Contacts of the strand formed by residues 68 - 74 (chain B) in PDB entry 3OP5
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 CYS 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A LYS* 3.3 35.7 - - - -
37B TRP* 3.9 13.2 - - + -
53B LEU* 3.7 2.1 - - - +
54B ALA* 2.8 41.8 + - + +
55B ASP* 4.4 1.6 - - - +
66B ALA* 4.1 3.8 - - - +
67B PRO* 1.3 82.1 - - - +
69B VAL* 1.3 65.4 + - - +
114B TRP* 4.0 13.7 - - - -
130B ILE* 4.0 11.7 - - + -
131B MET 3.3 13.9 - - - +
133B ARG* 3.8 4.3 - - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.6 28.3 - - + -
51B ILE* 3.8 13.5 - - + -
52B TYR 3.3 9.6 - - - +
53B LEU* 4.4 1.6 - - + -
54B ALA* 4.1 4.0 - - - +
68B CYS* 1.3 79.0 - - - +
70B VAL* 1.3 60.3 + - - +
71B LYS* 5.3 0.7 - - + +
129B MET 3.7 0.9 - - - +
130B ILE* 3.5 4.5 - - - +
131B MET* 3.0 40.8 + - + +
132B ASP 3.9 5.6 - - - +
133B ARG* 3.9 11.2 - - + -
365B REB 3.6 45.3 - - + +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.1 17.9 - - + -
29B ILE* 3.9 11.2 - - + -
39B VAL* 4.3 11.2 - - + -
50B CYS 3.8 1.0 - - - +
51B ILE* 3.4 6.6 - - - -
52B TYR* 2.8 58.4 + - + +
54B ALA* 4.1 16.6 - - + +
69B VAL* 1.3 72.9 - - - +
71B LYS* 1.4 59.9 + - - +
72B VAL* 4.0 1.0 + - + +
128B PHE* 3.8 34.8 - - + -
129B MET 3.3 9.6 - - - +
130B ILE* 4.3 6.3 - - + -
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Residues in contact with LYS 71 (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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48B PHE 5.8 0.2 - - - +
49B GLY* 4.9 7.1 - - - +
50B CYS 3.6 4.9 - - - +
51B ILE* 4.2 19.9 - - + +
69B VAL* 4.1 1.5 - - + -
70B VAL* 1.4 69.7 - - - +
72B VAL* 1.4 64.8 + - - +
73B GLU* 4.8 12.2 + - + +
80B LEU* 3.8 21.4 - - + +
83B GLU* 3.3 28.7 - - - +
127B ARG 3.8 0.9 - - - +
128B PHE* 3.2 3.7 - - - -
129B MET* 2.8 41.2 + - + +
131B MET* 3.8 25.6 - - + -
365B REB 3.6 34.1 - - + +
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Residues in contact with VAL 72 (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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22B GLN* 3.6 26.2 - - + +
23B PHE* 3.3 35.4 - - + -
50B CYS* 2.9 40.2 + - - +
52B TYR* 4.4 1.1 - - + -
70B VAL* 4.3 5.6 - - + +
71B LYS* 1.4 77.5 - - - +
73B GLU* 1.3 75.2 + - - +
80B LEU* 4.9 0.2 - - - -
119B HIS* 5.6 1.1 - - + -
126B TYR* 3.6 21.3 - - + -
127B ARG 3.5 13.5 - - - +
128B PHE* 4.3 7.2 - - + -
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Residues in contact with GLU 73 (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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49B GLY* 3.9 22.0 - - - -
50B CYS* 4.1 1.2 + - - -
71B LYS* 4.8 9.7 + - - +
72B VAL* 1.3 79.4 - - - +
74B PRO* 1.4 83.5 - - + +
77B ASN* 3.9 29.7 + - + +
80B LEU* 3.7 31.6 - - + +
126B TYR* 3.5 9.1 - - - -
127B ARG* 2.9 25.4 + - - +
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Residues in contact with PRO 74 (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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73B GLU* 1.4 99.1 - - + +
75B SER* 1.3 60.3 + - - +
76B ASP* 3.1 22.4 - - - +
77B ASN* 2.9 32.6 + - + +
80B LEU* 5.2 0.7 - - - +
124B LYS* 6.5 0.2 - - + -
125B SER 3.7 5.4 - - - +
126B TYR* 3.6 26.8 - - + -
127B ARG* 4.8 1.6 - - - +
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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