Contacts of the strand formed by residues 67 - 73 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.2 37.2 - - + -
57B LEU* 4.9 1.6 - - + -
58B LEU 3.8 5.8 - - - +
59B THR* 4.2 6.5 - - + -
65B TYR 3.3 10.1 - - - +
66B LYS* 1.4 104.9 - - + +
68B TRP* 1.3 59.8 + - - +
84B LEU* 4.3 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.6 24.9 - - + -
33B ILE* 3.8 19.1 - - + -
35B ASN* 2.9 39.9 - - + -
36B LYS 4.7 0.2 - - - -
37B PRO* 3.5 27.1 - - + +
38B GLU* 5.2 4.7 - - + +
41B ILE* 3.2 23.6 - - + -
58B LEU* 2.8 19.3 + - + +
59B THR* 4.6 2.2 - - - -
60B SER 5.1 0.4 - - - +
66B LYS 4.3 3.6 - - - +
67B PRO* 1.3 77.1 - - - +
69B ALA* 1.3 77.4 + - + +
83B MET* 3.4 28.7 - - + +
84B LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.3 12.1 - - + -
57B LEU* 3.6 4.9 - - - +
58B LEU* 3.0 31.9 + - + +
68B TRP* 1.3 102.0 - - + +
70B LEU* 1.3 61.0 + - - +
81B ILE* 5.0 1.3 - - + -
82B LYS 3.5 8.5 - - - +
83B MET* 3.8 19.7 - - - -
84B LEU* 3.8 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 5.4 0.9 - - + +
8B ILE* 5.3 8.7 - - + +
11B GLU* 3.6 34.1 - - + +
12B THR* 4.0 14.4 - - + -
55B VAL* 4.2 12.6 - - + -
56B MET 3.3 13.7 - - - +
57B LEU* 4.4 9.6 - - + -
69B ALA* 1.3 73.8 - - - +
71B VAL* 1.3 99.7 + - - +
72B ILE* 3.8 15.0 - - + -
80B LYS 3.9 0.2 - - - +
81B ILE* 3.5 0.7 - - - +
82B LYS* 2.8 44.8 + - + +
84B LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.2 9.2 - - + -
33B ILE* 4.0 19.3 - - + -
54B ASN 3.7 1.9 - - - +
55B VAL 3.7 0.5 - - - -
56B MET* 2.8 64.2 + - + +
58B LEU* 4.0 19.3 - - + -
70B LEU* 1.3 83.0 - - - +
72B ILE* 1.3 66.8 + - - +
79B ASN* 3.5 33.7 - - + +
80B LYS 3.6 4.0 - - - +
81B ILE* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.8 26.9 - - + -
53B GLU* 3.7 40.6 - - + +
54B ASN 3.8 1.1 - - - -
55B VAL* 4.4 15.0 - - + -
70B LEU* 3.8 12.3 - - + -
71B VAL* 1.3 79.9 - - - +
73B GLN* 1.3 61.3 + - - +
74B ASP 4.2 0.4 - - - -
78B GLU 3.6 1.6 - - - +
79B ASN* 3.3 2.9 - - - -
80B LYS* 2.9 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN* 5.5 0.2 + - - -
194A PRO* 2.9 35.8 + - - +
195A LEU* 4.4 1.0 - - - +
198A SER* 5.8 1.2 + - - -
53B GLU* 3.3 6.2 - - - -
54B ASN* 2.9 62.8 + - + +
56B MET* 3.5 19.7 - - + +
72B ILE* 1.3 72.0 - - - +
74B ASP* 1.3 68.9 + - - +
77B GLY* 4.1 14.2 + - - +
78B GLU 3.5 4.3 - - - -
79B ASN* 3.2 26.4 + - - +
80B LYS* 5.3 0.2 - - - -
----------------------------------------------------------
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