Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 1OZ7
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 PHE 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 3.7 6.3 - - - -
21A LYS 2.9 22.7 + - - +
62A MET* 5.4 1.6 - - + -
63A TYR* 5.2 11.4 - + + -
64A LYS* 3.4 57.4 - - + +
65A ILE 4.6 0.2 - - - +
66A TRP* 3.5 27.7 - + + +
102A VAL* 5.3 0.4 - - + -
115A THR* 4.1 11.7 - - - -
119A ASN* 3.4 35.6 + - + -
120A THR* 1.3 79.0 - - - +
122A PRO* 1.3 79.3 - - + +
123A PHE* 4.0 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE 3.4 15.7 - - - +
18A LYS* 3.9 21.5 - - + +
19A GLU 4.2 5.4 - - - +
20A PRO* 4.1 13.7 - - + -
59A ILE* 4.0 20.4 - - + -
62A MET* 3.8 24.9 - - + -
64A LYS 3.4 16.6 - - - +
65A ILE* 3.6 6.3 - - + -
66A TRP* 3.0 19.2 + - - +
121A PHE* 1.3 92.9 - - + +
123A PHE* 1.3 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.3 4.2 - - - +
17A PHE* 2.7 55.9 + + + -
19A GLU* 3.1 28.7 - - + -
21A LYS* 4.0 17.5 - - + -
26A ALA* 3.6 19.5 - - + -
29A PHE* 3.3 41.7 - + + -
30A CYS* 3.7 19.1 - - - -
39A LEU* 3.9 5.8 - - + -
59A ILE* 4.2 0.9 - - - +
65A ILE* 3.8 12.1 - - - -
66A TRP* 3.8 18.6 - - + -
121A PHE 4.0 2.2 - - - +
122A PRO* 1.3 81.5 - - - +
124A MET* 1.3 57.8 + - - +
125A CYS* 3.6 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 6.2 2.2 - - + -
15A MET 3.3 8.5 - - - +
16A LEU* 4.5 7.9 - - + -
30A CYS* 4.4 0.9 - - - -
39A LEU* 3.6 7.6 - - - +
40A LEU* 2.9 39.2 + - + -
51A VAL* 4.5 17.9 - - + -
54A VAL* 5.4 3.4 - - + -
55A VAL* 5.3 2.5 - - + -
65A ILE* 4.6 7.0 - - + -
66A TRP 3.5 9.9 + - - +
67A THR* 5.8 1.3 - - + -
103A LEU* 6.3 0.2 - - + -
123A PHE* 1.3 78.2 - - - +
125A CYS* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 4.0 13.7 - - + -
14A TYR* 3.4 7.1 - - - +
15A MET 2.7 27.6 + - - +
17A PHE* 3.5 29.6 - - + -
29A PHE* 4.0 2.9 - - - -
30A CYS* 2.0 52.7 - - + +
33A GLN* 4.7 2.5 - - - -
38A HIS 3.4 4.3 - - - -
40A LEU* 4.6 0.7 - - - +
123A PHE* 3.6 10.1 - - - -
124A MET* 1.3 77.1 - - - +
126A LYS* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 4.6 0.8 - - - -
12A TYR* 3.7 35.7 - - + -
13A CYS 3.2 13.0 - - - +
14A TYR* 3.6 23.6 - - + -
36A ASP 4.0 0.7 - - - +
37A GLY* 3.1 1.2 - - - -
38A HIS* 2.8 32.9 + - - +
39A LEU 4.9 0.9 - - - +
40A LEU* 4.0 13.2 - - + -
41A SER* 2.8 42.0 + - - +
43A GLU* 4.1 10.1 + - - -
47A GLU* 2.8 26.3 + - - +
125A CYS* 1.3 79.8 - - - +
127A TYR* 1.3 69.1 + - - +
81B ASP* 4.4 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PRO* 2.8 37.6 - - + +
6A TRP* 3.3 47.1 - + - -
12A TYR* 3.6 5.7 - - - -
13A CYS* 3.0 44.7 + - + +
33A GLN* 5.2 3.1 - - + -
34A GLY* 5.0 18.6 - - - -
35A LYS 4.5 6.3 - - - +
36A ASP 3.8 2.5 - - - +
37A GLY* 3.3 22.4 - - - +
126A LYS* 1.3 80.6 - - - +
128A PRO* 1.3 78.2 - - + +
129A VAL* 4.2 13.4 - - + +
----------------------------------------------------------
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