Contacts of the strand formed by residues 83 - 89 (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 LEU 83 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.9 20.5 - - + +
33B SER* 4.4 11.4 - - - +
34B GLN* 4.1 18.8 - - + +
45B LEU* 3.8 17.3 - - + -
69B VAL 3.3 1.4 - - - +
70B TYR* 3.2 4.4 - - - -
71B LEU 2.9 31.1 + - - +
82B GLY* 1.3 72.1 - - - -
84B GLN* 1.3 70.1 + - - +
85B ILE* 3.6 26.7 + - + +
112B LEU* 4.1 15.9 - - + -
119B THR* 3.3 40.6 - - + +
120B GLN* 4.2 2.2 - - - -
121B GLY 4.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.1 10.8 - - + +
69B VAL 3.6 4.0 - - - -
70B TYR* 3.0 43.1 + - + -
82B GLY 3.6 3.6 + - - -
83B LEU* 1.3 74.7 - - - +
85B ILE* 1.3 62.7 + - - +
86B HIS* 3.7 16.0 + - - +
118B ARG* 3.6 26.1 + - - +
119B THR 4.9 2.5 + - - +
120B GLN* 2.7 40.6 + - + +
121B GLY 2.8 23.7 + - - -
281B TMP 3.8 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.5 26.9 - - + -
68B THR* 3.4 4.2 - - - +
69B VAL* 2.7 44.0 + - + +
71B LEU* 3.9 30.7 - - + -
83B LEU* 3.7 20.2 - - + +
84B GLN* 1.3 81.4 - - - +
86B HIS* 1.3 67.1 + - - +
87B LEU* 3.6 27.2 + - + -
107B LEU* 3.9 6.5 - - + -
110B ILE* 4.0 13.9 - - + -
121B GLY* 3.4 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.6 2.8 - - + +
67B THR 3.8 2.2 - - - -
68B THR* 2.7 40.4 + - + +
84B GLN* 3.7 13.4 - - - -
85B ILE* 1.3 71.9 - - - +
87B LEU* 1.3 63.6 + - - +
88B PHE* 3.6 24.1 - + + -
120B GLN* 3.6 27.8 + - + -
121B GLY 2.9 11.1 + - - +
122B LEU* 3.6 3.5 - - + -
123B SER* 2.9 25.8 + - - -
281B TMP 3.3 24.6 + - - -
5D A 3.6 35.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.2 6.9 - - - +
67B THR* 2.8 52.2 + - + +
69B VAL* 4.7 14.4 - - + -
85B ILE* 3.6 27.4 - - + +
86B HIS* 1.3 73.2 - - - +
88B PHE* 1.3 60.8 + - - +
95B LEU* 3.6 4.1 - - + +
96B PRO* 3.8 31.9 - - + -
105B LEU* 4.9 1.3 - - + -
107B LEU* 3.9 19.5 - - + -
110B ILE* 3.7 11.4 - - + -
123B SER* 3.5 17.3 - - - -
127B PHE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 4.1 0.4 - - - -
64B ASP* 4.1 9.9 - - + +
65B TRP 3.1 15.3 - - - -
66B VAL* 3.5 23.1 - - + -
86B HIS* 3.6 28.5 - - + -
87B LEU* 1.3 73.9 - - - +
89B SER* 1.3 65.2 + - - +
90B LYS* 6.0 0.7 - - + -
95B LEU* 3.9 1.8 - - - -
122B LEU* 4.9 4.7 - - + -
123B SER* 2.8 19.8 + - - +
124B LYS 5.2 0.9 - - - +
125B ASP* 5.2 2.1 - - - +
127B PHE* 3.6 14.4 - - - -
150B ARG* 4.2 4.7 + - - -
2D G 3.7 14.4 - - - +
4D T 3.4 69.8 - + + +
5D A 3.5 21.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP* 3.7 1.7 - - - +
65B TRP* 3.0 37.3 + - - +
88B PHE* 1.3 78.2 - - - +
90B LYS* 1.3 62.8 + - - +
91B GLN 3.2 5.3 + - - -
92B GLY 2.8 17.7 + - - -
94B ASP* 2.4 33.2 + - - -
95B LEU* 3.9 13.0 - - - -
125B ASP 6.0 0.4 - - - -
150B ARG* 3.1 13.5 + - - +
----------------------------------------------------------
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