Contacts of the strand formed by residues 103 - 112 (chain B) in PDB entry 3O4O
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ASP 2.8 10.5 - - - -
7B TRP* 4.9 3.4 - - - -
32B HIS* 3.2 36.8 + - - -
94B CYS 3.6 0.5 - - - +
95B MET* 2.7 32.9 - - - +
96B LEU* 3.0 23.3 + - - +
101B TYR* 3.9 6.4 - - - -
102B CYS* 1.3 83.6 - - - +
104B LYS* 1.3 55.1 + - - +
105B VAL* 5.8 0.2 - - - -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B CYS* 5.2 11.2 - - + -
5B ASP 2.9 7.2 + - - +
6B ASP* 3.2 40.5 + - + +
7B TRP* 3.0 29.7 + - - -
51B TYR* 3.8 18.4 + - - +
59B LEU* 5.4 9.5 - - - +
93B THR* 4.0 11.0 - - + -
94B CYS 3.2 6.3 - - - +
95B MET* 3.6 18.4 - - + -
102B CYS* 4.9 0.6 - - - -
103B SER* 1.3 74.6 - - - +
105B VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ASP* 4.7 0.4 - - - -
7B TRP* 3.6 22.9 - - + +
8B GLY 4.2 3.6 - - - +
10B ASP* 3.9 15.9 - - - +
27B CYS* 4.7 1.6 - - - -
28B PRO* 4.6 21.8 - - + +
31B GLU* 3.9 16.4 - - + +
93B THR* 3.2 24.5 - - - -
94B CYS* 3.2 32.5 + - - +
103B SER 5.6 0.2 - - - +
104B LYS* 1.3 80.0 - - - +
106B ALA* 1.3 75.2 + - - +
107B PHE* 4.9 2.0 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B TRP 4.1 4.0 + - - +
9B LEU* 2.7 47.2 - - + +
10B ASP* 3.0 6.1 + - - +
91B ASN* 5.0 4.7 - - + -
92B TYR 2.8 17.5 - - - +
93B THR* 3.7 10.3 - - - +
105B VAL* 1.3 81.0 - - - +
107B PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 4.6 14.6 - - + +
13B ARG 5.2 4.0 - - - +
15B ILE* 4.3 21.1 - - + +
25B ILE* 3.4 29.4 - - + -
26B LYS 4.3 1.6 - - - -
28B PRO* 3.8 33.9 - - + -
50B TRP* 3.5 38.6 - + - -
91B ASN* 4.3 0.4 - - - -
92B TYR* 3.0 37.7 + + + +
94B CYS* 4.7 5.4 - - - -
105B VAL 4.9 1.3 - - - -
106B ALA* 1.3 81.1 - - - +
108B PRO* 1.3 72.9 - - + +
109B LEU* 3.2 10.0 + - + -
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Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.0 20.2 - - + -
10B ASP 4.3 10.1 - - - +
11B THR* 4.6 3.4 - - + +
14B GLN* 3.3 41.0 - - + +
15B ILE* 3.6 22.9 + - - +
90B GLY 4.0 2.7 - - - +
91B ASN* 3.0 26.9 - - - +
107B PHE* 1.3 81.7 - - + +
109B LEU* 1.3 59.9 + - - +
110B GLU* 3.7 6.9 + - + +
1D NAG 4.7 9.4 - - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.5 29.4 - - + -
17B VAL* 3.9 23.3 - - + -
23B ALA* 5.8 1.8 - - + -
25B ILE* 4.4 13.5 - - + -
81B PHE* 4.3 26.5 - - + -
84B THR* 5.6 2.0 - - - +
88B ASP* 4.8 3.8 - - + +
89B THR* 3.1 8.9 - - - +
90B GLY 3.0 39.5 + - - +
92B TYR* 4.1 22.0 - - + +
107B PHE* 3.2 9.7 + - + +
108B PRO* 1.3 70.5 - - - +
110B GLU* 1.3 65.1 + - - +
111B VAL* 4.8 10.1 - - + -
1D NAG 6.1 1.1 - - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN* 2.5 38.8 - - - +
15B ILE 3.3 20.3 + - - +
16B GLN* 3.6 25.8 + - + +
17B VAL 3.2 22.2 + - - -
89B THR* 4.0 10.3 - - + -
108B PRO* 4.2 8.5 - - + +
109B LEU* 1.3 74.4 - - - +
111B VAL* 1.3 64.0 + - - +
112B VAL* 3.7 4.8 + - + +
1D NAG 6.4 1.3 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.5 9.6 - - + +
18B PHE 4.7 0.2 - - - -
19B GLU* 3.8 27.4 - - + -
84B THR* 3.9 15.0 - - - +
85B LEU 3.8 15.9 - - - +
86B LEU* 3.6 35.1 - - + +
88B ASP* 4.1 4.9 - - + -
89B THR* 3.1 32.9 + - - +
109B LEU* 3.7 9.6 + - + -
110B GLU* 1.3 72.4 - - - +
112B VAL* 1.3 65.0 + - - +
113B GLN* 4.1 1.7 + - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLN* 3.3 39.5 - - + +
17B VAL 2.6 15.6 + - - +
18B PHE* 3.4 7.1 - - + -
19B GLU* 2.9 27.8 + - - -
110B GLU* 4.0 5.4 - - + +
111B VAL* 1.3 76.7 - - - +
113B GLN* 1.3 77.7 + - - +
120B SER* 4.1 4.3 - - - +
121B PRO* 3.4 29.4 - - + -
122B MET* 4.0 18.6 - - + +
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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