Contacts of the helix formed by residues 66 - 76 (chain B) in PDB entry 1JYQ
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 PRO 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS 4.7 0.7 - - - +
65B ILE* 1.3 92.5 - - + +
67B ARG* 1.3 66.4 + - - +
68B ALA* 4.1 11.0 - - + +
69B LYS* 3.0 27.8 + - + +
70B ALA* 3.0 12.3 + - - +
86B ARG* 4.4 0.9 - - - -
89B GLU* 3.5 29.4 - - + +
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Residues in contact with ARG 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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65B ILE 3.8 1.0 + - - -
66B PRO* 1.3 71.4 - - - +
68B ALA* 1.4 63.9 + - - +
70B ALA* 3.1 4.9 + - - +
71B GLU* 3.0 34.0 + - - +
86B ARG* 3.7 23.8 - - - +
89B GLU* 4.8 1.4 + - - +
107B HIS* 3.2 41.4 + - + +
200H MAZ 2.8 74.8 + - - -
201H PTR 2.8 42.3 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PRO* 3.2 7.7 - - + +
67B ARG* 1.4 81.9 - - - +
69B LYS* 1.3 56.8 + - - +
71B GLU* 3.4 12.3 + - - +
72B GLU* 3.0 26.7 + - - +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.1 17.3 - - + -
66B PRO* 3.0 29.2 + - + +
68B ALA* 1.3 76.1 - - - +
70B ALA* 1.3 61.7 + - - +
72B GLU* 3.3 13.7 + - + +
73B MET* 2.9 64.3 + - + +
76B LYS* 5.6 3.8 - - - +
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Residues in contact with ALA 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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65B ILE* 4.1 8.2 - - + +
66B PRO 3.0 6.2 + - - +
67B ARG 3.1 8.7 + - - +
69B LYS* 1.3 77.9 - - - +
71B GLU* 1.3 57.6 + - - +
73B MET* 3.8 1.0 - - - +
74B LEU* 2.9 36.4 + - - +
84B LEU* 4.1 14.1 - - + -
86B ARG* 3.8 18.6 - - - +
98B SER* 3.6 30.1 - - - +
105B VAL* 4.9 0.2 - - - -
107B HIS* 4.6 0.2 - - + -
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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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67B ARG* 3.0 22.3 + - - +
68B ALA* 3.7 13.0 - - - +
69B LYS 3.2 0.2 - - - -
70B ALA* 1.3 77.5 - - - +
72B GLU* 1.3 58.0 + - - +
75B SER* 2.9 36.3 + - - -
105B VAL* 3.9 22.4 - - + +
107B HIS* 2.5 40.2 + - + +
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Residues in contact with GLU 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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68B ALA 3.0 17.4 + - - +
69B LYS* 3.7 19.1 - - + +
71B GLU* 1.3 76.6 - - - +
73B MET* 1.3 64.9 + - - +
75B SER* 3.2 18.2 + - - -
76B LYS* 3.4 40.0 + - - +
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Residues in contact with MET 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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62B PHE* 3.4 32.5 - - + -
65B ILE* 3.9 23.8 - - - -
69B LYS* 2.9 48.8 + - - +
70B ALA* 3.8 2.5 - - - +
72B GLU* 1.3 77.7 - - - +
74B LEU* 1.3 64.9 + - + +
76B LYS* 3.3 29.2 + - - +
77B GLN* 3.7 12.9 + - - +
84B LEU* 3.9 7.6 - - + -
151B ILE* 3.7 22.7 - - + -
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Residues in contact with LEU 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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70B ALA 2.9 18.2 + - - +
73B MET* 1.3 69.9 - - - +
75B SER* 1.3 66.2 + - - +
76B LYS 3.0 2.0 - - - -
77B GLN* 3.0 20.1 + - + +
82B ALA* 3.7 19.5 - - + +
83B PHE* 3.9 6.5 - - - +
84B LEU* 4.3 9.2 - - + -
98B SER* 3.2 48.9 - - - +
99B VAL* 3.7 6.7 - - - +
100B LYS* 3.5 15.9 - - + +
105B VAL* 3.8 18.8 - - + -
151B ILE* 3.8 33.4 - - + -
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Residues in contact with SER 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 GLU* 2.9 17.6 + - - -
72B GLU* 3.2 16.8 + - - -
74B LEU* 1.3 77.0 - - - +
76B LYS* 1.3 65.0 + - - +
77B GLN 3.9 0.7 - - - +
100B LYS* 3.3 21.6 + - - +
103B ASN 6.1 1.1 - - - -
105B VAL* 3.9 11.8 - - - +
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Residues in contact with LYS 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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69B LYS* 5.6 3.8 - - - +
72B GLU* 3.4 42.4 + - - +
73B MET* 3.3 19.8 + - - +
74B LEU 3.0 1.0 - - - -
75B SER* 1.3 81.8 - - - +
77B GLN* 1.3 65.4 + - - +
78B ARG* 3.7 6.6 + - - +
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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