Contacts of the helix formed by residues 66 - 87 (chain B) in PDB entry 4U9W
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 GLU 66 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 5.3 0.4 - - - +
64B GLY 4.1 2.6 + - - +
65B LEU* 1.3 75.5 - - - +
67B PRO* 1.3 76.9 - - + +
68B ALA* 4.4 7.2 - - + +
69B THR* 2.8 35.3 + - - +
70B VAL* 3.2 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU 3.5 6.0 - - - +
66B GLU* 1.3 97.1 - - + +
68B ALA* 1.3 57.1 + - - +
70B VAL* 3.3 11.5 + - + +
71B ASP* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.1 5.9 - - + +
67B PRO* 1.3 78.1 - - - +
69B THR* 1.3 60.8 + - - +
71B ASP* 3.3 10.7 + - - +
72B TRP* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.5 12.8 - - + -
66B GLU* 2.8 26.3 + - - +
68B ALA* 1.3 77.3 - - - +
70B VAL* 1.3 58.8 + - - +
72B TRP* 3.1 19.7 + - + -
73B ALA* 2.9 26.6 + - + +
110B ILE* 4.0 27.6 - - + -
112B TRP* 3.5 34.2 - - + -
118B PRO* 5.0 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.1 15.3 - - + +
65B LEU* 3.9 31.0 - - + +
66B GLU 3.2 11.4 + - - +
67B PRO* 3.4 13.2 - - + +
69B THR* 1.3 76.3 - - - +
71B ASP* 1.3 65.0 + - - +
73B ALA* 3.2 7.2 + - - +
74B PHE* 3.1 24.7 + - + +
98B ARG* 5.9 2.2 - - + +
101B MET* 5.1 5.2 - - + +
102B THR* 3.7 29.4 - - + -
108B TYR* 5.7 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 2.9 21.6 + - - +
68B ALA* 3.5 13.8 - - - +
69B THR 3.3 0.2 - - - -
70B VAL* 1.3 80.0 - - - +
72B TRP* 1.3 58.2 + - - +
74B PHE* 3.5 6.1 + - - +
75B ASP* 2.8 43.5 + - - +
98B ARG* 4.8 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 2.8 14.4 + - - +
69B THR* 3.3 19.1 - - + +
71B ASP* 1.3 77.8 - - - +
73B ALA* 1.3 75.9 + - + +
75B ASP* 3.5 8.4 + - + +
76B LEU* 2.9 41.6 + - + +
110B ILE* 4.3 12.1 - - + -
118B PRO* 3.1 54.8 + - + -
119B VAL 3.7 6.3 - - - -
120B ALA 3.7 31.9 - - - -
121B PHE* 3.8 24.5 - + + -
143B GLU* 3.0 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 6.5 0.4 - - + -
69B THR* 2.9 16.3 + - + +
70B VAL* 3.7 6.5 - - - +
72B TRP* 1.3 88.7 - - + +
74B PHE* 1.3 56.5 + - - +
76B LEU* 3.3 0.6 + - - -
77B THR* 2.7 36.6 + - - -
101B MET* 3.7 9.6 - - + -
108B TYR* 4.4 9.4 - - + +
110B ILE* 5.7 0.7 - - + -
121B PHE* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.1 17.9 + - + +
71B ASP* 3.7 4.7 - - - +
73B ALA* 1.3 76.5 - - - +
75B ASP* 1.3 70.6 + - - +
77B THR* 3.1 2.3 + - - -
78B LYS* 2.8 45.4 + - + +
92B TRP* 4.1 9.2 - + - -
94B ASP* 3.6 49.4 - - - -
97B LYS* 4.1 10.3 - - + -
98B ARG* 3.2 58.8 - - + +
101B MET* 3.6 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASP* 2.8 35.1 + - - +
72B TRP* 3.8 7.2 - - + +
74B PHE* 1.3 89.5 - - - +
76B LEU* 1.3 57.8 + - - +
78B LYS* 3.4 6.8 + - - +
79B THR* 2.8 36.1 + - - +
98B ARG* 5.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 2.9 45.6 + - + +
73B ALA 3.7 3.6 - - - +
75B ASP* 1.3 78.1 - - - +
77B THR* 1.3 56.4 + - - +
79B THR* 3.3 7.7 + - + -
80B ASN* 2.9 60.0 + - - +
119B VAL 4.6 0.2 - - - +
121B PHE* 4.1 4.7 - - + -
141B GLN* 3.6 35.9 - - + +
142B LEU 3.8 14.4 - - - +
143B GLU* 3.8 24.9 - - - +
144B SER 5.4 0.2 - - - +
