Contacts of the helix formed by residues 66 - 76 (chain B) in PDB entry 1R1P
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 3.8 13.0 - - - -
58A PRO* 6.0 0.9 - - - -
64B GLY 3.6 2.4 + - - -
65B LEU* 1.3 76.3 - - - +
67B ARG* 1.3 65.7 + - - +
68B HIS* 3.5 6.8 + - - +
69B GLN* 2.9 44.6 + - - +
70B ALA* 3.0 22.0 + - - +
85B ARG* 4.2 0.7 - - - +
88B GLN* 3.6 21.3 - - - -
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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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66B SER* 1.3 71.3 - - - +
68B HIS* 1.3 77.2 + - + +
70B ALA* 3.3 3.1 + - - +
71B GLU* 3.0 31.3 + - - +
85B ARG* 3.7 22.2 - - - +
88B GLN* 3.0 17.9 + - - +
106B HIS* 3.5 37.7 + - + +
556F ASP* 3.4 32.7 + - - +
557F ASP* 2.8 41.4 + - - +
558F PTR 2.7 48.6 + - - +
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Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 3.2 6.1 + - - +
67B ARG* 1.3 98.6 - - + +
69B GLN* 1.3 62.7 + - + +
71B GLU* 3.2 26.9 + - - +
72B ASN* 3.0 31.5 + - - +
88B GLN* 4.7 0.6 + - - -
556F ASP* 5.4 2.5 - - - -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 4.3 2.9 - - - +
65B LEU* 3.4 26.4 - - + +
66B SER* 2.9 43.8 + - - +
68B HIS* 1.3 77.4 - - + +
70B ALA* 1.3 63.6 + - - +
72B ASN* 3.3 9.4 + - - +
73B LEU* 3.0 25.8 + - - +
73D LEU* 4.4 16.1 - - - +
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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 LEU* 3.8 11.8 - - + +
66B SER 3.0 16.2 + - - +
67B ARG 3.6 4.5 - - - +
69B GLN* 1.3 78.8 - - - +
71B GLU* 1.3 62.6 + - - +
73B LEU* 3.3 0.7 + - - +
74B LEU* 3.0 31.1 + - - +
83B ILE* 4.0 18.6 - - + -
85B ARG* 4.0 11.2 - - - -
97B SER* 3.7 24.5 - - - +
104B VAL* 5.0 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 25.9 + - - +
68B HIS* 3.2 27.9 + - - +
70B ALA* 1.3 74.1 - - - +
72B ASN* 1.3 71.4 + - - +
75B MET* 3.0 32.4 + - + +
104B VAL* 3.8 24.2 - - + +
106B HIS* 2.9 35.4 + - + +
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Residues in contact with ASN 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 HIS* 3.0 25.3 + - - +
69B GLN* 3.8 8.3 - - - +
71B GLU* 1.3 79.9 - - - +
73B LEU* 1.4 64.6 + - - +
75B MET* 3.4 12.8 + - - +
76B GLY 3.7 5.4 + - - -
76D GLY* 6.4 1.6 - - - -
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Residues in contact with LEU 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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65B LEU* 4.2 3.8 - - + -
69B GLN 3.0 17.5 + - - +
70B ALA 3.6 3.6 - - - +
72B ASN* 1.4 76.6 - - - +
74B LEU* 1.3 58.4 + - + +
76B GLY* 3.1 21.7 + - - -
77B LYS* 3.9 27.8 + - - +
83B ILE* 3.4 27.1 - - + -
72D ASN* 3.3 44.6 - - + +
75D MET* 3.7 36.8 - - + -
76D GLY 6.0 0.2 - - - +
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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 3.0 20.7 + - - +
73B LEU* 1.3 73.2 - - - +
75B MET* 1.3 60.2 + - - +
76B GLY 3.1 2.5 - - - -
77B LYS* 2.9 32.4 + - + +
81B PHE* 3.7 18.2 - - + +
82B PHE* 3.6 27.6 - - - +
83B ILE* 4.1 20.0 - - + +
97B SER* 3.4 43.3 - - - +
98B VAL 4.1 1.1 - - - +
99B ARG* 3.1 21.0 + - + +
104B VAL* 3.6 16.8 - - + -
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Residues in contact with MET 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* 3.0 23.5 + - + +
72B ASN* 3.7 7.6 - - - +
73B LEU 3.2 0.2 - - - -
74B LEU* 1.3 77.7 - - - +
76B GLY* 1.3 56.3 + - - +
77B LYS 3.3 2.6 + - - +
99B ARG* 3.0 53.6 + - - +
102B ASP 3.8 13.5 - - - +
103B ASP* 3.6 28.9 - - - -
104B VAL* 3.8 7.6 - - + -
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Residues in contact with GLY 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 ASN 3.7 4.4 + - - -
73B LEU 3.1 9.9 + - - -
74B LEU 3.1 1.4 - - - -
75B MET* 1.3 76.0 - - - +
77B LYS* 1.3 64.4 + - - +
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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