Contacts of the strand formed by residues 67 - 73 (chain N) in PDB entry 2ZHX
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 PRO 67 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N ILE* 3.9 33.2 - - + -
59N THR* 4.2 12.1 - - + -
65N TYR 3.8 6.5 - - - +
66N LYS* 1.3 90.5 - - + +
68N TRP* 1.3 61.2 + - - +
84N LEU* 4.3 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 68 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 3.8 7.9 - - + -
33N ILE* 3.8 24.9 - - + -
35N ASN* 3.1 34.5 - - + -
36N LYS 4.5 0.2 - - - -
37N PRO* 3.3 37.0 - - + +
38N GLU 5.0 1.4 - - - +
41N ILE* 3.3 24.0 - - + -
58N LEU* 3.2 19.2 + - + +
59N THR* 4.3 4.5 - - - -
60N SER 5.0 0.4 - - - +
66N LYS 4.3 4.3 - - - +
67N PRO* 1.3 77.5 - - - +
69N ALA* 1.3 88.8 + - + +
83N MET* 3.8 2.4 - - - +
84N LEU* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ILE* 4.2 9.0 - - + -
57N LEU* 3.6 3.8 - - - +
58N LEU* 2.9 40.2 + - + +
68N TRP* 1.3 106.3 - - + +
70N LEU* 1.3 61.7 + - - +
71N VAL* 5.1 0.7 - - + -
81N ILE* 5.1 3.4 - - + -
82N LYS 3.3 13.7 - - - +
83N MET* 4.8 2.0 - - - -
84N LEU* 3.9 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N ILE 5.6 0.2 - - - +
8N ILE* 5.7 6.1 - - + -
11N GLU* 3.7 30.7 - - + +
12N THR* 3.6 27.6 - - + -
55N VAL* 4.5 8.7 - - + -
56N MET 3.3 13.0 - - - +
57N LEU* 5.2 4.3 - - + -
69N ALA* 1.3 74.5 - - - +
71N VAL* 1.3 78.3 + - - +
72N ILE* 3.9 16.2 - - + -
80N LYS 3.5 3.3 - - - +
82N LYS* 2.8 52.6 + - + +
84N LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195M LEU* 4.0 14.1 - - + -
33N ILE* 4.2 11.2 - - + -
54N ASN 3.5 1.6 - - - +
55N VAL* 3.7 1.0 - - - -
56N MET* 2.8 57.2 + - + +
58N LEU* 3.4 28.5 - - + -
70N LEU* 1.3 80.1 - - - +
72N ILE* 1.3 63.9 + - - +
73N GLN 3.9 0.2 - - - -
79N ASN* 3.5 38.8 - - + +
80N LYS 3.9 2.7 - - - +
81N ILE* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N THR* 4.0 24.2 - - + -
53N GLU* 3.9 24.5 - - + -
54N ASN 3.7 2.0 - - - -
55N VAL* 4.4 19.5 - - + -
70N LEU* 3.9 12.1 - - + -
71N VAL* 1.3 76.1 - - - +
73N GLN* 1.3 60.2 + - - +
74N ASP* 5.1 2.3 - - + +
78N GLU 3.8 3.6 - - - +
80N LYS* 3.1 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ASN* 5.4 0.5 + - - -
194M PRO* 2.7 41.0 + - - +
195M LEU* 3.9 3.2 - - - +
198M SER* 5.3 2.9 + - - -
53N GLU* 2.9 7.8 - - - +
54N ASN* 2.7 57.3 + - + +
56N MET* 3.5 17.9 - - + +
71N VAL 3.9 1.4 - - - -
72N ILE* 1.3 72.3 - - - +
74N ASP* 1.3 63.6 + - - +
77N GLY* 3.4 26.9 + - - +
78N GLU 3.8 2.0 - - - -
79N ASN* 3.2 23.1 + - - +
----------------------------------------------------------
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