Contacts of the helix formed by residues 84 - 96 (chain B) in PDB entry 1UU1
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 GLY 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY* 2.6 22.1 + - - -
83B ASN* 1.3 75.9 - - - +
85B ALA* 1.3 63.4 + - - -
86B ASP 2.8 7.2 + - - -
87B GLU 3.1 6.6 + - - -
88B ILE 3.7 1.0 + - - -
210B ARG* 3.2 21.6 + - - -
211B VAL 3.8 0.2 - - - -
212B GLY 3.8 10.3 - - - -
1335B PMP 3.2 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY* 1.3 71.6 - - - -
86B ASP* 1.3 61.6 + - - +
88B ILE* 3.1 17.4 + - - +
89B ILE* 3.1 26.7 + - - +
173B ASP* 5.4 0.7 - - - +
175B ALA* 5.7 0.7 - - + -
197B ILE* 3.5 23.1 - - + -
198B ARG 3.6 12.8 - - - +
199B THR* 4.1 3.8 - - - -
212B GLY* 3.7 4.1 - - - -
1335B PMP 2.5 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.9 12.5 - - + +
230A PRO* 4.4 7.1 - - - +
231A PHE* 4.7 1.9 + - - -
83B ASN 4.7 1.3 - - - +
84B GLY 2.8 0.8 - - - -
85B ALA* 1.3 77.0 - - - +
87B GLU* 1.3 56.1 + - - +
89B ILE* 3.4 7.2 + - - +
90B TYR* 2.9 28.1 + - - +
106B TYR* 2.4 32.5 + - - -
112B PHE* 3.5 25.2 - - - -
210B ARG* 3.7 11.9 + - - +
1335B PMP 2.7 23.3 + - - +
1336B HSA 3.0 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 4.5 1.9 + - - -
87A GLU* 5.2 0.5 - - - +
229A LEU* 3.7 28.0 - - + +
82B GLY* 3.7 1.7 - - - -
83B ASN* 2.9 39.2 + - - +
84B GLY 3.1 3.2 + - - -
86B ASP* 1.3 76.9 - - - +
88B ILE* 1.3 59.0 + - - +
90B TYR* 3.9 2.0 - - + -
91B VAL* 2.7 50.0 + - + +
224B TYR* 4.4 3.7 + - - +
228B ARG* 5.3 0.9 - - - -
229B LEU* 3.8 24.6 + - - +
232B ASN* 2.8 40.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY* 3.7 11.7 - - - +
84B GLY 3.8 3.6 - - - +
85B ALA* 3.3 15.0 - - - +
87B GLU* 1.3 78.4 - - - +
89B ILE* 1.3 56.8 + - - +
91B VAL* 3.5 1.2 - - - +
92B MET* 2.9 42.0 + - - +
197B ILE* 4.0 22.7 - - + -
212B GLY 3.7 7.4 - - - -
213B TYR* 3.5 30.1 - - - +
214B VAL* 3.3 37.9 - - + -
220B PHE* 5.9 0.2 - - + -
224B TYR* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 3.1 18.0 + - + +
86B ASP* 3.6 7.2 - - - +
88B ILE* 1.3 72.8 - - - +
90B TYR* 1.3 68.6 + - - +
92B MET* 3.1 8.1 + - - +
93B MET* 2.9 34.2 + - + +
106B TYR* 3.8 18.4 - - + -
109B TYR* 3.6 32.1 - - + -
112B PHE* 4.3 13.9 - - + -
143B PHE* 3.9 17.3 - - + -
173B ASP* 3.3 24.7 - - - +
197B ILE* 4.0 18.4 - - + -
1335B PMP 4.1 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.7 9.4 - + - -
91A VAL* 4.1 10.3 - - + +
94A LEU* 3.4 25.5 - - + +
227A VAL* 2.5 33.1 + - - +
228A ARG 4.5 1.6 - - - -
