Contacts of the strand formed by residues 65 - 72 (chain B) in PDB entry 1QZG
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 TRP 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 5.0 17.0 - + - -
93A ASN* 6.1 2.2 - - + -
55B SER* 4.8 0.7 - - - -
56B ARG* 3.6 27.6 - - - -
57B GLN* 3.7 44.1 - - + +
63B LYS 5.2 0.7 - - - -
64B ASP* 1.3 74.7 - - - +
66B VAL* 1.3 59.2 + - - +
88B PHE* 3.1 7.1 - - - -
89B SER* 3.0 37.0 + - - +
92B GLY* 3.2 32.2 - - - +
93B ASN* 3.3 50.3 - - + +
95B LEU* 3.6 14.4 - - + -
----------------------------------------------------------
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 PRO 4.1 2.3 - - - +
55B SER* 3.3 2.1 - - - -
56B ARG* 2.8 51.3 + - + +
58B SER* 3.5 18.6 - - - +
65B TRP* 1.3 75.8 - - - +
67B THR* 1.3 72.9 + - - +
68B THR* 4.5 7.6 - - - +
86B HIS* 4.6 3.4 - - + -
87B LEU 3.2 8.7 - - - +
88B PHE* 3.5 31.2 - - + -
95B LEU* 3.6 3.5 - - - +
5D A 3.7 28.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
52B PHE* 5.7 0.5 - - - +
53B THR* 2.7 22.9 + - - -
54B PRO* 4.3 1.1 - - - +
55B SER* 3.7 20.2 + - - +
56B ARG* 6.0 0.4 - - - +
66B VAL* 1.3 77.6 - - - +
68B THR* 1.3 63.3 + - - +
69B VAL* 4.9 7.4 - - + +
85B ILE 3.9 0.3 - - - +
86B HIS* 3.8 1.0 - - - -
87B LEU* 2.8 60.6 + - + +
95B LEU* 4.0 16.4 - - + -
96B PRO* 4.3 10.2 + - + +
98B ILE* 5.2 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.1 4.3 - - - +
53B THR* 2.9 46.8 + - - +
56B ARG* 5.9 0.2 + - - -
66B VAL* 4.5 2.9 - - - +
67B THR* 1.3 75.2 + - - +
69B VAL* 1.3 72.1 + - - +
70B TYR* 4.0 24.0 - - + +
84B GLN* 4.1 9.0 - - + +
85B ILE 3.4 10.8 - - - +
86B HIS* 2.7 35.8 + - + +
5D A 4.4 10.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
49B VAL* 5.0 4.5 - - + -
51B ASP 3.5 7.9 - - - +
52B PHE* 4.2 1.3 - - + +
67B THR* 4.9 3.4 - - + +
68B THR* 1.3 84.4 - - - +
70B TYR* 1.3 64.2 + - - +
71B LEU* 4.8 4.0 - - + -
83B LEU 3.3 1.7 - - - +
84B GLN* 3.6 0.7 - - - -
85B ILE* 2.7 66.4 + - + +
87B LEU* 4.7 13.5 - - + -
98B ILE* 3.3 33.7 - - + -
105B LEU* 4.3 22.0 - - + -
107B LEU* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 5.7 1.3 - - - -
48B ILE 3.6 0.3 - - - +
49B VAL* 3.7 2.6 - - - -
50B LYS* 2.7 33.1 + - - +
51B ASP* 2.9 37.7 + - + +
52B PHE* 4.7 1.8 - - - -
53B THR* 5.6 2.7 - - - -
68B THR* 4.0 17.1 - - + +
69B VAL* 1.3 76.8 - - - +
71B LEU* 1.3 57.7 + - - +
81B ILE* 3.6 45.8 - - + +
82B GLY 4.1 9.9 - - - -
83B LEU 3.2 5.2 - - - +
84B GLN* 3.0 46.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.6 18.3 - - + +
45B LEU* 3.9 28.3 - - + -
47B GLY* 3.3 44.0 - - - +
48B ILE 3.5 9.9 - - - +
49B VAL* 4.0 4.7 - - + +
69B VAL* 3.9 3.3 - - + -
70B TYR* 1.3 72.8 - - - +
72B TRP* 1.3 59.7 + - - +
82B GLY* 3.1 4.2 - - - -
83B LEU* 2.9 30.2 + - + +
85B ILE* 3.9 23.6 - - + -
105B LEU* 4.2 22.0 - - + +
107B LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.0 3.8 - - - -
47B GLY* 3.2 3.8 - - - -
48B ILE* 2.7 56.0 + - + +
50B LYS* 3.7 38.6 - - + +
71B LEU* 1.3 74.8 - - - +
73B ASP* 1.3 77.8 + - - +
74B PRO* 3.8 12.6 - - + -
76B CYS* 3.6 33.1 + - + -
77B ASP 3.7 9.7 + - - -
78B THR* 4.1 0.6 - - - +
80B SER 3.8 12.6 - - - -
81B ILE 4.2 4.7 - - - +
82B GLY* 4.5 2.2 - - - -
165B LEU* 4.2 7.0 - - + -
168B ILE* 3.8 22.0 - - + -
169B TRP* 3.8 33.2 - + + -
172B GLN* 3.8 24.7 - - + -
----------------------------------------------------------
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