
56T GLU 3.5 35.9 - - - -
57T CYS* 3.6 8.3 - - + -
75T VAL* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T ALA* 3.1 10.6 - - - +
10T TYR* 2.9 61.1 + - + +
11T ASN* 4.4 13.5 - - + +
25T TRP* 1.3 81.9 - - - +
27T PRO* 1.4 77.4 - - + +
28T LYS* 4.3 8.4 + - - +
55T THR* 5.9 0.8 - - - +
----------------------------------------------------------
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