147B ARG* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA 2.7 22.6 + - - -
74B PHE 3.6 4.5 - - - -
76B LEU* 1.3 76.5 - - - +
78B LYS* 1.3 52.2 + - - +
80B ASN 3.2 0.7 + - - -
81B MET* 2.6 50.5 + - + +
92B TRP* 4.4 14.1 - - + -
97B LYS* 4.7 4.0 - - + -
101B MET* 3.5 14.2 - - - +
121B PHE* 3.2 20.8 - - - -
139B GLU* 3.6 31.0 - - + +
141B GLN* 3.9 9.9 - - - +
1E SER* 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 2.8 32.3 + - + +
75B ASP* 3.6 7.4 - - - +
77B THR* 1.3 73.9 - - - +
79B THR* 1.3 66.1 + - - +
82B GLN* 3.1 50.8 + - - +
92B TRP* 3.3 33.7 - - + +
94B ASP* 2.4 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP* 2.8 26.6 + - - +
76B LEU* 3.6 9.4 - - + -
78B LYS* 1.3 75.1 - - - +
80B ASN* 1.3 68.8 + - - +
82B GLN 4.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 2.9 32.1 + - - +
77B THR 3.8 0.4 - - - +
79B THR* 1.3 86.4 - - - +
81B MET* 1.3 64.8 + - - +
83B THR* 5.4 1.0 + - - -
84B MET* 3.3 20.4 + - - +
141B GLN* 2.7 31.8 + - - +
142B LEU 3.6 11.3 + - - -
147B ARG* 3.0 30.4 + - - +
301B COA 3.7 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 2.6 26.7 + - + +
80B ASN* 1.3 85.0 - - - +
82B GLN* 1.3 65.1 + - - +
83B THR 3.4 2.2 - - - -
84B MET* 3.1 30.4 + - + +
85B TYR* 2.9 37.2 + - + -
92B TRP* 4.6 1.6 - - + -
141B GLN* 3.4 31.4 - - - +
176B PHE* 4.1 17.0 - - + -
179B ASN* 3.8 13.2 - - - +
301B COA 3.9 16.8 - - + -
1E SER* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR 4.2 0.2 + - - -
78B LYS* 3.1 42.4 + - - +
79B THR 4.8 0.6 + - - -
80B ASN 3.8 0.4 - - - -
81B MET* 1.3 76.3 - - - +
83B THR* 1.3 59.4 + - - +
85B TYR* 3.0 3.6 + - - +
86B GLU* 2.7 54.3 + - - +
92B TRP* 3.5 47.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN 5.6 1.5 - - - -
81B MET 3.4 0.6 - - - -
82B GLN* 1.3 76.7 - - - +
84B MET* 1.3 60.4 + - + +
86B GLU* 2.9 18.4 + - + +
87B GLN* 2.8 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 3.3 26.7 - - + +
81B MET* 3.1 25.8 + - + +
83B THR* 1.3 80.4 - - + +
85B TYR* 1.3 60.4 + - - +
87B GLN* 3.5 17.2 + - - +
88B SER* 3.4 9.4 + - - -
176B PHE* 3.6 17.8 - - + -
178B HIS* 3.0 33.7 + - + +
179B ASN* 3.4 45.3 - - - +
301B COA 4.7 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 5.4 0.2 - - + -
81B MET* 2.9 38.4 + - + +
82B GLN 3.3 7.6 - - - +
84B MET* 1.3 74.3 - - - +
86B GLU* 1.3 63.7 + - - +
87B GLN 3.1 0.2 - - - -
88B SER* 2.9 22.3 + - - -
90B TRP* 3.4 28.3 - + + -
91B GLY* 3.1 30.2 + - - -
92B TRP* 3.6 29.4 - + + +
93B LYS 5.6 0.4 - - - -
97B LYS* 2.8 38.3 + - - -
176B PHE* 3.6 16.2 - + - -
1E SER* 2.8 27.7 + - - -
2E GLY* 3.4 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLN* 2.7 50.2 + - - +
83B THR* 2.9 18.7 + - + +
85B TYR* 1.3 73.4 - - - +
87B GLN* 1.3 60.2 + - + +
88B SER 3.2 6.1 + - - +
91B GLY* 4.3 6.5 - - - -
92B TRP* 4.1 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 2.8 36.4 + - + +
84B MET* 3.5 25.1 - - - +
85B TYR 3.1 0.6 - - - -
86B GLU* 1.3 79.1 - - + +
88B SER* 1.3 56.3 + - - +
178B HIS* 3.6 26.3 + - + +
210B SER* 4.7 2.9 + - - -
----------------------------------------------------------
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