Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 2YYU
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 ILE 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 1.3 93.3 + - - +
68A PRO* 1.3 74.2 - - + +
69A ASN* 5.0 7.4 - - + +
70A THR* 3.2 31.4 - - - +
71A VAL* 3.1 17.7 + - - +
123B LEU* 3.8 13.4 - - + +
124B THR* 3.8 21.3 - - - +
125B SER* 3.7 18.8 - - - +
2301B C5P 3.8 49.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP 4.3 1.8 - - - +
67A ILE* 1.3 84.5 - - + +
69A ASN* 1.3 65.5 + - - +
71A VAL* 3.1 4.3 + - - +
72A LYS 3.0 17.7 + - - -
92A GLY 5.8 0.9 - - - +
95A ARG* 3.3 39.3 - - + +
96A MET* 4.0 32.5 - - + +
99A ALA* 3.6 18.9 - - + +
125B SER* 3.3 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.6 9.9 - - + +
68A PRO* 1.3 78.2 - - - +
70A THR* 1.3 64.6 + - - +
72A LYS* 3.3 14.0 + - - +
73A GLN* 3.1 42.0 + - - +
2301B C5P 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.8 24.2 + - + +
67A ILE* 3.2 33.0 + - - +
68A PRO 3.2 0.8 - - - -
69A ASN* 1.3 81.0 + - - +
71A VAL* 1.3 57.9 + - - +
73A GLN* 3.5 5.0 + - - +
74A ALA* 3.0 26.6 + - - +
12B ASP* 5.6 4.0 + - - +
36B GLY* 5.7 2.2 - - - -
37B MET* 4.5 21.5 - - + +
38B GLU* 5.0 6.5 - - + +
2301B C5P 4.8 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.4 20.4 - - + -
65A HIS 4.7 0.4 - - - -
66A ASP* 3.5 33.4 - - + +
67A ILE 3.1 14.1 + - - +
68A PRO 3.1 7.5 + - - +
70A THR* 1.3 73.2 - - - +
72A LYS* 1.3 59.9 + - - +
74A ALA* 3.6 5.9 - - - +
75A MET* 2.9 32.8 + - + +
88A VAL* 4.6 4.9 - - + -
96A MET* 3.6 21.3 - - + +
100A ALA* 3.9 25.6 - - + -
37B MET* 5.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO 3.0 13.0 + - - +
69A ASN* 3.5 18.2 - - - +
71A VAL* 1.3 75.5 - - - +
73A GLN* 1.3 71.5 + - - +
75A MET 3.1 2.1 + - - -
76A LYS* 2.9 34.8 + - - +
99A ALA* 3.6 26.7 - - + +
102A GLU* 3.0 46.5 + - + +
103A GLY* 3.3 17.2 - - - +
106A ALA* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 3.1 35.5 + - - +
70A THR* 4.0 4.9 - - - +
72A LYS* 1.3 83.6 - - - +
74A ALA* 1.3 60.7 + - - +
76A LYS* 3.2 40.7 + - - +
77A GLY 3.1 15.8 + - - -
80A ARG* 4.9 1.7 + - - +
14B PRO* 6.0 1.0 - - - +
38B GLU* 3.4 37.5 + - + +
42B GLN* 4.0 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.6 24.9 - - + -
70A THR 3.0 19.5 + - - +
71A VAL* 3.6 2.7 - - - +
73A GLN* 1.3 78.6 - - - +
75A MET* 1.3 57.4 + - - +
77A GLY* 3.0 5.2 + - - -
78A LEU* 2.9 30.6 + - - +
37B MET* 3.9 22.2 - - + -
38B GLU* 4.2 11.2 - - - +
41B TYR* 4.6 5.7 - - + +
42B GLN* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.1 13.2 - - + -
71A VAL* 2.9 22.3 + - + +
72A LYS 3.7 2.9 - - - +
74A ALA* 1.3 72.3 - - - +
76A LYS* 1.3 67.0 + - - +
77A GLY 2.9 2.0 - - - -
78A LEU* 3.9 20.0 - - - +
79A ALA* 2.9 26.3 + - - +
86A VAL* 3.6 24.2 - - + -
87A ASN 3.8 7.9 - - - +
88A VAL* 3.5 31.6 - - + -
100A ALA* 3.5 31.9 - - + +
103A GLY* 3.9 2.0 - - - -
104A LEU* 3.6 23.1 - - + +
117A CYS* 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 2.9 19.4 + - - +
73A GLN* 3.2 45.9 + - - +
75A MET* 1.3 77.6 - - - +
77A GLY* 1.3 61.2 + - - +
80A ARG* 3.2 51.2 + - - +
103A GLY* 3.0 15.6 + - - +
106A ALA* 3.6 26.7 - - + +
107A GLY* 3.5 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN 3.1 6.5 + - - -
74A ALA 3.0 8.4 + - - -
75A MET 2.9 0.4 - - - -
76A LYS* 1.3 77.9 - - - +
78A LEU* 1.3 63.3 + - - +
80A ARG* 3.3 7.8 + - - +
81A VAL* 3.0 29.2 + - - +
42B GLN* 3.6 35.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.1 7.2 - - - +
60A LEU* 3.5 30.7 - - + +
62A LEU* 4.0 14.4 - - + -
64A LEU* 4.0 16.2 - - + -
74A ALA 2.9 16.3 + - - +
75A MET* 3.1 28.2 + - - +
77A GLY* 1.3 74.5 - - - +
79A ALA* 1.3 61.8 + - - +
81A VAL* 2.8 24.3 - - + +
83A ALA* 3.5 13.7 + - - +
86A VAL* 4.2 16.6 - - + -
104A LEU* 5.0 1.6 - - + -
41B TYR* 3.9 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET 2.9 15.8 + - - +
78A LEU* 1.3 77.3 - - - +
80A ARG* 1.3 62.5 + - - +
82A GLY* 3.3 13.9 + - - -
104A LEU* 3.5 27.6 - - + +
107A GLY* 3.6 17.9 - - - +
108A THR* 4.0 1.2 - - - +
109A PRO* 5.2 5.2 - - - +
115A PRO* 3.9 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 4.9 1.8 + - - +
76A LYS* 3.2 34.5 + - - +
77A GLY* 3.3 12.4 + - - +
79A ALA* 1.3 74.9 - - - +
81A VAL* 1.3 61.5 + - + +
82A GLY* 3.2 2.6 - - - -
106A ALA 5.4 0.6 + - - -
107A GLY* 3.1 24.9 - - - +
109A PRO* 6.1 1.1 - - - -
14B PRO* 4.3 10.5 - - - +
42B GLN* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.1 6.5 - - - +
45A PRO* 3.8 31.6 - - + +
48A VAL* 3.5 24.2 - - + +
49A ALA* 4.6 5.5 + - - +
52A LYS* 3.9 6.1 - - - +
60A LEU* 4.4 11.9 - - + -
77A GLY 3.0 16.4 - - - +
78A LEU* 2.8 31.9 - - + +
80A ARG* 1.3 78.9 - - + +
82A GLY* 1.3 58.2 + - - +
83A ALA* 3.8 11.7 - - + +
41B TYR 4.2 6.7 - - - +
42B GLN* 5.2 4.3 - - + -
----------------------------------------------------------
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