Contacts of the helix formed by residues 63 - 75 (chain B) in PDB entry 5DPS
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 5.1 2.8 + - - -
61B ASP 3.3 7.4 + - - +
62B LEU* 1.3 78.8 - - - +
64B VAL* 1.3 65.2 + - - +
65B GLY* 3.5 4.4 + - - -
66B GLN* 3.0 46.8 + - - +
67B PHE* 3.1 18.0 + - - +
94B THR 4.4 4.7 - - - -
95B SER* 4.6 9.6 - - - +
96B ALA 3.3 11.9 - - - +
97B THR* 4.1 6.7 - - + +
98B MET* 4.5 1.6 - - - -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 1.3 71.8 - - - +
65B GLY* 1.3 56.0 + - - +
67B PHE* 3.0 3.6 + - - +
68B TYR* 2.8 51.6 + - + -
85B PHE* 4.0 13.2 - - + -
92B PRO* 4.2 9.4 - - + -
93B PRO 3.5 14.4 - - - +
94B THR* 3.5 15.9 - - - +
96B ALA* 2.8 26.8 + - + +
97B THR 4.6 0.7 - - - +
98B MET* 4.3 12.3 - - - -
101B LEU* 3.7 28.9 - - + -
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Residues in contact with GLY 65 (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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119A GLU* 4.0 14.1 - - - +
63B THR* 3.2 3.6 + - - -
64B VAL* 1.3 76.0 - - - +
66B GLN* 1.3 61.0 + - - +
68B TYR* 3.4 8.0 + - - +
69B PHE* 3.2 21.0 + - - +
94B THR* 3.1 31.3 + - - -
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Residues in contact with GLN 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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61B ASP 4.4 1.4 - - - +
62B LEU* 3.6 27.8 - - + +
63B THR* 3.0 46.8 + - - +
65B GLY* 1.3 75.7 - - - +
67B PHE* 1.3 63.7 + - - +
69B PHE* 3.4 9.2 + - - +
70B LEU* 3.1 22.5 + - - +
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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
----------------------------------------------------------
38B VAL* 4.4 6.7 - - + -
40B VAL* 3.7 31.6 - - + -
56B TYR* 4.4 11.2 - + + -
58B VAL* 4.1 17.9 - - + -
62B LEU* 4.0 18.6 - - + +
63B THR 3.1 10.7 + - - +
64B VAL 3.0 8.8 + - - +
66B GLN* 1.3 76.0 - - - +
68B TYR* 1.3 64.6 + - - +
70B LEU* 3.3 25.5 + - + +
71B ILE* 3.0 42.7 + - + +
85B PHE* 3.6 24.5 - + + -
98B MET* 4.0 26.0 - - + -
114B ILE* 4.0 16.2 - - + -
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 3.4 55.0 - - - +
64B VAL* 2.8 40.7 + - + -
65B GLY* 3.5 7.9 - - - +
66B GLN 3.3 0.2 - - - -
67B PHE* 1.3 77.0 - - - +
69B PHE* 1.3 52.2 + - - +
71B ILE* 3.3 2.3 + - - +
72B ARG* 2.8 39.8 + - - +
83B LEU* 3.4 31.4 - - + +
84B PHE* 3.7 2.1 - - - -
85B PHE* 2.9 59.7 + + - +
91B ILE* 4.1 9.9 - - - +
92B PRO* 4.5 2.6 + - - +
94B THR* 4.0 12.3 + - + -
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Residues in contact with PHE 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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65B GLY 3.2 10.7 + - - +
66B GLN* 3.6 11.4 - - - +
68B TYR* 1.3 79.8 - - - +
70B LEU* 1.3 68.2 + - + +
72B ARG* 3.3 14.7 + - - +
73B LYS* 3.1 62.5 + - + +
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Residues in contact with LEU 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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56B TYR* 4.3 9.0 - - + -
58B VAL* 5.9 3.4 - - + -
62B LEU* 5.2 8.7 - - + -
66B GLN 3.1 11.1 + - - +
67B PHE* 3.5 28.0 - - + +
69B PHE* 1.3 85.7 - - + +
71B ILE* 1.3 76.2 + - + +
73B LYS* 3.4 3.5 + - - +
74B ARG* 3.3 68.8 + - - +
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Residues in contact with ILE 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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40B VAL* 4.5 4.3 - - + -
51B LEU* 3.9 28.3 - - + -
56B TYR* 4.5 7.0 - - + -
67B PHE* 3.0 40.5 + - + +
68B TYR 3.8 3.1 - - - +
70B LEU* 1.3 89.9 - - + +
72B ARG* 1.3 64.0 + - - +
74B ARG* 3.1 13.5 + - - +
75B ILE* 3.1 28.6 + - + +
83B LEU* 4.3 12.8 - - + -
85B PHE* 3.8 24.9 - - + -
116B TYR* 4.7 13.7 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 3.5 25.9 - - - +
68B TYR* 2.8 24.2 + - - +
69B PHE* 3.5 16.2 - - - +
70B LEU 3.3 0.2 - - - -
71B ILE* 1.3 73.8 - - - +
73B LYS* 1.3 71.2 + - + +
75B ILE* 3.3 8.6 + - - +
76B HIS 3.0 18.4 + - - -
77B LEU* 3.1 50.0 + - + +
78B ARG 2.9 23.6 + - - -
79B ALA* 4.1 20.0 + - - +
81B ASP* 3.3 22.0 + - - +
83B LEU* 4.1 17.3 - - + +
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Residues in contact with LYS 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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69B PHE* 3.1 59.3 + - + +
70B LEU* 3.8 6.1 - - - +
71B ILE 3.3 0.2 - - - -
72B ARG* 1.3 86.0 - - + +
74B ARG* 1.3 67.1 + - - +
75B ILE 3.5 0.3 + - - -
76B HIS* 3.5 20.5 + - - +
77B LEU 5.3 5.3 + - - +
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Residues in contact with ARG 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 ASP 4.7 5.0 - - - +
51B LEU* 3.6 18.0 - - + +
56B TYR* 3.9 27.5 + - - +
70B LEU* 3.3 54.5 + - - +
71B ILE* 3.1 10.1 + - - +
73B LYS* 1.3 86.7 - - - +
75B ILE* 1.3 58.3 + - - +
76B HIS* 3.4 14.1 + - - -
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Residues in contact with ILE 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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48B ILE* 4.1 7.2 - - + -
49B GLY* 3.5 36.6 + - - +
50B ASP 4.1 4.5 - - - +
51B LEU* 3.9 19.3 - - + -
71B ILE* 3.1 18.4 + - + +
72B ARG* 3.3 10.1 + - - +
74B ARG* 1.3 79.9 - - - +
76B HIS* 1.3 71.0 + - - +
77B LEU* 3.7 37.4 - - + +
83B LEU* 4.3 8.5 - - + -
116B TYR* 3.9 27.1 - - + +
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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