Contacts of the helix formed by residues 67 - 82 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 5.7 0.4 - - - -
123A LEU* 3.7 14.1 - - + +
124A THR* 4.2 4.0 - - - +
125A SER* 3.6 17.5 - - - +
1301A C5P 3.8 61.2 - - + +
66B ASP* 1.3 92.8 + - - +
68B PRO* 1.3 76.3 - - + +
69B ASN* 4.3 8.1 - - + +
70B THR* 3.1 30.2 - - - +
71B VAL* 3.1 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 5.7 0.4 - - + -
125A SER* 3.5 18.8 - - - +
66B ASP 3.6 1.7 - - - +
67B ILE* 1.3 87.8 - - + +
69B ASN* 1.3 58.5 + - - +
71B VAL* 3.2 3.1 + - - +
72B LYS 2.9 23.9 + - - -
92B GLY 5.8 0.7 - - - +
95B ARG* 3.8 30.3 - - + +
96B MET* 4.0 19.7 - - + +
99B ALA* 3.4 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.5 10.2 - - + +
68B PRO* 1.3 78.3 - - - +
70B THR* 1.3 67.4 + - - +
72B LYS* 3.1 13.3 + - - +
73B GLN* 2.9 44.3 + - - +
99B ALA* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY* 6.0 1.3 - - - -
37A MET* 4.4 23.1 - - + +
38A GLU* 5.1 5.8 - - + +
1301A C5P 5.0 8.0 + - - -
66B ASP* 3.8 25.3 + - + +
67B ILE* 3.1 32.6 + - - +
69B ASN* 1.3 80.1 + - - +
71B VAL* 1.3 63.7 + - - +
73B GLN* 3.3 5.6 + - - +
74B ALA* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 5.2 1.1 - - - -
64B LEU* 4.1 27.8 - - + -
66B ASP* 3.5 32.5 - - + +
67B ILE 3.1 12.9 + - - +
68B PRO 3.6 6.7 - - - +
70B THR* 1.3 76.8 - - - +
72B LYS* 1.3 57.1 + - - +
74B ALA* 3.2 7.5 + - - +
75B MET* 2.8 29.6 + - + +
88B VAL* 4.7 3.6 - - + -
96B MET* 3.6 19.7 - - + +
100B ALA* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO 2.9 13.6 + - - +
69B ASN* 3.3 16.8 - - - +
71B VAL* 1.3 76.5 - - - +
73B GLN* 1.3 69.5 + - - +
75B MET* 3.2 2.7 + - - -
76B LYS* 3.2 40.3 + - - +
99B ALA* 3.5 27.3 + - + +
102B GLU* 2.9 44.0 + - + +
103B GLY* 3.3 17.3 - - - +
106B ALA* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.0 41.1 - - + +
69B ASN* 2.9 41.8 + - - +
70B THR* 3.8 5.2 - - - +
72B LYS* 1.3 78.9 - - - +
74B ALA* 1.3 62.8 + - - +
76B LYS* 3.1 52.0 + - - +
77B GLY* 3.4 8.7 + - - -
80B ARG* 5.1 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 4.1 22.0 - - + -
38A GLU* 4.4 12.0 - - - +
41A TYR* 4.3 8.2 - - + +
64B LEU* 3.7 20.4 - - + -
70B THR 2.9 16.8 + - - +
71B VAL* 3.2 5.1 + - - +
73B GLN* 1.3 78.5 - - - +
75B MET* 1.3 61.6 + - - +
77B GLY* 3.2 4.1 + - - -
78B LEU* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.0 10.8 - - + -
71B VAL* 2.8 21.6 + - + +
72B LYS 3.7 4.7 - - - +
74B ALA* 1.3 73.9 - - - +
76B LYS* 1.3 66.2 + - - +
78B LEU* 3.1 21.5 + - - +
79B ALA* 2.8 25.3 + - - +
86B VAL* 3.5 24.0 - - + -
87B ASN 4.0 5.6 - - - +
88B VAL* 3.4 32.5 - - + -
100B ALA* 3.5 32.3 - - + +
103B GLY* 4.0 1.8 - - - -
104B LEU* 3.7 21.8 - - + +
117B CYS* 4.2 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 3.2 28.7 + - - +
73B GLN* 3.1 44.3 + - - +
74B ALA 3.3 0.2 - - - -
75B MET* 1.3 75.7 - - - +
77B GLY* 1.3 63.8 + - - +
79B ALA* 3.2 4.7 + - - +
80B ARG* 3.0 47.5 + - - +
103B GLY* 3.2 22.6 + - - +
106B ALA* 3.5 24.8 - - + +
107B GLY* 3.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 6.5 0.2 - - - -
42A GLN* 5.5 6.7 - - - -
73B GLN 3.4 5.7 + - - -
74B ALA 3.2 6.3 + - - -
75B MET 3.2 0.4 - - - -
76B LYS* 1.3 80.3 - - - +
78B LEU* 1.3 58.9 + - - +
80B ARG* 3.0 23.4 + - - +
81B VAL* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.6 34.1 - - + +
40B TYR* 4.9 5.2 - - - +
60B LEU* 3.8 22.2 - - + +
62B LEU* 4.4 7.9 - - + -
64B LEU* 4.1 20.4 - - + -
74B ALA 3.0 22.4 + - - +
75B MET* 3.1 32.7 + - - +
77B GLY* 1.3 77.3 - - - +
79B ALA* 1.3 58.4 + - - +
81B VAL* 2.9 25.6 - - + +
83B ALA* 3.3 15.2 + - - +
86B VAL* 4.2 20.2 - - + -
104B LEU* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B MET 2.8 15.9 + - - +
76B LYS 3.5 3.4 - - - +
77B GLY 3.1 0.2 - - - -
78B LEU* 1.3 77.2 - - - +
80B ARG* 1.3 62.4 + - - +
82B GLY* 3.6 10.4 + - - -
83B ALA 4.7 0.3 + - - +
104B LEU* 3.7 17.2 - - + +
107B GLY* 3.4 27.5 - - - +
108B THR* 3.8 6.1 + - - +
115B PRO* 4.0 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 5.2 8.9 + - - -
73B GLN 5.1 1.6 + - - -
76B LYS* 3.0 41.3 + - - +
77B GLY* 3.0 24.6 + - - +
79B ALA* 1.3 75.6 - - - +
81B VAL* 1.3 62.7 + - - +
82B GLY* 3.1 3.5 + - - -
106B ALA 5.1 1.6 + - - -
107B GLY* 3.8 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR 6.1 0.2 - - - +
40B TYR* 4.6 4.9 - - - +
45B PRO* 4.0 28.9 - - + +
48B VAL* 3.8 30.0 - - + +
49B ALA* 5.0 5.9 + - + +
52B LYS* 3.8 5.7 - - - +
60B LEU* 4.2 16.8 - - + -
77B GLY 2.8 10.2 + - - +
78B LEU* 2.9 32.8 - - + +
80B ARG* 1.3 77.1 - - - +
82B GLY* 1.3 57.4 + - - +
83B ALA 3.7 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 4.6 1.3 - - - -
52B LYS* 2.9 42.5 + - - +
58B VAL* 5.1 0.3 - - - +
79B ALA 3.6 8.9 + - - -
80B ARG 3.1 4.7 - - - -
81B VAL* 1.3 81.1 - - - +
83B ALA* 1.3 67.4 + - - +
84B ASP* 3.5 4.7 + - - +
----------------------------------------------------------
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