Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 2RCY
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL* 1.3 77.0 - - - +
68B PRO* 1.4 73.5 - - + +
69B ASP* 3.2 26.3 + - - +
70B ILE* 3.2 16.9 + - + +
71B ALA* 3.1 17.8 + - - +
264B NAP 3.7 41.6 - - + +
225C SER* 5.1 5.6 - - - -
226C PRO* 3.5 47.9 + - + +
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Residues in contact with PRO 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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66B VAL 3.7 0.2 - - - -
67B LYS* 1.4 89.0 - - + +
69B ASP* 1.3 62.6 + - - +
70B ILE 3.3 0.7 + - - -
71B ALA* 3.5 12.6 + - + +
72B GLY 4.3 3.1 + - - -
91B CYS* 4.5 1.3 - - + -
92B GLY 3.6 26.0 - - - +
94B LEU* 3.9 31.7 - - + +
102B MSE 5.0 1.9 - - - +
260B MSE 3.8 22.0 - - + -
264B NAP 3.3 25.8 - - + +
225C SER* 5.9 2.9 - - - -
226C PRO 6.1 0.7 - - - +
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Residues in contact with ASP 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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67B LYS* 3.2 39.0 + - - +
68B PRO* 1.3 79.9 - - - +
70B ILE* 1.3 78.0 + - - +
72B GLY* 4.9 2.7 + - - -
73B SER 5.7 0.2 + - - -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.0 12.8 - - + -
67B LYS* 3.3 24.7 - - + +
69B ASP* 1.3 92.7 - - - +
71B ALA* 1.3 63.2 + - - +
72B GLY 3.2 3.1 - - - -
73B SER* 3.0 26.9 + - - +
74B VAL* 3.2 13.6 + - + +
264B NAP 3.4 45.5 - - + +
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Residues in contact with ALA 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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64B CYS* 4.5 4.9 - - - -
66B VAL* 3.8 19.3 - - + -
67B LYS 3.1 13.7 + - - +
68B PRO 3.5 10.7 + - - +
70B ILE* 1.3 76.0 - - - +
72B GLY* 1.3 60.0 + - - +
74B VAL* 4.3 1.3 - - - -
75B LEU* 3.0 37.5 + - + +
91B CYS* 4.0 10.1 - - - -
94B LEU* 3.7 20.6 - - + -
102B MSE 4.3 2.0 - - - -
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Residues in contact with GLY 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 PRO 4.3 3.0 + - - -
69B ASP 4.9 2.3 + - - -
70B ILE* 3.2 1.4 - - - +
71B ALA* 1.3 78.7 - - - +
73B SER* 1.3 55.7 + - - +
75B LEU* 4.5 1.0 - - - +
76B ASN* 3.3 24.9 + - - +
102B MSE 3.9 31.9 - - - +
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Residues in contact with SER 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 ASP 5.7 0.2 + - - -
70B ILE* 3.0 21.5 + - - +
72B GLY* 1.3 75.1 - - - +
74B VAL* 1.3 64.8 + - - +
76B ASN* 3.5 6.5 + - - +
77B ASN* 3.0 36.0 + - - +
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Residues in contact with VAL 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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10B MSE 3.8 26.7 - - + -
52B ASN* 3.7 19.0 - - - +
64B CYS* 5.1 4.0 - - - -
66B VAL* 4.4 15.3 - - + -
70B ILE* 3.2 22.3 + - + +
71B ALA* 4.0 7.0 - - - +
72B GLY 3.5 0.2 - - - -
73B SER* 1.3 82.0 + - - +
75B LEU* 1.3 62.2 + - + +
77B ASN* 3.4 19.2 + - - +
78B ILE* 3.4 14.9 + - - +
264B NAP 3.7 30.1 - - + +
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Residues in contact with LEU 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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10B MSE 5.3 1.1 - - - -
64B CYS* 4.2 24.7 - - + -
71B ALA* 3.0 23.4 + - + +
72B GLY 4.6 0.2 - - - +
74B VAL* 1.3 75.3 - - - +
76B ASN* 1.3 60.0 + - - +
77B ASN 3.3 0.2 - - - -
78B ILE* 3.4 24.5 - - + +
79B LYS* 3.1 22.3 + - - +
87B LEU* 3.8 29.4 - - + -
89B SER* 6.1 0.2 - - - -
99B LEU* 3.9 22.4 - - + -
102B MSE 3.7 30.1 - - + -
103B VAL* 3.4 24.4 - - + +
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Residues in contact with ASN 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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72B GLY 3.3 18.6 + - - +
73B SER* 3.7 9.0 - - - +
74B VAL 3.2 0.4 - - - -
75B LEU* 1.3 79.4 - - - +
77B ASN* 1.3 64.9 + - - +
79B LYS* 3.4 24.1 - - - +
80B PRO* 4.2 3.5 - - - +
102B MSE 4.5 13.5 + - - +
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Residues in contact with ASN 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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52B ASN* 5.9 1.1 - - + -
53B GLU* 3.3 28.0 + - - +
73B SER* 3.0 23.3 + - - +
74B VAL* 3.7 10.8 - - - +
75B LEU 3.3 0.4 - - - -
76B ASN* 1.3 84.4 - - - +
78B ILE* 1.3 57.7 + - + +
79B LYS 3.3 1.3 - - - -
80B PRO* 3.4 6.4 - - - +
81B TYR* 3.4 22.0 - - - -
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Residues in contact with ILE 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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10B MSE 3.7 23.3 - - + -
52B ASN* 3.4 43.5 - - + +
53B GLU* 3.9 3.4 - - + +
56B ALA* 3.9 9.8 - - + +
62B ILE* 4.5 1.8 - - + -
74B VAL 3.4 13.4 + - - +
75B LEU* 3.4 33.4 - - + +
77B ASN* 1.3 76.5 - - + +
79B LYS* 1.3 64.4 + - - +
80B PRO* 3.3 3.1 - - - -
81B TYR* 3.0 23.2 + - - +
82B LEU* 3.4 36.7 - - + +
87B LEU* 4.4 4.9 - - + -
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Residues in contact with LYS 79 (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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75B LEU 3.1 12.6 + - - +
76B ASN* 3.4 25.4 - - - +
78B ILE* 1.3 76.5 - - - +
80B PRO* 1.4 62.0 - - + +
81B TYR 3.1 4.0 + - - -
82B LEU* 3.7 18.0 + - - +
102B MSE 3.7 15.9 - - - +
103B VAL* 3.6 37.2 + - + +
104B GLY* 4.4 2.4 - - - +
107B ASN* 4.7 4.7 + - - +
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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