Contacts of the strand formed by residues 82 - 94 (chain C) in PDB entry 4OBZ
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ILE 3.2 14.6 - - - -
77C HIS* 3.5 23.2 + - - -
81C GLY* 1.3 73.4 - - - -
83C LEU* 1.4 69.4 + - - +
122D PRO* 3.4 36.2 + - - +
126D PHE* 3.4 13.8 - - - -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TRP* 3.4 50.5 - - + +
74C PHE* 3.8 8.9 - - + -
75C ASP* 3.3 5.4 - - - +
76C ILE* 3.0 44.3 + - + +
77C HIS* 5.9 0.2 + - - -
78C TYR* 3.7 19.1 - - + -
82C SER* 1.4 76.5 - - - +
84C SER* 1.3 62.8 + - - +
118D ALA* 3.4 29.4 - - + -
120D LYS 3.3 13.5 - - - +
121D GLN* 4.0 8.7 - - + -
122D PRO* 4.2 3.1 - - - -
126D PHE* 3.8 11.0 - - + -
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.3 21.3 - - - -
75C ASP* 3.7 16.3 + - - -
83C LEU* 1.3 76.8 + - - +
85C GLY* 1.3 58.7 + - - +
118D ALA* 3.5 4.3 - - - -
119D THR* 2.9 19.0 + - - -
120D LYS* 2.8 38.0 + - - +
122D PRO* 4.9 3.8 - - - +
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C SER* 3.5 9.5 + - - -
74C PHE* 3.2 28.2 + - - +
84C SER* 1.3 77.2 - - - +
86C TYR* 1.3 65.3 + - - +
117D GLU 3.4 12.6 - - - -
119D THR* 3.4 16.2 - - - -
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Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C SER* 4.0 4.7 - - - -
45C HIS* 3.4 27.3 + - + -
61C SER* 4.9 2.6 + - - -
67C TYR* 4.6 7.5 + - - -
71C GLY* 3.5 25.4 - - - +
72C THR 3.3 5.8 - - - +
73C SER* 4.6 1.8 - - - +
74C PHE* 3.3 8.7 - - - -
85C GLY* 1.3 74.1 - - - +
87C LEU* 1.3 72.1 + - - +
88C SER* 3.7 5.6 - - - -
117D GLU* 2.8 67.6 + - + +
119D THR* 3.9 27.4 - - + -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 6.1 1.8 - - - +
67C TYR* 5.3 0.2 + - - -
70C ASN* 3.1 33.2 + - - +
71C GLY 3.1 22.7 + - - -
72C THR* 2.7 30.4 + - + +
74C PHE* 4.2 19.3 - - + -
86C TYR* 1.3 77.4 - - - +
88C SER* 1.3 66.6 + - - +
114D VAL* 4.1 9.0 - - + -
115D PHE 3.4 19.3 - - - +
116D GLY* 4.2 6.7 - - - -
144D VAL 5.5 0.9 - - - +
145D ASN* 4.5 9.0 - - + +
147D VAL* 4.0 30.3 - - + -
1E NAG 4.1 4.9 - - - +
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C TYR* 3.1 26.9 + - - -
68C VAL 4.0 3.8 - - - -
70C ASN* 4.5 5.6 - - - +
86C TYR* 3.7 2.9 - - - -
87C LEU* 1.3 76.2 + - - +
89C GLN* 1.3 58.1 + - - +
114D VAL* 3.4 5.7 - - - +
115D PHE* 2.8 52.0 + - - +
117D GLU* 2.7 30.6 + - - -
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C THR 4.6 0.2 - - - -
67C TYR* 3.5 4.0 - - - -
68C VAL* 2.8 71.4 + - + +
70C ASN* 5.8 4.3 - - + -
88C SER* 1.3 76.0 - - - +
90C ASP* 1.3 65.7 + - - +
112D ARG* 3.5 43.0 + - - +
113D GLN 3.3 13.5 - - - +
114D VAL* 3.8 18.5 - - + +
115D PHE* 4.1 1.3 - - - -
1E NAG 5.1 1.8 + - - -
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Residues in contact with ASP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 3.8 6.3 - - + -
22C GLY* 3.2 13.1 - - - -
59C TYR* 2.6 25.4 + - - +
64C SER* 2.7 17.7 + - - -
66C THR* 2.7 39.4 + - - -
67C TYR* 3.7 6.7 - - - -
89C GLN* 1.3 74.4 - - - +
91C THR* 1.3 66.8 + - - +
92C VAL* 4.2 2.2 - - - +
112D ARG* 4.6 3.4 - - - +
113D GLN* 3.0 35.7 + - - +
115D PHE* 3.8 17.4 - - + -
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Residues in contact with THR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY 3.6 0.7 - - - +
21C ILE* 3.4 5.7 - - - -
22C GLY 2.9 28.0 + - - +
23C THR* 4.3 9.0 - - - +
66C THR* 3.6 26.9 + - - +
90C ASP* 1.3 78.1 + - - +
92C VAL* 1.4 64.7 + - - +
93C SER* 4.1 3.5 + - - +
109D LYS* 4.2 32.1 - - + +
110D VAL 3.5 13.0 - - - +
111D GLU* 4.2 18.1 - - + +
112D ARG 4.6 1.6 + - - -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.1 19.3 - - + -
20C GLY 3.3 8.5 - - - +
21C ILE* 4.5 10.3 - - + -
39C LEU* 3.7 28.3 - - + -
90C ASP 4.2 2.7 - - - +
91C THR* 1.4 74.4 - - - +
93C SER* 1.3 66.1 + - - +
94C VAL* 4.4 10.7 - - + +
108D VAL* 4.1 0.3 - - - +
109D LYS* 3.6 1.4 - - - -
110D VAL* 2.7 51.2 + - + +
113D GLN* 3.7 21.1 - - + +
115D PHE* 5.4 1.6 - - + -
135D LEU* 4.8 6.7 - - + -
150D VAL* 4.9 7.2 - - + -
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.5 3.8 - - - +
20C GLY* 2.8 33.3 + - - -
22C GLY 4.5 3.6 + - - -
25C PRO* 3.7 10.0 - - - +
91C THR* 4.6 2.3 + - - +
92C VAL* 1.3 71.8 - - - +
94C VAL* 1.3 69.2 + - - +
95C PRO 3.1 5.8 - - - +
96C CYS 3.6 20.9 - - - -
97C GLN* 3.6 9.4 - - - -
108D VAL 3.4 4.9 - - - -
109D LYS* 3.5 28.7 + - - +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ILE* 3.5 6.6 - - + +
5C GLU* 3.5 33.0 - - + +
18C GLU 5.0 0.2 - - - -
19C ILE* 3.8 17.3 - - + -
32C PHE* 4.6 7.4 - - + -
92C VAL* 4.2 12.8 + - + +
93C SER* 1.3 78.7 - - - +
95C PRO* 1.4 62.6 + - + +
97C GLN* 3.7 1.6 - - - -
107D GLY* 3.4 0.9 - - - -
108D VAL* 2.9 45.9 + - + +
110D VAL* 5.8 1.8 - - + -
135D LEU* 4.8 7.9 - - + -
150D VAL* 5.5 5.2 - - + -
183D LEU* 3.9 22.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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