Contacts of the helix formed by residues 70 - 82 (chain B) in PDB entry 5DPR
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 ASN 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B HIS 3.3 4.9 + - - +
69B VAL* 1.3 80.0 - - - +
71B MET* 1.3 63.9 + - - +
72B SER* 2.3 29.7 + - - -
73B GLU* 2.9 41.3 + - - +
74B LEU* 3.1 16.6 + - - +
102B VAL 3.4 9.2 - - - +
103B SER* 3.7 15.4 + - - +
104B THR 3.4 21.3 - - - +
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Residues in contact with MET 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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70B ASN* 1.3 71.3 - - - +
72B SER* 1.3 56.2 + - - +
74B LEU* 3.6 17.1 - - + +
75B VAL* 2.7 41.3 + - + +
92B LEU* 3.8 15.7 - - + -
94B VAL* 3.7 15.9 - - + -
99B MET* 3.2 45.1 - - + +
101B SER 4.4 7.4 - - - +
102B VAL* 3.6 11.5 + - - +
104B THR 4.1 3.3 + - - +
106B ILE* 4.7 12.5 - - + +
109B ILE* 4.9 15.5 - - + -
122B MET* 3.6 33.2 - - - -
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Residues in contact with SER 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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70B ASN* 2.3 32.6 + - - -
71B MET* 1.3 76.2 - - - +
73B GLU* 1.3 58.7 + - - +
75B VAL* 3.5 7.8 + - - +
76B LYS* 3.2 33.4 + - - +
102B VAL* 3.2 29.4 + - - +
103B SER* 5.0 0.5 - - - -
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Residues in contact with GLU 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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68B HIS 4.6 1.2 - - - +
69B VAL* 3.6 18.3 - - + +
70B ASN* 2.9 47.7 + - - +
72B SER* 1.3 76.3 - - - +
74B LEU* 1.3 64.1 + - - +
76B LYS* 3.2 11.8 + - + +
77B ILE* 3.1 30.4 + - + +
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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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44B VAL* 5.2 0.2 - - + -
46B ILE* 4.7 6.1 - - + -
63B PHE* 6.0 1.3 - - + -
65B VAL* 4.4 24.2 - - + -
69B VAL* 4.1 6.8 - - + +
70B ASN 3.1 13.4 + - - +
71B MET* 3.6 19.5 - - + +
73B GLU* 1.3 74.7 - - - +
75B VAL* 1.3 65.7 + - - +
77B ILE* 3.2 16.1 + - + -
78B ILE* 3.1 41.2 + - + +
92B LEU* 4.0 7.6 - - + -
106B ILE* 4.7 9.4 - - + -
122B MET* 3.5 41.1 - - + -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 2.7 29.8 + - + +
72B SER* 3.7 8.5 - - - +
73B GLU 3.3 0.2 - - - -
74B LEU* 1.3 72.7 - - - +
76B LYS* 1.3 61.8 + - + +
78B ILE 3.6 0.2 + - - -
79B ARG* 3.0 37.2 + - - +
90B PHE* 3.9 26.6 - - + +
91B PHE* 6.2 0.2 - - - -
92B LEU* 4.1 32.8 - - + +
99B MET* 5.1 8.7 - - + -
102B VAL* 6.0 0.7 - - + -
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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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72B SER* 3.2 19.1 + - - +
73B GLU* 3.2 13.4 + - + +
75B VAL* 1.3 83.1 - - + +
77B ILE* 1.3 57.2 + - - +
79B ARG* 3.6 10.5 + - - +
80B ARG* 3.1 51.9 + - - +
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Residues in contact with ILE 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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63B PHE* 6.1 2.5 - - + -
69B VAL* 5.0 11.0 - - + -
73B GLU* 3.1 21.2 + - + +
74B LEU* 3.2 18.3 + - + +
76B LYS* 1.3 72.8 - - + +
78B ILE* 1.3 74.8 + - + +
79B ARG 3.1 1.8 - - - -
80B ARG* 3.4 28.3 + - - +
81B ARG* 3.1 25.6 + - + +
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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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46B ILE* 3.4 38.4 - - + -
58B LEU* 3.8 24.9 - - + -
63B PHE* 3.9 25.6 - - + -
74B LEU* 3.1 30.0 + - + +
77B ILE* 1.3 81.1 - - + +
79B ARG* 1.3 56.8 + - - +
81B ARG* 3.4 7.4 + - - +
82B LEU* 3.0 31.7 + - + +
90B PHE* 4.1 22.9 - - + -
92B LEU* 4.4 5.6 - - + -
124B TYR* 4.8 1.3 - - + -
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Residues in contact with ARG 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 VAL* 3.0 31.5 + - - +
76B LYS* 3.6 11.7 - - - +
78B ILE* 1.3 75.2 - - - +
80B ARG* 1.3 64.1 + - + +
81B ARG 3.1 1.1 - - - -
82B LEU* 3.2 7.4 + - - +
83B GLN 3.2 15.6 + - - -
84B LEU* 3.3 33.9 + - + +
85B ASN 3.3 13.4 + - - -
86B PRO* 3.2 24.9 + - - +
88B GLN 2.7 24.0 + - - -
90B PHE* 2.9 40.9 - - + +
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Residues in contact with ARG 80 (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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76B LYS* 3.1 42.3 + - - +
77B ILE* 3.4 28.0 + - - +
79B ARG* 1.3 75.8 - - + +
81B ARG* 1.3 61.6 + - - +
83B GLN* 3.2 20.3 + - - +
84B LEU 5.2 1.1 - - - +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.9 12.5 - - + +
59B ASP* 2.8 44.2 + - - +
60B LYS* 3.6 17.6 - - - +
63B PHE* 4.0 30.0 - - - -
77B ILE* 3.1 17.5 + - - +
78B ILE* 3.4 13.2 - - - +
79B ARG 3.1 0.2 - - - -
80B ARG* 1.3 77.6 - - - +
82B LEU* 1.3 60.7 + - - +
83B GLN* 3.1 16.8 + - - +
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Residues in contact with LEU 82 (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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55B LEU* 5.1 0.9 - - + -
56B PRO* 3.6 45.7 - - + +
57B VAL 4.3 1.8 - - - +
58B LEU* 3.5 30.1 - - + +
78B ILE* 3.0 17.7 + - + +
79B ARG 3.2 1.3 + - - +
81B ARG* 1.3 74.8 - - - +
83B GLN* 1.3 73.8 + - - +
84B LEU* 3.3 26.0 + - + +
90B PHE* 3.6 34.3 - - + -
124B TYR* 3.7 22.7 - - + +
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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