Contacts of the helix formed by residues 87 - 102 (chain B) in PDB entry 1U75
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 LYS 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG 4.7 9.0 + - - +
32A GLU* 3.5 42.2 + - + +
33A ASP* 5.5 0.8 - - - +
34A ASP* 4.2 8.6 + - - +
35A GLU* 3.8 20.8 + - - +
85B ILE* 3.6 2.8 - - + +
86B LYS* 1.3 80.4 - - - +
88B LYS* 1.3 62.8 + - - +
89B THR* 4.3 24.3 + - - +
90B GLU* 4.3 19.5 - - + +
91B ARG* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 3.6 28.6 - - + +
86B LYS 4.0 0.6 + - - +
87B LYS* 1.3 74.9 - - - +
89B THR* 1.3 56.8 + - - +
90B GLU 3.3 1.8 - - - -
91B ARG* 3.3 3.8 + - - +
92B GLU* 2.8 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 5.5 6.5 - - - +
87B LYS* 4.3 22.9 + - - +
88B LYS* 1.3 77.5 + - - +
90B GLU* 1.3 57.3 + - - +
92B GLU* 3.4 14.8 + - - +
93B ASP* 3.1 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 2.4 32.7 - - - +
35A GLU* 6.5 0.4 - - - -
39A TYR* 3.5 31.9 - - + -
9B ILE* 3.2 38.7 - - + +
13B LYS* 3.3 17.2 + - - -
85B ILE* 3.3 29.9 - - + +
87B LYS* 4.3 13.6 - - + +
88B LYS 3.3 1.2 - - - +
89B THR* 1.3 77.2 - - - +
91B ARG* 1.3 60.0 + - - +
92B GLU 3.2 0.2 - - - -
93B ASP* 3.4 1.5 + - - -
94B LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 2.6 47.1 + - - -
66B GLU* 4.0 1.8 + - - +
68B LEU* 2.8 38.6 - - + +
69B GLU* 2.2 44.1 + - - +
85B ILE* 1.5 54.5 + - + -
86B LYS* 3.2 13.4 + - - +
87B LYS 3.0 24.9 + - - +
88B LYS* 3.3 3.9 + - - +
90B GLU* 1.3 74.6 - - - +
92B GLU* 1.3 59.4 + - - +
94B LEU* 3.5 3.1 + - - +
95B ILE* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 5.8 3.9 - - - -
62B GLU* 5.9 0.7 - - - +
65B MET* 3.7 20.8 - - + +
88B LYS* 2.8 32.6 + - - +
89B THR* 3.4 14.6 + - - +
91B ARG* 1.3 77.1 - - - +
93B ASP* 1.3 61.7 + - - +
95B ILE* 3.7 5.3 + - - +
96B ALA* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.9 3.7 + - - +
1B GLY* 3.4 8.1 - - - -
2B ASP* 3.0 64.3 + - - +
5B LYS* 4.4 7.3 - - + +
6B GLY* 3.2 15.1 - - - +
9B ILE* 4.0 10.8 - - + -
89B THR* 3.1 23.7 + - - +
90B GLU* 3.4 4.9 + - - +
91B ARG 3.3 0.2 - - - -
92B GLU* 1.3 84.3 - - - +
94B LEU* 1.3 61.7 + - - +
96B ALA* 4.3 0.4 - - - -
97B TYR 3.5 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLY 4.0 7.9 - - - +
9B ILE* 3.8 21.5 - - + +
10B PHE* 4.0 27.4 - - + -
14B CYS* 4.7 2.0 - - - -
68B LEU* 4.1 32.1 - - + -
85B ILE* 4.2 12.8 - - + -
90B GLU 3.0 16.3 + - - +
91B ARG* 4.0 5.2 - - - +
92B GLU 3.4 0.2 - - - -
93B ASP* 1.3 74.1 - - - +
95B ILE* 1.3 61.5 + - + +
97B TYR* 3.5 2.1 + - + +
98B LEU* 3.0 52.3 + - + +