229A LEU* 4.0 34.8 - - + -
86B ASP 2.9 18.0 + - - +
87B GLU* 3.5 8.5 - - + +
89B ILE* 1.3 77.0 - - - +
91B VAL* 1.3 71.0 + - + +
93B MET* 3.1 21.7 + - - +
94B LEU* 3.5 14.7 + - + +
112B PHE* 4.0 26.0 - + + -
115B ALA* 4.9 3.4 - - + -
116B VAL* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.9 22.7 - - + +
87B GLU* 2.7 43.2 + - + +
88B ILE 3.5 1.8 - - - +
90B TYR* 1.3 78.7 - - + +
92B MET* 1.3 58.2 + - - +
94B LEU* 2.7 37.0 + - - +
95B MET* 3.2 12.1 + - + +
224B TYR* 3.1 40.6 - - + -
227B VAL* 4.4 8.1 - - + -
228B ARG* 4.4 13.2 - - + -
229B LEU 5.4 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
88B ILE* 2.9 31.3 + - + +
89B ILE 3.1 6.5 + - - +
91B VAL* 1.3 77.4 - - - +
93B MET* 1.3 61.8 + - - +
95B MET* 2.9 27.7 + - + -
96B PHE* 3.1 28.9 + - + -
141B VAL* 3.9 10.9 - - + +
143B PHE* 4.0 11.2 - - + -
169B PHE* 3.6 25.8 - - + -
171B ALA* 3.3 27.8 - - + -
195B ALA* 4.2 5.4 - - + -
197B ILE* 3.9 24.9 - - - -
220B PHE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.9 24.2 + - + +
90B TYR* 3.5 8.3 - - - +
91B VAL 3.0 0.6 - - - -
92B MET* 1.3 76.7 - - - +
94B LEU* 1.3 63.5 + - + +
96B PHE 3.8 13.9 - - - +
99B SER* 3.5 30.3 + - - +
101B PHE* 4.0 7.2 - - + -
109B TYR* 3.2 29.4 - - - +
112B PHE* 3.9 14.8 - - - -
113B ALA* 3.6 32.8 - - + -
116B VAL* 5.5 4.3 - - + -
118B ALA* 4.1 22.7 - - + +
141B VAL* 5.2 0.4 - - - -
143B PHE* 3.9 19.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
90A TYR* 3.6 30.7 - - + +
94A LEU* 3.8 16.6 - - + -
115A ALA 4.9 4.0 - - - +
116A VAL* 3.6 27.4 - - + +
90B TYR* 3.7 14.1 - - + +
91B VAL* 2.7 21.2 + - - +
93B MET* 1.3 74.3 - - - +
95B MET* 1.3 62.0 + - - +
96B PHE 3.6 2.6 - - - +
116B VAL* 2.9 40.6 - - + -
227B VAL* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 5.8 5.4 - - + -
91B VAL* 3.3 8.3 - - + +
92B MET* 2.9 51.8 + - + +
94B LEU* 1.3 81.8 - - - +
96B PHE* 1.3 71.3 + - + +
220B PHE* 3.9 17.0 - - + -
223B ALA* 4.7 5.2 - - - -
224B TYR* 3.8 42.4 - - + -
227B VAL* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 5.0 14.4 - - + -
92B MET* 3.1 19.1 + - + -
93B MET* 3.8 12.8 + - - +
94B LEU 3.6 1.9 - - - +
95B MET* 1.3 91.3 - - + +
97B ASP* 1.3 66.2 + - - +
98B ARG* 3.3 3.2 + - - +
99B SER* 5.7 0.3 + - - -
118B ALA* 6.0 0.2 - - - +
139B GLY* 3.5 14.4 - - - +
140B ASP 4.0 11.7 - - - -
141B VAL* 3.0 43.3 - - + -
169B PHE* 3.6 41.7 - + + -
220B PHE* 4.1 22.0 - + - -
----------------------------------------------------------
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