Contacts of the strand formed by residues 67 - 74 (chain C) in PDB entry 1ZSV
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 GLN 67 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.1 2.6 - - - +
41C ALA* 3.3 25.2 + - + +
43C PHE 3.1 15.5 - - - +
44C LEU* 3.5 15.6 - - + +
66C GLN* 1.3 76.3 - - - +
68C VAL* 1.3 64.5 + - - +
69C ALA* 3.7 13.2 - - + +
86C LEU* 3.3 7.8 - - - +
87C ALA* 2.7 45.2 + - + +
89C PRO* 3.8 18.2 - - + +
90C GLY 3.5 18.0 + - - -
92C THR* 3.1 23.7 + - - +
93C THR 5.0 0.7 - - - +
95C SER* 5.0 3.5 + - - -
119C LEU* 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA* 3.8 1.7 - - - -
42C LEU* 2.9 40.1 + - + -
43C PHE* 2.9 21.0 + - + +
67C GLN* 1.3 71.4 - - - +
69C ALA* 1.3 60.8 + - - +
84C ILE* 3.7 28.0 - - + -
85C VAL 3.4 4.7 - - - +
86C LEU* 3.9 18.8 - - + -
105C LEU* 5.5 1.8 - - + -
115C LEU* 3.8 34.5 - - + +
118C ALA* 4.6 2.7 - - + -
119C LEU* 3.9 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.8 25.6 - - + -
40C GLU 3.2 13.5 - - - +
42C LEU* 4.3 4.9 - - - +
67C GLN* 3.7 21.3 - - + +
68C VAL* 1.3 73.3 - - - +
70C LYS* 1.3 59.7 + - - +
84C ILE* 3.4 6.2 - - - +
85C VAL* 2.9 41.7 + - + +
87C ALA* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.4 4.2 - - - -
40C GLU* 2.8 41.7 + - + +
42C LEU* 4.1 25.2 - - + +
69C ALA* 1.3 72.8 - - - +
71C VAL* 1.3 64.5 + - - +
72C VAL* 3.2 15.8 + - + +
82C GLY* 3.7 24.7 - - - +
83C THR 3.4 2.5 - - - -
84C ILE* 3.7 14.6 - - + -
415C CL 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 4.0 8.3 - - + -
38C LEU 3.5 4.3 - - - -
39C LEU* 3.5 20.2 - - + -
70C LYS* 1.3 70.5 - - - +
72C VAL* 1.3 56.8 + - - +
73C GLU 3.5 22.7 - - - +
79C LEU* 3.5 24.5 - - + +
80C PRO 3.4 24.0 - - - +
81C LYS* 3.2 6.7 - - - -
82C GLY* 2.7 29.8 + - - -
83C THR* 2.7 33.3 + - + +
85C VAL* 4.5 5.8 - - + -
415C CL 3.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.0 37.4 + - + +
40C GLU* 3.4 43.5 - - + +
70C LYS* 3.2 17.9 + - + +
71C VAL* 1.3 74.2 - - - +
73C GLU* 1.3 59.8 + - + +
81C LYS* 3.2 19.7 - - - +
94C HIS* 5.2 4.0 - - + -
415C CL 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.9 16.8 - - + -
37C VAL* 3.3 6.9 - - - +
38C LEU* 2.9 51.0 + - + -
71C VAL* 3.5 4.8 - - - +
72C VAL* 1.3 80.1 - - - +
74C SER* 1.3 62.0 + - - +
81C LYS* 4.0 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.2 2.4 - - - +
36C GLU 3.7 3.6 - - - -
37C VAL* 3.5 4.0 - - - +
71C VAL* 4.0 4.5 - - - -
73C GLU* 1.3 77.1 - - - +
75C LYS* 1.3 66.5 + - - +
76C ASN 2.8 26.5 + - - -
79C LEU 2.7 29.4 + - - -
80C PRO* 4.2 2.5 - - - -
81C LYS* 3.4 29.6 + - - +
----------------------------------------------------------
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