Contacts of the helix formed by residues 87 - 97 (chain B) in PDB entry 2UUG
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 PRO 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE 4.4 0.7 - - - +
86B PRO* 1.3 86.7 - - + +
88B SER* 1.3 55.9 + - - +
90B LEU* 3.4 11.7 + - + +
91B ASN* 3.0 36.3 + - - -
190B PRO* 3.5 28.5 - - + -
19D GLN* 4.1 24.2 - - + +
20D GLU* 3.8 14.8 - - + +
45D THR* 3.8 22.7 - - + +
46D ALA 5.1 1.3 - - - +
47D TYR* 5.1 3.6 - - + -
54D ASN* 3.9 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 5.4 2.7 - - - -
77B PHE* 4.6 17.7 - - - -
87B PRO* 1.3 76.2 - - - +
89B LEU* 1.3 59.1 + - - +
91B ASN* 3.2 4.7 + - - +
92B MET* 3.0 31.6 + - - +
187B ASP* 5.0 0.5 + - - -
188B PRO* 3.8 20.5 - - - +
189B SER* 3.4 18.9 + - - +
20D GLU* 3.0 34.1 + - - -
22D ILE* 4.1 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 4.8 1.7 + - - +
77B PHE* 3.5 24.0 - - + +
79B VAL* 4.3 0.4 - - + -
85B ILE* 3.8 13.5 - - + -
86B PRO* 3.2 22.0 + - + +
88B SER* 1.3 75.1 - - - +
90B LEU* 1.3 61.1 + - - +
92B MET* 3.0 27.1 + - + +
93B TYR* 2.9 43.7 + - + +
109B GLY* 3.3 38.6 - - - +
111B LEU* 3.4 26.0 - - + -
114B TRP* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.6 27.5 - - + +
86B PRO 2.8 17.3 + - - +
87B PRO* 3.5 11.9 - - + +
89B LEU* 1.3 76.4 - - - +
91B ASN* 1.3 59.4 + - - +
93B TYR* 3.2 7.9 + - + +
94B LYS* 3.0 54.3 + - - +
105B ARG* 3.9 32.1 - - - +
47D TYR* 5.0 18.4 - - + -
54D ASN* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO 3.0 15.8 + - - +
88B SER 3.2 4.9 + - - +
90B LEU* 1.3 76.2 - - - +
92B MET* 1.3 64.9 + - - +
94B LYS* 3.7 20.9 - - - +
95B GLU 3.2 16.8 + - - -
188B PRO 2.8 30.2 - - - +
190B PRO* 3.7 15.7 - - - +
193B ALA* 3.5 11.2 - - + +
197B PHE* 3.5 8.7 - - + -
198B PHE* 3.2 38.5 - - + -
54D ASN* 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 5.2 0.9 - - + -
77B PHE* 3.8 32.1 - - + -
88B SER 3.0 18.0 + - - +
89B LEU* 3.0 30.9 + - + +
91B ASN* 1.3 75.4 - - - +
93B TYR* 1.3 65.3 + - + +
95B GLU* 3.4 3.3 + - - +
96B LEU* 3.1 30.7 + - + +
111B LEU* 4.5 0.2 - - + -
114B TRP* 4.0 26.0 - - + -
121B LEU* 5.9 0.2 - - + -
164B TRP* 3.6 34.3 - - + -
188B PRO* 4.1 3.6 - - + -
197B PHE* 3.9 24.2 - - + -
203B PHE* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.7 31.6 - - + -
89B LEU* 2.9 27.6 + - + -
90B LEU* 3.2 10.7 + - + +
92B MET* 1.3 78.3 - - - +
94B LYS* 1.3 61.2 + - - +
96B LEU* 3.1 21.4 + - + +
97B GLU* 3.0 29.7 + - - +
103B PHE* 3.8 7.4 - + + -
105B ARG* 4.3 17.9 - - - -
106B PRO* 3.6 31.6 - - + -
108B HIS 2.7 29.3 + - - -
109B GLY* 3.5 3.1 - - - -
110B TYR 4.4 0.2 + - - -
111B LEU* 3.3 31.1 - - + +
114B TRP* 4.8 1.6 - + - -
222B PRO* 3.7 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.0 42.5 + - - +
91B ASN* 3.8 29.4 - - - +
92B MET 3.3 0.2 - - - -
93B TYR* 1.3 77.8 - - - +
95B GLU* 1.3 58.5 + - - +
97B GLU* 3.4 7.9 + - - +
98B ASN* 3.1 36.6 + - - +
105B ARG* 3.8 28.3 - - - +
198B PHE* 3.8 15.7 - - + -
54D ASN* 5.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN 3.2 16.6 + - - +
92B MET 3.8 4.9 - - - +
93B TYR 3.3 0.2 - - - -
94B LYS* 1.3 76.0 - - - +
96B LEU* 1.3 54.9 + - - +
98B ASN* 3.7 6.6 + - - +
99B THR* 2.6 43.9 + - - +
197B PHE* 3.8 21.3 - - + +
198B PHE* 3.6 10.0 - - + +
199B GLY* 2.7 27.4 + - - -
200B CYS* 3.4 4.8 + - - -
201B ASN* 2.9 34.1 + - - -
203B PHE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B MET 3.1 24.8 + - - +
93B TYR* 3.1 12.3 + - + +
95B GLU* 1.3 77.3 - - - +
97B GLU* 1.3 59.0 + - - +
99B THR* 3.8 1.8 - - - -
100B ILE* 2.9 41.6 + - + +
103B PHE* 3.6 34.3 - - + +
114B TRP* 3.9 26.7 - - + -
203B PHE* 3.5 33.2 - - + -
220B TRP* 3.3 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLY* 5.8 3.5 - - - -
93B TYR 3.0 20.1 + - - +
94B LYS* 3.4 8.4 - - - +
96B LEU* 1.3 76.7 - - - +
98B ASN* 1.3 72.6 + - - +
99B THR 3.4 0.9 + - - -
100B ILE 4.2 7.4 + - - +
103B PHE* 3.6 33.7 - - + +
105B ARG* 2.7 49.6 + - - +
----------------------------------------------------------
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