Contacts of the strand formed by residues 84 - 90 (chain N) in PDB entry 3INU
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 84 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N GLN* 3.8 26.9 - - + +
38N GLN 3.2 17.7 - - - +
39N LYS* 4.0 6.7 - - + +
40N PRO* 5.1 4.0 - - - -
82N ASP 3.3 7.3 + - - +
83N VAL* 1.3 78.1 - - - +
85N VAL* 1.3 65.5 + - - +
86N TYR* 3.9 7.0 - - + -
102N THR 3.7 0.3 - - - +
103N LYS* 3.5 4.7 - - - +
104N VAL* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N TYR 4.0 0.5 - - - +
37N GLN* 3.8 1.4 - - - -
38N GLN* 2.9 39.7 + - + +
40N PRO* 5.9 0.2 - - - +
84N ALA* 1.3 78.8 - - - +
86N TYR* 1.3 64.9 + - - +
87N TYR* 3.6 35.4 + - + +
100N GLY 5.2 0.9 - - - +
101N GLY* 4.0 2.9 - - - -
102N THR 3.2 20.9 - - - +
103N LYS* 4.2 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N GLN* 2.8 9.0 + - - -
21N ILE* 3.9 17.7 - - + -
35N TRP* 4.8 4.3 - - + -
36N TYR 3.3 13.2 - - - +
37N GLN* 2.9 28.5 + - + -
47N LEU* 3.6 24.2 - - + -
62N PHE* 3.6 14.3 - + - -
73N LEU* 3.7 21.1 - - + -
75N ILE* 3.7 10.3 - - + +
82N ASP 2.6 28.3 + - - -
84N ALA* 3.9 8.7 - - + -
85N VAL* 1.3 76.3 - - - +
87N TYR* 1.3 62.5 + - - +
101N GLY* 3.1 1.2 - - - -
102N THR 2.6 38.0 + - - +
104N VAL* 3.3 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M GLN* 3.4 20.2 + - - -
43M LYS 3.8 7.1 + - - -
44M GLY* 4.1 12.6 - - - -
45M LEU* 3.7 29.6 - - + -
6N GLN* 3.4 3.6 - - - +
34N ALA 3.8 0.2 - - - +
35N TRP* 3.3 8.2 - - - -
36N TYR* 2.7 46.4 + - + +
38N GLN* 3.4 26.9 + - + -
85N VAL* 3.6 30.0 - - + +
86N TYR* 1.3 74.6 - - - +
88N CYS* 1.3 65.7 + - - +
98N PHE* 4.5 7.9 - - + -
99N GLY 3.4 14.8 - - - -
100N GLY 3.7 8.1 + - - -
101N GLY* 3.3 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N MET* 4.1 11.4 - - + -
6N GLN* 3.0 29.2 + - - -
23N CYS* 2.1 48.0 - - + -
33N LEU* 4.9 2.5 - - + -
34N ALA 3.2 8.3 - - - +
35N TRP* 3.6 21.0 - - + -
87N TYR* 1.3 76.2 - - - +
89N GLN* 1.3 61.2 + - - +
98N PHE* 3.4 5.4 - - - +
99N GLY 2.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M PHE* 3.7 20.6 + - - +
4N MET* 4.3 5.2 - - - -
33N LEU* 3.5 4.3 - - - +
34N ALA* 2.8 33.1 + - + +
36N TYR* 2.6 40.6 + - + -
88N CYS* 1.3 76.5 - - - +
90N GLN* 1.3 65.5 + - - +
91N TYR* 3.6 31.9 + - - +
96N LEU* 3.8 9.7 - - - +
97N THR 3.3 17.5 - - - +
98N PHE* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2N LEU* 3.9 24.2 - - + +
4N MET* 3.5 30.1 - - + +
27N VAL* 3.8 18.6 - - - -
32N TYR 3.6 5.2 - - - +
33N LEU* 4.7 0.7 - - + +
89N GLN* 1.3 79.8 + - - +
91N TYR* 1.3 59.6 + - - +
92N TYR* 2.7 35.3 + - - +
93N SER 3.2 16.1 + - - -
95N PRO 3.2 19.0 + - - -
96N LEU* 3.7 1.7 - - - -
97N THR* 2.9 46.7 + - - +
----------------------------------------------------------
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