Contacts of the strand formed by residues 68 - 73 (chain A) in PDB entry 1Z10
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 VAL 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 3.8 28.3 - - + +
35A PRO* 3.9 9.9 - - - +
65A TYR 4.3 5.0 - - - +
66A GLY 3.2 1.2 - - - +
67A PRO* 1.3 85.7 - - + +
69A PHE* 1.3 65.6 + - - +
79A VAL* 3.9 14.6 - - + -
80A VAL 3.2 2.7 - - - -
81A LEU* 4.1 8.5 - - + -
86A ALA* 3.8 23.1 - - + -
380A PHE* 3.9 22.2 - - + -
381A ARG* 3.9 15.0 - - - +
383A PHE* 4.3 18.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 3.7 5.4 - - - -
35A PRO 3.2 16.2 - - - +
37A PRO* 4.9 0.9 - - + -
58A LEU* 3.3 34.8 - - + -
61A ILE* 3.6 24.9 - - + -
62A SER* 3.6 15.3 - - - -
65A TYR* 3.9 15.5 - - + -
66A GLY 3.5 15.9 - - - +
68A VAL* 1.3 77.1 - - - +
70A THR* 1.3 72.5 + - - +
71A ILE* 4.1 12.3 - - + -
79A VAL* 3.2 4.7 - - - +
80A VAL* 2.7 80.4 + - + -
82A CYS* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 8.2 - - + +
34A PRO* 2.8 45.1 + - - +
35A PRO 3.1 6.5 + - - -
36A GLY* 3.5 20.0 - - - -
37A PRO* 3.7 5.4 - - - +
45A ASN* 4.7 0.5 - - - +
69A PHE* 1.3 81.0 - - - +
71A ILE* 1.3 64.3 + - - +
72A HIS* 3.8 15.7 + - + -
77A ARG* 3.7 35.0 - - + -
78A VAL 3.3 7.6 - - - +
79A VAL* 4.2 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 4.0 9.0 - - + -
45A ASN* 3.6 29.8 - - + +
49A LEU* 4.1 4.5 - - + -
58A LEU* 3.9 14.8 - - + -
61A ILE* 3.4 33.2 - - + -
69A PHE* 4.1 11.2 - - + -
70A THR* 1.3 75.6 - - - +
72A HIS* 1.3 64.5 + - - +
73A LEU* 3.9 30.3 - - + -
76A ARG 3.6 0.3 - - - +
77A ARG* 3.7 2.3 - - - -
78A VAL* 2.8 38.5 + - + +
80A VAL* 3.7 21.1 - - + -
392A TYR* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.8 0.4 - - + -
37A PRO 4.6 2.8 + - - -
39A PRO* 3.5 31.8 - - + +
44A GLY* 3.6 18.2 - - - -
45A ASN* 2.8 51.9 + - - +
46A TYR 4.3 0.2 + - - -
49A LEU* 4.6 0.3 - - - +
70A THR* 3.8 23.3 - - + +
71A ILE* 1.3 73.6 - - - +
73A LEU* 1.3 65.5 + - - +
74A GLY 3.1 7.8 + - - +
75A PRO* 5.1 3.8 - - + -
76A ARG 3.2 4.7 - - - -
77A ARG* 3.2 35.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.9 17.0 - - + -
54A MET* 3.9 26.9 - - + -
58A LEU* 5.0 0.9 - - + -
71A ILE* 3.9 21.5 - - + -
72A HIS* 1.3 69.6 - - - +
74A GLY* 1.3 63.0 + - - +
75A PRO* 3.3 1.6 - - - +
76A ARG* 2.7 39.6 + - + +
78A VAL* 4.1 15.0 - - + -
218A GLN* 6.3 0.2 - - - +
221A GLU* 5.0 4.5 - - + +
222A MET* 3.7 29.9 - - + -
392A TYR* 3.5 42.0 - - + +
----------------------------------------------------------
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