Contacts of the strand formed by residues 64 - 72 (chain B) in PDB entry 4ZHF
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 TYR 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.6 4.9 - + - -
24B ASP* 2.6 46.9 + - + -
27B PHE* 3.5 17.3 - + - +
28B GLN* 4.2 5.6 - - + -
56B TYR* 3.9 32.8 - + + -
57B GLU 3.2 20.9 - - - +
58B LEU* 3.7 20.0 - - + -
63B SER* 1.3 73.3 - - - +
65B ASN* 1.3 63.1 + - - +
66B VAL* 3.7 17.9 + - + -
82B THR* 3.4 9.0 - - - +
83B PHE* 3.0 37.6 + + + -
92B PHE* 3.5 41.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE 3.3 2.6 - - - +
56B TYR* 3.7 0.7 - - - -
57B GLU* 2.8 56.9 + - + +
59B LYS* 3.3 40.3 + - + +
64B TYR* 1.3 71.0 - - - +
66B VAL* 1.3 60.9 + - - +
67B THR* 4.1 4.6 + - - +
80B ILE* 4.8 14.0 - - + +
81B ARG 3.8 3.8 - - - -
82B THR* 3.9 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B THR* 3.5 30.5 - - + -
55B ILE 3.3 5.2 - - - +
56B TYR* 4.0 16.2 - - + -
64B TYR* 3.7 17.5 - - + +
65B ASN* 1.3 77.4 - - - +
67B THR* 1.3 60.0 + - - +
80B ILE* 3.3 3.0 - - - +
81B ARG* 2.8 67.4 + - - +
83B PHE* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA 3.8 0.5 - - - +
54B THR* 3.3 1.5 - - - -
55B ILE* 2.6 54.4 + - + +
57B GLU* 5.5 4.3 + - - -
65B ASN* 4.8 3.8 + - - +
66B VAL* 1.3 78.0 + - - +
68B SER* 1.3 68.7 + - - +
69B VAL* 4.6 4.9 - - + -
78B TYR* 4.3 19.3 - - + -
79B TRP 3.4 3.8 - - - +
80B ILE* 3.9 29.3 - - + +
81B ARG* 3.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 4.5 1.1 - - - -
53B ALA 3.1 5.2 - - - -
54B THR* 2.5 25.2 + - - -
67B THR* 1.3 73.7 - - - +
69B VAL* 1.3 62.4 + - - +
70B LEU* 3.9 11.8 - - - +
77B ASP 3.5 1.2 - - - +
78B TYR* 3.3 6.9 - - - +
79B TRP* 2.9 35.7 + - - -
81B ARG* 3.1 18.5 + - - +
202B 4OL 3.6 14.7 - - - -
204B SO4 3.1 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 6.0 1.1 - - - -
52B TYR* 3.1 19.9 - - - +
53B ALA* 2.8 22.4 + - + +
55B ILE* 4.2 25.1 - - + -
67B THR* 4.6 3.8 - - + -
68B SER* 1.3 75.6 - - - +
70B LEU* 1.3 63.3 + - - +
76B CYS* 4.7 0.7 - - + -
77B ASP 3.4 4.3 - - - +
78B TYR* 3.6 36.6 - - + -
175B CYS* 3.5 38.8 - - + +
176B ILE* 3.6 9.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
49B GLN* 5.6 2.5 - - - +
52B TYR* 3.7 24.2 - - + +
68B SER* 3.9 26.2 - - - +
69B VAL* 1.3 79.9 - - - +
71B PHE* 1.3 63.5 + - - +
72B ARG* 3.8 14.7 + - + -
75B LYS 3.5 0.3 - - - +
76B CYS* 3.4 4.7 - - - -
77B ASP* 2.8 45.6 + - + +
79B TRP* 5.3 3.1 - - + +
175B CYS* 4.3 5.1 - - - -
176B ILE* 5.0 0.4 - - - -
202B 4OL 3.6 49.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 3.9 39.8 + - + +
51B MET 5.3 1.4 + - - -
70B LEU* 1.3 70.5 - - - +
72B ARG* 1.3 62.6 + - - +
74B LYS* 3.5 42.0 - - + -
75B LYS 3.5 12.3 - - - -
172B ILE* 3.7 27.1 - - + +
174B GLN* 3.8 46.0 - - + +
175B CYS* 3.6 20.3 - - - +
176B ILE* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.8 16.8 - - + +
71B PHE* 1.3 77.1 - - - +
73B LYS* 1.3 80.2 + - - +
74B LYS 3.0 1.3 - - - +
75B LYS* 3.0 22.3 + - - +
77B ASP* 2.6 60.5 + - + +
202B 4OL 6.1 4.2 - - - -
----------------------------------------------------------
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