Contacts of the helix formed by residues 92 - 103 (chain B) in PDB entry 4AUP
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 SER 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.8 7.4 + - - -
91B LEU* 1.3 73.3 - - - +
93B PRO* 1.3 63.0 - - - +
94B VAL 3.4 2.5 - - - -
95B SER* 3.4 11.8 + - - -
96B ASP* 2.9 46.4 + - - -
1213B ACT 3.2 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.7 11.7 - - + +
92B SER* 1.3 88.0 - - - +
94B VAL* 1.4 54.0 + - + +
96B ASP* 4.0 4.2 - - + +
97B THR* 2.7 37.8 + - - -
118B PRO* 6.1 0.9 - - + -
120B ASN* 5.2 13.2 - - + +
121B LEU* 3.7 21.6 - - + +
157B GLN* 3.9 7.9 - - + +
1213B ACT 3.3 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 1.4 76.5 - - + +
95B SER* 1.3 61.7 + - - +
97B THR 3.4 0.5 + - - -
98B ASP* 3.1 28.8 + - - +
157B GLN* 4.0 25.8 - - + +
159B ARG* 3.5 38.7 + - - +
1213B ACT 3.4 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B SER* 3.4 14.1 + - - -
94B VAL* 1.3 73.4 - - - +
96B ASP* 1.3 62.4 + - - +
98B ASP* 3.3 6.2 + - - +
99B ARG* 2.8 29.7 + - - +
1213B ACT 3.2 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 5.4 4.2 - - - -
91B LEU* 6.2 0.3 - - - +
92B SER* 2.9 36.5 + - - +
93B PRO* 4.0 4.7 - - + +
95B SER* 1.3 75.4 + - - +
97B THR* 1.4 60.9 + - - +
99B ARG* 3.3 21.8 + - - +
100B LEU* 2.9 36.3 + - - +
118B PRO* 3.4 34.4 - - + +
121B LEU* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO 2.7 23.4 + - - -
94B VAL 3.6 5.2 - - - -
95B SER 3.4 0.2 - - - -
96B ASP* 1.4 74.3 - - - +
98B ASP* 1.3 58.3 + - - +
100B LEU* 3.2 3.5 + - - +
101B LEU* 2.9 36.3 + - + +
121B LEU* 3.5 11.7 - - - +
149B PHE* 3.7 20.1 - - + -
153B ASN* 3.8 23.1 - - + +
154B TYR* 3.9 13.9 - - + -
157B GLN* 2.9 13.3 + - - +
159B ARG* 3.7 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.1 19.9 + - - +
95B SER* 3.9 5.3 - - - +
96B ASP 3.2 0.2 - - - -
97B THR* 1.3 72.8 - - - +
99B ARG* 1.3 65.2 + - - +
101B LEU* 4.1 0.2 - - - +
102B TYR* 3.1 42.7 + - + +
103B SER* 4.0 2.6 + - - -
154B TYR* 2.5 30.1 + - - -
159B ARG* 2.9 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASP* 5.2 4.5 - - - -
99A ARG* 3.3 57.6 - - - +
95B SER* 2.8 18.4 + - - +
96B ASP* 3.7 20.9 + - - +
98B ASP* 1.3 76.7 - - - +
100B LEU* 1.3 82.7 + - - +
103B SER* 3.0 39.2 + - - +
104B THR* 2.8 35.2 + - - +
117B ASN* 5.1 2.6 + - - -
118B PRO* 5.0 5.3 - - - +
1212B SCN 5.1 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP 2.9 20.7 + - - +
97B THR 3.2 3.6 + - - +
99B ARG* 1.3 103.7 - - - +
101B LEU* 1.3 50.6 + - - +
104B THR* 3.5 19.5 - - + +
108B ALA 5.1 0.2 - - - +
109B PHE* 3.6 16.9 - - + -
112B ALA* 3.7 25.1 - - + -
117B ASN 4.1 0.7 - - - +
118B PRO* 4.0 18.4 - - + -
121B LEU* 4.2 1.8 - - + -
123B TRP* 3.7 25.4 - - + -
146B ARG* 2.8 32.1 + - - -
149B PHE* 3.8 19.3 - - + -
1212B SCN 5.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 2.9 22.8 + - + +
98B ASP* 4.1 0.2 - - - +
100B LEU* 1.3 80.4 - - - +
102B TYR* 1.3 86.4 + - + +
104B THR 4.9 0.2 - - - +
146B ARG* 3.6 38.7 + - + +
149B PHE* 3.9 9.6 - - + -
150B GLY* 3.7 28.5 - - - +
154B TYR* 3.5 31.9 - - + -
168B ILE* 4.4 9.4 - - + -
171B ASN* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 3.1 35.5 + - + +
101B LEU* 1.3 88.6 - - + +
103B SER* 1.3 64.2 + - - +
104B THR 3.7 2.5 - - - -
154B TYR* 3.1 32.3 + - - -
167B ARG* 3.6 52.3 - - + +
168B ILE* 3.8 11.4 - - - +
171B ASN* 3.8 28.0 + - + +
174B LYS* 5.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 2.9 29.3 + - - +
1212A ACT 4.6 0.8 - - - +
98B ASP 4.3 3.3 + - - -
99B ARG* 3.0 21.9 + - - +
102B TYR* 1.3 85.9 + - - +
104B THR* 1.3 65.9 + - - +
----------------------------------------------------------
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