Contacts of the strand formed by residues 87 - 98 (chain C) in PDB entry 3U53
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 3.3 3.7 - - - +
84C ALA 2.5 38.9 + - - +
85C ARG 3.3 2.2 - - - +
86C ASN* 1.3 76.9 - - - +
88C PRO* 1.3 69.1 - - + +
89C LYS* 3.5 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG 5.7 1.2 + - - -
82C TYR 3.4 7.2 - - - +
83C VAL* 4.0 18.4 - - + -
86C ASN 4.6 2.0 - - - +
87C LYS* 1.3 85.3 - - + +
89C LYS* 1.3 64.3 + - - +
90C THR* 4.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG 5.4 3.6 - - - +
80C LEU 3.7 0.9 - - - +
81C ASN* 3.6 1.7 - - - +
82C TYR* 2.8 67.1 + - + +
84C ALA* 3.6 17.0 + - + -
87C LYS* 3.5 38.2 - - - +
88C PRO* 1.3 75.5 - - - +
90C THR* 1.3 64.4 + - - +
91C VAL* 4.3 3.8 - - + -
159C SO4 3.8 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.3 36.0 - - + +
5C ALA* 2.7 26.2 + - - +
79C GLU* 4.2 20.9 - - + +
80C LEU 3.3 4.9 - - - +
81C ASN* 2.8 24.3 + - - +
88C PRO 4.3 1.1 + - - -
89C LYS* 1.3 73.2 + - - +
91C VAL* 1.3 69.1 + - - +
92C ILE* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ALA* 3.1 17.7 - - + +
42C LYS* 3.9 23.6 - - + -
78C ARG 3.8 0.3 - - - +
79C GLU* 3.3 3.5 - - - +
80C LEU* 2.7 42.6 + - + +
82C TYR* 3.8 32.8 - - + +
89C LYS* 4.9 2.7 - - + -
90C THR* 1.3 81.0 - - - +
92C ILE* 1.3 70.2 + - - +
93C TYR* 3.6 36.3 - - + +
131C MET* 6.1 0.4 - - + -
159C SO4 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.9 17.7 - - - +
5C ALA 2.8 14.9 + - - +
6C CYS* 3.2 7.6 - - - +
7C GLY 2.9 25.3 + - - +
51C ASP* 3.9 22.2 - - - +
77C LYS* 4.1 22.4 - - + +
78C ARG 3.5 9.0 - - - +
79C GLU* 3.8 27.8 - - + +
90C THR* 4.8 4.0 - - + -
91C VAL* 1.3 78.9 - - - +
93C TYR* 1.3 63.7 + - - +
94C TRP* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLY* 3.5 31.4 - - - -
8C LEU 3.8 2.2 - - - -
9C ILE* 3.9 29.4 - - + -
39C THR* 4.0 1.2 + - - -
40C PRO* 3.5 20.4 - - + +
41C PRO 3.9 6.7 - - - -
42C LYS* 3.6 26.4 - - + +
76C PHE* 4.5 1.6 - - - -
77C LYS* 3.4 6.9 - - - +
78C ARG* 2.9 38.2 + - + +
80C LEU* 3.7 20.0 - - + -
91C VAL* 3.6 21.9 - - + +
92C ILE* 1.3 73.0 - - - +
94C TRP* 1.3 64.4 + - - +
131C MET* 3.2 38.5 - - + +
134C ALA* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 4.1 15.9 - - + -
53B GLU* 3.0 26.6 + - + +
6C CYS* 4.4 2.7 - - + -
7C GLY 3.3 11.2 + - - -
8C LEU* 3.3 18.0 - - + -
9C ILE* 2.6 34.2 + - - +
51C ASP* 3.8 39.3 - - + -
52C LEU* 3.5 30.0 - - + +
55C ALA* 4.2 2.5 - - + -
72C ILE* 4.6 12.3 - - + -
73C ILE 5.2 1.3 - - - -
76C PHE* 3.4 26.0 - - - -
77C LYS* 3.5 27.4 - - + +
92C ILE* 3.6 32.3 - - + -
93C TYR* 1.3 78.0 - - - +
95C LEU* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.4 31.2 - - + +
11C PHE* 3.7 17.0 - - + -
26C PHE* 4.5 5.4 - - + -
72C ILE* 3.7 7.3 - - - +
73C ILE* 3.0 36.2 + - + +
76C PHE* 3.7 41.3 + - + -
94C TRP* 1.3 75.9 - - - +
96C ALA* 1.3 62.2 + - - +
138C GLY* 4.0 17.5 - - - +
141C PHE* 3.9 20.6 - - + -
142C LEU* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.8 33.4 - - + -
9C ILE 3.1 6.9 + - - -
10C ILE* 3.5 12.3 - - + +
11C PHE* 3.1 27.4 + - - -
70C LEU* 4.3 9.2 - - + -
71C THR 3.0 13.5 - - - +
72C ILE* 4.0 6.7 - - + -
73C ILE 4.6 0.2 - - - +
94C TRP 4.0 0.4 + - - -
95C LEU* 1.3 75.8 - - - +
97C GLU* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 3.3 31.7 - - + +
13C ARG* 3.2 49.2 + - - +
70C LEU* 3.4 3.4 - - - -
71C THR* 2.8 38.6 + - - +
73C ILE* 4.1 14.6 - - + +
96C ALA* 1.3 72.6 - - - +
98C VAL* 1.3 76.2 + - - +
160C SO4 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.8 25.8 - - + -
11C PHE 3.1 15.1 + - - +
12C ARG* 3.6 13.0 - - + -
65C ILE* 4.4 3.6 - - + -
69C GLN 3.7 5.6 - - - +
70C LEU* 4.1 13.0 - - + -
71C THR* 5.5 0.7 - - - -
97C GLU* 1.3 84.3 - - - +
99C LYS* 1.3 64.3 + - - +
100C ASP 3.5 22.4 - - - +
101C TYR* 4.4 0.7 - - - -
103C VAL* 3.8 21.5 - - + -
116C TRP* 4.2 6.1 - - + -
160C SO4 3.3 29.1 + - - +
----------------------------------------------------------
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