Contacts of the strand formed by residues 65 - 75 (chain B) in PDB entry 5C58
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 THR 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A THR* 3.3 29.5 - - - +
23B TRP* 3.7 27.1 - - + +
26B THR* 4.4 8.2 + - - +
27B PHE* 3.1 28.4 - - + -
59B SER 3.0 24.8 + - - -
62B ASN* 3.3 14.9 + - - -
64B VAL* 1.3 78.4 - - - +
66B ALA* 1.3 62.1 - - - +
95B GLY 3.9 9.2 - - - +
96B ASP* 3.6 11.0 + - - +
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Residues in contact with ALA 66 (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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23B TRP* 3.8 8.9 - - - -
27B PHE* 4.0 4.0 - - - -
57B ILE 3.2 22.2 - - - +
58B SER* 3.7 8.7 - - - +
64B VAL 3.5 4.8 + - - +
65B THR* 1.3 75.6 - - - +
67B PHE* 1.3 68.4 + - - +
95B GLY 3.1 28.8 + - - +
97B GLY 5.2 0.9 - - - +
98B LEU* 3.8 28.0 - - + -
108B ILE* 4.7 2.9 - - + -
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Residues in contact with PHE 67 (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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23B TRP* 3.7 17.5 - + - -
27B PHE* 4.4 5.4 - + - -
55B TYR* 4.5 8.7 - + - -
56B ALA* 3.4 21.1 - - - +
57B ILE* 3.6 34.0 + - + -
66B ALA* 1.3 79.6 - - - +
68B VAL* 1.3 70.3 + - - +
69B ALA* 4.6 11.7 - - + -
92B LEU* 3.8 18.2 - - + -
93B SER 3.4 14.4 - - - +
94B PHE* 3.7 19.5 - + + -
108B ILE* 4.4 2.7 - - - -
136B VAL* 4.3 12.1 - - + -
139B LEU* 3.6 44.9 - - + -
140B MET* 4.3 5.6 - - + -
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Residues in contact with VAL 68 (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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54B GLN* 3.4 39.0 - - + +
55B TYR 3.2 10.5 - - - +
56B ALA* 3.8 13.2 - - + -
67B PHE* 1.3 79.4 - - - +
69B ALA* 1.3 62.9 + - - +
70B GLY* 3.8 1.8 + - - +
91B SER* 5.2 0.3 + - - -
92B LEU* 3.4 7.9 - - - +
93B SER* 3.1 39.3 + - - +
98B LEU* 4.0 8.5 - - + -
106B TYR* 4.2 15.0 - - + +
107B SER* 5.4 0.2 - - - -
108B ILE* 3.8 21.3 - - + -
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Residues in contact with ALA 69 (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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54B GLN* 3.1 3.4 - - - -
55B TYR* 2.7 42.9 + - + +
67B PHE* 4.3 8.3 - - + -
68B VAL* 1.3 69.7 - - - +
70B GLY* 1.3 61.9 + - - +
73B LEU* 3.7 15.8 - - + +
89B LEU* 4.1 15.7 - - + -
91B SER 3.9 5.2 - - - -
92B LEU* 4.0 13.9 - - + -
136B VAL* 4.6 14.8 - - + -
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Residues in contact with GLY 70 (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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53B SER 3.5 8.3 - - - -
54B GLN* 3.8 11.0 - - - -
68B VAL* 3.8 4.2 + - - +
69B ALA* 1.3 74.7 - - - +
71B GLY* 1.3 58.8 + - - -
73B LEU* 5.0 2.2 - - - +
88B GLN 4.1 0.2 - - - +
89B LEU* 3.7 6.1 - - - +
90B ASP* 3.0 20.3 + - - -
91B SER* 3.2 34.0 + - - +
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Residues in contact with GLY 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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53B SER* 2.7 32.2 + - - +
70B GLY* 1.3 73.7 - - - -
72B ASN* 1.3 62.9 + - - +
73B LEU* 4.1 0.4 - - - -
88B GLN* 3.4 8.7 - - - -
90B ASP* 3.7 15.9 - - - +
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Residues in contact with ASN 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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52B GLY 3.8 8.7 + - - -
53B SER* 5.7 0.8 - - - +
71B GLY* 1.3 76.2 + - - +
73B LEU* 1.3 62.0 + - - +
74B THR* 5.0 9.0 - - - +
87B GLY* 3.3 6.6 - - - -
88B GLN* 3.0 48.4 + - + +
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Residues in contact with LEU 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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45B PHE* 4.1 9.3 - - + -
51B SER* 3.2 3.4 - - - -
52B GLY 3.2 33.3 + - - +
54B GLN* 5.1 2.0 - - - +
55B TYR* 4.3 14.6 - - + +
69B ALA* 3.7 36.3 - - + +
70B GLY 5.1 0.7 - - - +
71B GLY 5.0 1.6 - - - -
72B ASN* 1.3 79.3 - - - +
74B THR* 1.3 67.0 + - - +
85B LEU* 4.0 24.9 - - + -
86B TYR 3.7 4.9 - - - +
88B GLN 3.7 28.0 - - - +
89B LEU* 4.2 7.4 - - + +
132B VAL* 4.0 22.2 - - + -
136B VAL* 5.4 0.4 - - + -
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Residues in contact with THR 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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50B LEU 3.7 4.9 - - - -
51B SER* 3.6 17.9 - - - +
72B ASN* 5.0 9.9 - - - +
73B LEU* 1.3 80.7 - - - +
75B TYR* 1.3 61.7 + - - +
84B THR 3.5 2.1 - - - +
85B LEU* 3.7 5.3 - - - -
86B TYR* 3.0 69.8 + - + +
87B GLY* 5.1 0.5 - - - -
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Residues in contact with TYR 75 (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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45B PHE* 4.0 11.7 - - + -
50B LEU* 2.9 46.3 + - + +
74B THR* 1.3 74.0 - - - +
76B THR* 1.3 61.5 + - - +
77B LEU* 3.5 34.8 - - + -
83B HIS* 2.7 42.5 + - - +
84B THR 3.3 14.4 - - - -
85B LEU* 4.3 4.3 - - + -
86B TYR* 5.2 0.4 - - - -
200B HEM 2.2 89.4 + + + -
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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