Contacts of the helix formed by residues 74 - 89 (chain B) in PDB entry 1U2X
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 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.8 4.2 - - - +
73B ASN* 1.3 90.4 - - + +
75B PRO* 1.3 85.1 - - + +
76B ILE* 4.4 11.2 - - + +
77B ASP* 2.9 26.9 + - - +
78B PHE 3.5 2.6 + - - -
98B ASN* 3.7 8.3 - - - +
101B MSE 3.2 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.6 24.9 - - + -
74B GLU* 1.3 99.0 - - + +
76B ILE* 1.3 57.7 + - - +
78B PHE* 3.0 12.2 + - + +
79B VAL* 3.0 25.3 + - - +
101B MSE 3.8 12.1 - - - -
104B TRP* 3.8 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.8 19.8 - - + -
60B GLU* 3.3 49.1 - - + +
61B VAL* 4.2 3.6 - - + +
64B ARG* 3.8 21.4 - - + +
74B GLU* 4.7 9.6 - - + -
75B PRO* 1.3 75.5 - - - +
77B ASP* 1.3 75.2 + - - +
79B VAL* 3.7 17.0 - - + -
80B ALA* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 2.8 37.6 + - - +
69B PRO* 4.0 11.2 - - + +
71B GLU 3.9 8.9 - - - +
72B ILE* 3.9 17.5 - - + -
73B ASN* 2.8 31.6 + - - +
74B GLU* 2.9 20.7 + - - +
76B ILE* 1.3 77.5 - - - +
78B PHE* 1.3 62.5 + - - +
80B ALA* 3.8 0.9 - - - +
81B ARG* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 14.4 - - + -
72B ILE* 3.9 24.2 - - + +
74B GLU 3.5 1.6 + - - +
75B PRO* 3.0 9.9 + - + +
77B ASP* 1.3 75.9 - - - +
79B VAL* 1.3 63.0 + - + +
81B ARG* 3.4 2.3 + - - +
82B LEU* 2.9 45.0 + - + +
104B TRP* 3.7 20.2 - + + -
105B PHE* 3.6 27.6 - + + -
109B PHE* 3.7 20.6 - + - -
185B PHE* 3.6 39.9 - + - -
208B PHE* 3.8 25.1 - + - -
210B VAL* 4.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.4 14.8 - - + -
53B ILE* 3.4 30.7 - - + -
56B PHE* 4.0 31.4 - - + -
61B VAL* 4.1 13.2 - - + -
75B PRO 3.0 9.2 + - - +
76B ILE* 3.5 30.5 - - + +
78B PHE* 1.3 82.7 - - + +
80B ALA* 1.3 61.5 + - - +
82B LEU* 3.8 3.3 - - - +
83B VAL* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 4.2 6.5 - - + +
64B ARG* 3.7 29.6 - - + +
65B ILE* 3.4 32.5 - - + +
69B PRO* 4.8 3.1 - - + -
76B ILE 3.1 19.4 + - - +
77B ASP* 3.8 3.1 - - - +
79B VAL* 1.3 80.5 - - + +
81B ARG* 1.3 64.6 + - - +
83B VAL* 3.4 0.3 + - - -
84B HIS* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 6.4 0.7 - - - +
68B TYR* 3.0 55.5 + - - -
69B PRO* 3.1 41.7 + - + +
70B ARG* 4.1 8.5 - - - +
72B ILE* 5.7 1.1 - - + -
77B ASP 3.1 19.0 + - - +
78B PHE* 4.1 1.1 - - - +
80B ALA* 1.3 76.7 - - - +
82B LEU* 1.3 63.9 + - - +
84B HIS* 3.4 9.0 + - - +
85B THR* 3.0 26.8 + - - -
90B LYS* 6.3 0.4 - - - +
92B ALA* 4.2 16.6 - - - +
93B ALA 5.2 1.8 + - - -
94B VAL* 3.5 33.2 - - + +
