Contacts of the helix formed by residues 59 - 73 (chain B) in PDB entry 1YYV
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 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ARG* 5.4 1.6 - - - -
57B GLY 3.7 3.2 + - - -
58B VAL* 1.3 77.8 - - - +
60B GLU* 1.3 58.8 + - - +
61B MLY 4.0 10.3 + - - +
62B MSE 2.8 40.1 + - - +
63B LEU* 3.0 29.5 + - - +
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Residues in contact with GLU 60 (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* 3.8 23.2 - - + -
52B ARG* 2.8 38.4 + - - +
59B SER* 1.3 69.7 - - - +
61B MLY 1.3 56.4 + - - +
63B LEU* 3.5 0.6 + - - -
64B ALA* 2.7 38.5 + - - +
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Residues in contact with MLY 61 (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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59B SER* 3.3 7.4 - - - +
60B GLU* 1.3 80.1 + - - +
62B MSE 1.3 87.6 + - - +
64B ALA* 3.6 6.1 - - - +
65B GLN* 2.9 50.8 + - - +
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Residues in contact with MSE 62 (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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33B TRP* 3.7 32.9 - - + +
58B VAL* 4.1 3.6 - - + -
59B SER* 2.8 28.6 + - - +
61B MLY 1.3 99.1 + - - +
63B LEU* 1.3 63.5 + - - +
65B GLN* 2.9 32.3 - - + +
66B SER* 3.0 30.0 + - - -
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Residues in contact with LEU 63 (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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33B TRP* 5.4 1.3 - - + -
37B ILE* 3.8 19.5 - - + -
48B PHE* 3.6 40.2 - - + +
51B LEU* 4.1 6.5 - - + -
52B ARG* 3.7 27.8 - - + +
55B MSE 3.7 25.4 - - - -
58B VAL* 3.8 12.5 - - + +
59B SER 3.0 18.7 + - - +
60B GLU 3.9 2.9 - - - +
62B MSE 1.3 74.4 - - - +
64B ALA* 1.3 65.6 + - - +
65B GLN 3.3 0.3 + - - -
66B SER* 3.3 3.6 + - - -
67B LEU* 3.0 40.4 + - + +
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Residues in contact with ALA 64 (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* 4.0 15.8 - - + -
60B GLU 2.7 24.0 + - - +
61B MLY 3.6 6.3 - - - +
63B LEU* 1.3 72.9 - - - +
65B GLN* 1.3 62.0 + - + +
67B LEU* 3.5 5.1 + - - +
68B GLN* 3.1 26.5 + - - +
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Residues in contact with GLN 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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61B MLY 2.9 42.5 + - - +
62B MSE 2.9 37.8 - - + +
63B LEU 3.3 0.2 - - - -
64B ALA* 1.3 73.7 - - + +
66B SER* 1.3 61.3 + - - +
68B GLN* 3.5 10.3 + - - +
69B ALA* 3.1 22.5 + - - +
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Residues in contact with SER 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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28B HIS 5.6 1.1 - - - -
31B SER* 4.4 6.1 + - - -
33B TRP* 3.4 22.0 - - - +
34B GLY* 4.2 10.6 + - - -
37B ILE* 3.5 22.9 - - - -
62B MSE 3.0 18.4 + - - -
63B LEU 4.1 0.2 - - - -
65B GLN* 1.3 74.6 - - - +
67B LEU* 1.3 57.8 + - - +
69B ALA* 3.3 5.7 + - - +
70B LEU* 3.0 32.2 + - - +
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Residues in contact with LEU 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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37B ILE* 3.8 33.9 - - + -
48B PHE* 3.7 31.4 - - + -
51B LEU* 4.0 14.1 - - + -
63B LEU* 3.0 31.4 + - + +
64B ALA* 3.8 4.7 - - - +
66B SER* 1.3 72.9 - - - +
68B GLN* 1.3 61.0 + - - +
70B LEU 3.5 0.3 + - - -
71B GLU* 2.9 32.7 + - - +
76B LEU* 3.6 11.0 - - + +
90B TYR* 3.8 45.2 - - + +
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Residues in contact with GLN 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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64B ALA 3.1 19.0 + - - +
65B GLN* 3.7 9.7 - - - +
66B SER 3.4 0.2 - - - -
67B LEU* 1.3 76.1 - - - +
69B ALA* 1.3 57.0 - - - +
71B GLU* 4.0 6.4 - - - +
72B GLN* 3.0 33.4 + - + +
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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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121A ARG* 4.0 2.3 + - - +
28B HIS* 3.9 36.6 - - + +
65B GLN 3.1 16.4 + - - +
66B SER* 3.3 6.7 + - - +
68B GLN* 1.3 77.5 - - - +
70B LEU* 1.3 57.4 + - - +
72B GLN* 3.9 3.7 - - - -
73B ASP* 3.1 36.7 + - - +
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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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28B HIS* 3.5 33.0 - - + +
29B VAL* 4.1 9.4 - - + -
34B GLY* 4.1 17.5 - - - +
37B ILE* 3.9 35.4 - - + -
38B LEU* 4.2 12.6 - - + -
66B SER* 3.0 19.8 + - - +
69B ALA* 1.3 76.6 - - + +
71B GLU* 1.3 59.7 + - - +
73B ASP* 3.6 1.1 + - - +
74B GLY 3.4 3.3 + - - -
75B PHE* 3.0 49.0 + - + +
76B LEU* 3.4 20.2 - - + -
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Residues in contact with GLU 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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120A GLN* 4.7 2.3 - - - +
67B LEU 2.9 18.4 + - - +
68B GLN* 4.0 6.9 - - - +
70B LEU* 1.3 73.9 - - - +
72B GLN* 1.3 64.7 + - - +
74B GLY* 3.0 14.9 + - - -
76B LEU* 3.5 32.1 - - + +
78B ARG* 3.6 60.2 + - + +
90B TYR* 4.6 4.8 - - + -
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Residues in contact with GLN 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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120A GLN* 3.7 7.6 - - - +
121A ARG* 3.2 76.3 + - + +
122A GLU* 4.1 14.5 + - - +
68B GLN* 3.0 21.9 + - + +
69B ALA* 4.1 1.3 - - - +
71B GLU* 1.3 75.9 - - - +
73B ASP* 1.3 58.6 + - - +
74B GLY 3.5 0.3 + - - -
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Residues in contact with ASP 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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117A VAL* 3.6 40.7 - - + +
120A GLN* 3.8 4.2 - - - +
121A ARG* 2.5 39.7 + - - -
25B VAL* 4.4 6.9 - - - +
28B HIS* 2.9 31.3 + - - +
69B ALA 3.1 19.0 + - - +
70B LEU 3.9 0.4 - - - +
71B GLU 3.2 0.4 - - - -
72B GLN* 1.3 73.8 - - - +
74B GLY* 1.3 60.0 + - - +
75B PHE* 3.5 31.8 - - + -
95B LEU* 4.2 2.1 - - - +
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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