Contacts of the strand formed by residues 42 - 47 (chain N) in PDB entry 2IAN
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 LEU 42 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N PHE* 4.5 13.3 - - + -
35N HIS 3.6 4.3 - - - +
36N GLN* 3.9 25.8 - - + +
40N GLY 3.5 5.1 + - - +
41N GLN* 1.3 78.9 - - - +
43N ILE* 1.3 62.0 + - - +
44N ASN 4.1 0.5 + - - -
85N PHE* 4.3 18.6 - - + -
43O LEU* 3.9 15.5 - - + -
90O PHE* 3.9 26.4 - - + -
101O PHE* 3.6 69.9 + - + +
102O GLY 5.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N PHE* 3.3 6.7 - - - +
35N HIS* 2.8 53.9 + - + +
37N ASN* 4.2 17.0 - - + +
41N GLN* 3.8 22.4 - - + +
42N LEU* 1.3 74.1 - - - +
44N ASN* 1.3 73.7 + - - +
45N LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N GLN* 2.6 30.5 + - - -
33N TRP 4.2 0.4 + - - -
34N PHE* 3.2 25.4 - - + -
42N LEU 4.1 1.4 + - - -
43N ILE* 1.3 84.7 - - - +
45N LEU* 1.3 62.6 + - - +
46N PHE* 3.2 26.5 + - - -
47N TYR 3.8 0.5 + - - -
98O THR* 3.4 21.3 - - + +
99O GLY 3.4 17.4 + - - +
100O TYR* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N TRP* 2.7 27.1 + - + +
34N PHE 3.5 20.6 - - - +
35N HIS* 3.6 24.9 - - + +
43N ILE* 4.4 7.2 - - + +
44N ASN* 1.3 79.9 - - - +
46N PHE* 1.3 88.7 + - + +
55N ASN* 4.9 9.2 + - - +
58N LEU* 4.3 21.1 - - + -
71N LEU* 4.2 8.7 - - + -
84N TYR* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N GLN* 3.2 7.6 - - - +
33N TRP* 2.9 31.9 + - + +
44N ASN* 3.2 8.9 + - - +
45N LEU* 1.3 97.3 - - + +
47N TYR* 1.3 64.7 + - - +
48N ILE* 4.2 12.6 - - + -
53N LYS* 3.9 34.5 - - + +
54N GLN 3.9 19.5 - - - -
55N ASN* 3.9 14.8 - - + -
58N LEU* 3.6 39.3 - - + -
59N SER* 3.8 16.4 - - - -
60N ALA* 4.0 11.7 - - + -
71N LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L ASP* 4.2 8.5 - - - +
69L GLU* 4.2 11.9 - - + -
70L GLN* 3.5 27.1 - - - +
30N ASN* 2.5 48.4 + - + -
31N LEU 4.0 0.4 - - - -
32N GLN* 3.8 15.7 - - + -
44N ASN* 3.8 4.0 + - - -
46N PHE* 1.3 69.5 - - - +
48N ILE* 1.3 59.9 + - - +
49N PRO* 3.4 31.7 - - + +
53N LYS* 2.8 37.1 + - - +
89N LEU* 6.3 0.4 - - + -
96O HIS 3.5 9.4 + - - -
97O GLY* 3.6 36.8 - - - -
98O THR* 3.6 25.0 + - - +
----------------------------------------------------------
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