208B PHE* 3.8 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.8 32.5 - - + -
49B ILE* 5.9 0.2 - - + -
52B LEU* 3.7 29.8 - - + -
78B PHE* 2.9 34.2 + - + +
79B VAL 3.8 3.1 - - - +
81B ARG* 1.3 77.6 - - - +
83B VAL* 1.3 53.6 + - + +
85B THR* 3.1 7.0 + - + -
86B LEU* 2.8 56.3 + - + +
185B PHE* 4.7 1.1 - - + -
187B PHE* 5.1 0.2 - - + -
208B PHE* 3.7 41.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.0 38.1 - - + -
61B VAL* 4.6 4.7 - - + -
65B ILE* 3.8 20.6 - - + -
79B VAL* 2.9 21.8 + - + +
80B ALA 3.9 2.7 - - - +
82B LEU* 1.3 76.4 - - + +
84B HIS* 1.3 57.6 + - - +
86B LEU* 3.2 12.9 + - + +
87B LYS* 3.0 30.3 + - + +
193B PHE* 4.3 19.0 - - + -
195B LEU* 4.2 16.6 - - + -
200B ILE* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.0 27.7 - - + +
68B TYR* 3.5 39.1 + + + -
80B ALA 3.1 16.4 + - - +
81B ARG* 3.6 11.9 - - - +
83B VAL* 1.3 79.0 - - - +
85B THR* 1.3 65.8 + - - +
87B LYS* 3.4 9.3 + - - +
88B LEU* 3.2 51.2 + - + +
90B LYS* 5.3 7.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.0 13.6 + - - -
82B LEU* 3.2 12.3 - - + +
84B HIS* 1.3 79.9 - - - +
86B LEU* 1.3 51.6 + - - +
88B LEU 3.2 1.0 + - - -
89B GLY* 2.7 36.2 + - - -
90B LYS* 3.2 36.4 + - - +
92B ALA* 3.5 20.3 - - + +
187B PHE* 3.5 26.5 - - + -
208B PHE* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.4 2.5 - - + -
49B ILE* 4.1 26.9 - - + -
53B ILE* 6.2 0.2 - - + -
82B LEU* 2.8 45.6 + - + +
83B VAL* 3.2 12.5 + - + +
85B THR* 1.3 74.0 - - - +
87B LYS* 1.3 63.1 + - - +
89B GLY* 3.4 7.9 + - - +
187B PHE* 3.5 44.2 - - + -
193B PHE* 3.9 30.3 - - + -
200B ILE* 4.7 1.5 - - - +
202B ILE* 3.7 20.6 - - + +
203B PRO* 3.5 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 3.0 17.4 + - + +
84B HIS* 3.7 10.1 - - - +
85B THR 3.3 0.2 - - - -
86B LEU* 1.3 79.8 - - - +
88B LEU* 1.3 73.2 + - + +
198B GLU* 4.4 23.4 + - - +
200B ILE* 3.9 34.0 - - + +
201B GLU 4.6 2.3 - - - +
203B PRO* 3.5 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B HIS* 3.2 41.7 + - + +
85B THR 3.2 1.6 + - - -
87B LYS* 1.3 93.8 - - + +
89B GLY* 1.3 64.1 + - - +
90B LYS* 3.1 40.5 + - + +
203B PRO* 3.6 7.7 - - - +
204B ASN* 3.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR 2.7 10.7 + - - -
86B LEU 3.4 3.4 + - - -
87B LYS 3.3 3.0 + - - -
88B LEU* 1.3 77.4 - - - +
90B LYS* 1.3 58.0 + - - -
91B PRO* 4.0 4.9 - - - +
187B PHE* 3.9 11.2 - - - -
203B PRO* 3.7 11.8 - - - +
204B ASN* 2.9 40.8 - - - +
205B SER 4.7 1.7 - - - +
----------------------------------------------------------
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