1101B HEC 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 3.9 10.1 - - + -
61B GLU* 3.3 55.4 - - + +
62B GLU* 5.4 2.0 - - - +
64B LEU* 4.0 6.3 - - + +
65B MET* 3.6 23.8 - - + -
68B LEU* 3.8 21.8 - - + -
91B ARG 3.1 21.5 + - - +
92B GLU* 4.0 6.1 - - - +
94B LEU* 1.3 76.1 - - + +
96B ALA* 1.3 66.9 + - - +
98B LEU* 3.4 12.7 + - + +
99B LYS* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 3.7 26.5 - - - +
2B ASP 4.0 2.7 - - - +
3B VAL* 3.8 8.6 - - + +
92B GLU 3.1 19.5 + - - +
93B ASP* 3.8 6.7 - - - +
94B LEU 3.3 0.4 - - - -
95B ILE* 1.3 77.9 - - - +
97B TYR* 1.4 62.2 + - - +
99B LYS* 3.2 33.5 + - - +
100B LYS 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.5 38.9 - - + +
6B GLY 3.8 16.4 - - - -
7B LYS* 3.6 35.4 + - + +
10B PHE* 3.6 36.7 - + + -
20B VAL* 4.1 9.6 - - + +
93B ASP 3.5 9.5 + - - +
94B LEU* 3.5 6.7 + - + +
96B ALA* 1.4 75.7 - - - +
98B LEU* 1.3 83.7 + - + +
100B LYS* 3.0 20.7 + - + +
101B ALA* 3.0 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.9 19.3 - - + -
20B VAL* 4.6 1.1 - - + -
32B LEU* 4.7 4.9 - - + -
35B LEU* 4.0 21.1 - - + -
36B PHE* 3.4 14.1 - - + -
64B LEU* 6.2 1.3 - - + -
94B LEU* 3.0 37.6 + - + +
95B ILE* 3.7 9.0 - - + +
96B ALA 3.4 0.2 - - - -
97B TYR* 1.3 91.7 - - + +
99B LYS* 1.4 51.9 + - - +
100B LYS 3.0 1.0 + - - -
101B ALA 4.7 0.2 - - - +
102B THR* 2.5 59.5 + - + -
1101B HEC 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 5.4 5.2 - - - -
36B PHE* 3.4 30.7 - - + -
61B GLU* 5.4 9.2 - - + +
95B ILE 3.3 11.2 + - - +
96B ALA* 3.2 24.0 - - - +
97B TYR 3.3 1.2 - - - -
98B LEU* 1.4 72.4 - - - +
100B LYS* 1.3 73.4 + - - +
102B THR* 4.3 1.1 - - - -
103B ASN* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.5 28.8 - - + +
96B ALA 3.9 1.1 + - - +
97B TYR* 3.0 25.4 + - + +
99B LYS* 1.3 91.5 - - - +
101B ALA* 1.3 64.7 + - + +
102B THR 3.2 1.0 + - - -
103B ASN 3.2 1.4 + - - -
104B GLU* 2.9 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.4 28.6 - - + +
21B GLU* 4.4 3.8 + - - +
97B TYR* 3.0 49.5 + - + +
98B LEU* 4.3 1.1 - - - +
100B LYS* 1.3 82.2 - - + +
102B THR* 1.3 57.7 + - - +
103B ASN 3.3 3.4 + - - -
104B GLU* 4.7 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.6 31.6 - - + -
32B LEU* 3.2 27.1 - - + +
33B HIS* 3.2 7.3 - - - -
34B GLY* 3.0 25.1 + - - -
35B LEU* 4.2 2.9 + - + +
36B PHE* 3.1 24.0 - - + -
98B LEU* 2.5 48.0 + - + +
99B LYS* 4.1 1.0 - - - -
101B ALA* 1.3 71.4 - - - +
103B ASN* 1.3 59.4 + - - +
----------------------------------------------------------
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