Contacts of the strand formed by residues 71 - 77 (chain B) in PDB entry 2QNU
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 ALA 71 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE 3.5 14.4 - - - +
64B PRO* 3.9 25.0 - - + +
70B GLU* 1.3 78.0 - - - +
72B VAL* 1.3 61.6 + - - +
94B LEU* 3.4 4.2 - - - -
95B LEU* 2.7 36.4 + - + +
96B PRO 4.1 13.2 + - - +
99B ALA* 5.3 1.8 - - + +
101B LEU* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 3.7 27.1 - - + -
60B PHE* 3.9 11.2 - - + -
61B ALA* 3.3 2.1 - - - +
62B ILE* 2.7 49.7 + - + +
67B LEU* 3.7 31.9 - - + -
70B GLU 4.5 5.4 - - - +
71B ALA* 1.3 79.2 - - - +
73B THR* 1.3 64.1 + - - +
92B ALA* 3.9 21.5 - - + -
93B CYS 3.6 8.3 - - - +
94B LEU* 4.6 6.5 - - + -
95B LEU* 4.9 2.0 - - - -
101B LEU* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 2.8 24.1 + - - -
61B ALA* 4.3 2.9 - - - +
72B VAL* 1.3 75.3 - - - +
74B GLY* 1.3 57.7 + - - +
92B ALA* 3.4 3.8 - - - +
93B CYS* 2.8 42.9 + - + +
95B LEU* 3.9 12.5 - - + +
101B LEU* 5.2 0.2 - - - -
104B LEU* 3.7 16.2 - - + +
111B TRP* 4.2 4.5 - - + -
112B PHE* 3.2 20.1 - - - -
142B PRO* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.3 1.4 - - - -
60B PHE* 2.9 35.9 + - - -
73B THR* 1.3 82.0 + - - +
75B VAL* 1.3 69.9 + - - +
91B VAL 3.2 12.3 - - - -
111B TRP* 4.0 13.9 - - - -
112B PHE* 3.6 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.1 7.6 - - + -
58B TRP 3.3 17.5 - - - +
59B ARG* 4.0 16.4 - - + +
60B PHE* 3.5 3.3 - - - -
74B GLY* 1.3 80.6 - - - +
76B VAL* 1.3 68.9 + - - +
90B THR* 3.5 2.3 - - - +
91B VAL 3.0 30.2 + - - +
112B PHE* 4.0 16.4 - - + +
115B VAL* 3.7 31.8 - - + +
116B GLU* 3.9 16.2 - - + -
119B LEU* 3.7 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 4.4 9.4 - - + -
32B TRP* 6.1 0.9 - - + -
33B LEU* 4.9 4.3 - - + -
56B PRO 4.3 1.4 - - - +
57B LEU* 3.5 4.3 - - - -
58B TRP* 2.9 54.2 + - + +
60B PHE* 4.3 14.6 - - + -
75B VAL* 1.3 76.3 - - - +
77B MSE 1.3 64.7 + - - +
78B PRO* 4.9 0.4 - - + -
88B PRO* 3.5 29.8 - - + -
89B LEU 3.5 3.1 - - - +
90B THR* 3.5 18.4 - - - +
183B TRP* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.6 31.4 - - + -
76B VAL* 1.3 75.3 - - - +
78B PRO* 1.3 93.0 - - + +
79B SER* 3.9 13.8 - - - +
88B PRO* 3.3 5.0 - - - +
89B LEU* 2.9 37.5 + - + +
119B LEU* 3.4 45.8 - - + +
120B LEU* 4.2 4.7 - - - -
122B THR* 3.7 11.2 - - - +
123B LEU* 4.0 29.4 - - + -
----------------------------------------------------------
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