Contacts of the helix formed by residues 65 - 78 (chain B) in PDB entry 4Y5O
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 LYS 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 6.1 0.2 - - - -
63B PRO 3.5 5.7 + - - +
64B VAL* 1.3 74.4 - - - +
66B TYR* 1.3 67.7 + - - +
67B GLU* 3.4 29.1 - - + +
68B ASP* 3.2 20.6 + - + +
69B VAL* 3.2 22.2 + - - +
97B GLN* 3.4 7.2 - - - +
100B LEU* 4.2 1.3 - - - -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL 3.9 0.2 + - - -
65B LYS* 1.3 72.5 - - - +
67B GLU* 1.3 76.6 + - - +
69B VAL* 2.9 21.9 + - + +
70B GLU* 3.1 42.1 + - + +
83B LEU* 3.9 22.0 - - + +
94B LEU* 2.8 31.4 + - + -
95B LYS* 3.3 27.3 + - - -
96B ASN* 3.8 21.1 - - - -
97B GLN* 2.7 34.9 + - - +
100B LEU* 3.8 22.0 - - + -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 3.4 32.4 - - + +
66B TYR* 1.3 91.0 + - + +
68B ASP* 1.3 58.2 + - - +
70B GLU* 3.4 19.0 + - - +
71B HIS* 2.9 27.5 + - - +
97B GLN* 4.2 5.2 + - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.6 23.2 - - - -
65B LYS* 3.2 26.8 + - + +
66B TYR 3.1 0.8 - - - -
67B GLU* 1.3 75.2 - - - +
69B VAL* 1.3 55.7 + - - +
71B HIS* 3.3 18.4 + - - +
72B LYS* 2.8 36.8 + - - +
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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
----------------------------------------------------------
47B ILE* 4.4 12.1 - - + -
49B PHE* 4.1 22.9 - - + -
60B PHE* 4.0 20.2 - - + -
64B VAL* 3.7 23.3 - - + -
65B LYS 3.2 14.7 + - - +
66B TYR* 2.9 10.2 + - + +
68B ASP* 1.3 73.8 - - - +
70B GLU* 1.3 63.6 + - - +
72B LYS* 3.3 3.5 + - - +
73B VAL* 3.0 22.6 + - + +
83B LEU* 4.1 22.2 - - + -
100B LEU* 4.2 12.1 - - + -
118B ILE* 5.4 2.7 - - + -
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Residues in contact with GLU 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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66B TYR* 3.1 53.1 + - + +
67B GLU* 3.6 25.3 - - - +
68B ASP 3.3 0.2 - - - -
69B VAL* 1.3 75.0 - - - +
71B HIS* 1.3 67.8 + - - +
73B VAL* 3.1 9.8 + - - +
74B THR* 3.0 26.7 + - - +
81B LEU 6.1 0.4 - - - +
83B LEU* 4.6 9.9 - - + -
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU 2.9 18.4 + - - +
68B ASP* 3.3 19.5 - - - +
70B GLU* 1.3 77.6 - - - +
72B LYS* 1.3 64.3 + - - +
74B THR* 3.2 7.8 + - - +
75B THR* 3.1 34.3 + - - -
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Residues in contact with LYS 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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58B ILE* 3.8 44.9 - - + +
59B ALA 4.8 2.8 + - - -
60B PHE* 3.8 25.9 - - + -
68B ASP* 2.8 23.2 + - - +
69B VAL 3.6 5.4 - - - +
70B GLU 3.2 0.2 - - - -
71B HIS* 1.3 75.5 - - + +
73B VAL* 1.3 62.5 + - + +
75B THR* 3.2 8.9 + - + -
76B VAL* 3.0 33.5 + - + +
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Residues in contact with VAL 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 PHE* 3.6 34.8 - - + -
69B VAL 3.0 20.1 + - - +
70B GLU* 3.1 6.9 + - - +
72B LYS* 1.3 74.1 - - - +
74B THR* 1.3 65.3 + - - +
76B VAL* 4.9 0.4 - - - -
77B PHE* 2.9 37.9 + - + +
79B GLN 4.6 0.2 - - - +
81B LEU* 3.8 43.7 - - + +
83B LEU* 3.8 17.7 - - + -
120B LEU* 4.1 5.6 - - + -
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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
----------------------------------------------------------
70B GLU* 3.0 13.4 + - - +
71B HIS* 3.2 12.9 + - - +
73B VAL* 1.3 76.9 - - - +
75B THR* 1.3 57.0 + - - +
78B GLY* 2.8 29.8 + - - -
79B GLN* 4.0 21.0 + - - +
80B PRO* 4.5 10.9 - - + +
81B LEU 5.4 0.5 + - - -
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Residues in contact with THR 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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71B HIS* 3.1 34.3 + - - -
72B LYS* 3.7 13.1 - - + +
73B VAL 3.2 0.2 - - - -
74B THR* 1.3 77.8 - - - +
76B VAL* 1.3 71.2 + - + +
77B PHE 3.5 0.2 + - - -
78B GLY* 3.8 4.5 + - - -
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Residues in contact with VAL 76 (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 ARG* 3.9 29.8 - - + +
58B ILE* 3.9 20.9 - - + -
72B LYS* 3.0 30.6 + - + +
75B THR* 1.3 83.0 - - + +
77B PHE* 1.3 91.3 + - + +
78B GLY 3.9 0.2 + - - -
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Residues in contact with PHE 77 (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 PHE* 4.1 17.9 - + + -
51B HIS* 3.7 36.3 - + + -
54B GLU* 4.9 16.4 - - + -
56B ARG* 4.1 23.1 - - + -
58B ILE* 5.4 0.9 - - + -
73B VAL* 2.9 22.8 + - + +
76B VAL* 1.3 99.5 - - + +
78B GLY* 1.3 62.9 + - - +
79B GLN* 3.1 14.8 + - + +
81B LEU* 3.7 18.6 - - + -
120B LEU* 3.5 26.2 - - + -
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Residues in contact with GLY 78 (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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74B THR* 2.8 21.2 + - - -
75B THR 3.8 4.2 + - - -
76B VAL 3.5 2.6 - - - -
77B PHE* 1.3 76.1 - - - +
79B GLN* 1.3 58.6 + - - +
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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