Contacts of the strand formed by residues 86 - 97 (chain C) in PDB entry 4UOW
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 86 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 4.3 3.6 - - - -
5C PRO* 3.4 10.9 - - - +
82C GLY* 3.6 0.3 - - - -
83C ASN* 3.0 33.9 + - - +
84C GLU 3.6 0.6 + - - -
85C PHE* 1.3 77.8 - - - +
87C SER* 1.3 61.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 5.3 0.4 - - - +
5C PRO* 3.8 10.0 - - - +
81C LEU 3.4 15.9 - - - -
82C GLY* 4.3 3.6 - - - -
86C GLY* 1.3 73.9 - - - -
88C ASP* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 3.6 16.9 - - - +
6C LYS* 3.5 19.3 + - - +
7C ILE* 2.7 41.4 + - + +
80C SER* 3.4 2.9 - - - -
81C LEU* 2.9 34.8 + - + +
87C SER* 1.3 76.7 - - - +
89C SER* 1.3 73.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.7 2.9 - - - +
78C THR* 4.3 11.9 - - - +
79C LEU 3.3 10.1 - - - -
80C SER* 4.2 11.2 - - - -
88C ASP* 1.3 85.7 + - - +
90C ALA* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.9 27.4 - - + -
10C LEU* 3.8 20.7 - - + +
78C THR* 3.3 3.8 - - - -
79C LEU* 2.9 31.1 + - + +
89C SER* 1.3 75.9 - - - +
91C THR* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.6 5.6 - - - +
11C PRO 3.4 10.4 - - - +
12C SER* 3.7 9.1 - - - +
76C LEU* 3.9 32.4 - - + +
77C TYR 3.2 4.5 - - - +
78C THR* 3.4 31.0 - - + +
90C ALA* 1.3 77.4 - - - +
92C VAL* 1.3 60.0 + - - +
93C ASN 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.8 11.0 - - + -
11C PRO* 3.3 20.6 - - + +
12C SER 3.4 4.0 - - - +
14C ILE* 3.7 39.0 - - + -
24C VAL* 4.9 8.5 - - + -
38C TRP* 3.9 20.6 - - + -
76C LEU* 4.6 1.8 - - - -
77C TYR* 2.8 52.7 + - + +
91C THR* 1.3 71.0 - - - +
93C ASN* 1.3 61.4 + - - +
94C ILE* 3.4 12.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER 2.8 13.2 + - - +
13C ASP* 3.3 23.3 + - - +
14C ILE 2.9 28.2 + - - +
75C GLY* 3.6 14.3 - - - +
76C LEU* 3.8 23.7 - - + +
91C THR 4.2 0.2 - - - -
92C VAL* 1.3 71.5 - - - +
94C ILE* 1.3 62.6 + - - +
95C HIS* 3.2 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.4 24.9 - - + +
16C ILE* 4.6 2.7 - - + -
22C LEU* 3.6 33.9 - - + -
24C VAL* 4.7 1.1 - - + -
64C LEU* 4.1 10.1 - - + -
66C ILE* 4.0 12.3 - - + -
73C ASP 4.9 1.8 - - - +
74C GLY* 3.4 3.5 - - - -
75C GLY 2.9 37.1 + - - +
77C TYR* 3.5 38.1 - - + -
92C VAL* 4.1 10.3 - - + +
93C ASN* 1.3 75.0 - - - +
95C HIS* 1.3 64.4 + - - +
96C ILE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASP* 2.9 30.5 + - + -
14C ILE 2.9 22.4 + - - +
15C SER* 3.3 21.3 - - - +
16C ILE* 3.0 27.0 + - - +
74C GLY* 5.0 0.7 - - - -
93C ASN* 3.2 37.8 + - - -
94C ILE* 1.3 73.5 + - - +
96C ILE* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.4 7.9 - - + +
18C GLU* 3.6 28.3 - - + +
69C VAL* 3.4 33.9 - - + -
70C GLN 3.9 2.2 - - - +
71C LYS* 3.0 48.7 + - + +
73C ASP* 4.3 2.7 - - + -
74C GLY* 3.5 33.1 - - - +
94C ILE* 3.8 18.4 - - + -
95C HIS* 1.3 82.7 - - - +
97C ARG* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.2 45.3 + - - -
16C ILE 3.0 14.0 + - - +
17C ASP* 2.8 40.3 + - - +
18C GLU* 3.0 32.9 + - - +
71C LYS* 4.7 4.3 - - - +
96C ILE* 1.3 73.9 - - - +
98C SER* 1.4 62.5 + - - +
83D ARG* 5.3 9.5 - - - +
85D ARG* 4.0 10.3 - - - +
90D GLU* 4.0 8.5 + - - -
----------------------------------------------------------
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