Contacts of the helix formed by residues 70 - 82 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A HIS 3.3 4.1 + - - +
69A VAL* 1.3 78.0 - - - +
71A MET* 1.3 67.5 - - - +
72A SER* 3.2 10.8 - - - +
73A GLU* 3.0 27.0 + - - +
74A LEU* 3.0 10.4 + - - +
103A SER* 3.1 37.7 - - - +
104A THR 3.6 7.2 - - - -
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASN* 1.3 71.2 - - - +
72A SER* 1.3 61.1 + - - +
74A LEU* 3.6 15.9 - - + +
75A VAL* 2.8 35.4 + - + +
92A LEU* 5.7 0.9 - - + -
94A VAL* 4.8 2.5 - - + -
99A MET* 3.2 47.8 - - + +
102A VAL* 3.5 13.4 + - + +
104A THR 3.9 3.7 + - - +
106A ILE* 3.6 40.2 - - + +
109A ILE* 3.7 20.6 - - + -
122A MET* 3.8 28.9 - - + -
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 3.8 11.1 - - - +
71A MET* 1.3 78.0 - - - +
73A GLU* 1.3 64.7 + - - +
75A VAL* 3.6 3.3 + - - +
76A LYS* 3.4 36.0 + - - +
99A MET 3.8 6.0 + - - -
100A VAL* 4.3 23.2 - - - +
101A SER 5.3 0.7 - - - -
102A VAL 3.1 18.7 + - - -
103A SER* 4.3 6.3 - - - -
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS 4.4 1.7 - - - +
69A VAL* 3.5 17.7 - - + +
70A ASN* 3.0 30.8 + - + +
72A SER* 1.3 81.1 + - - +
74A LEU* 1.3 63.9 + - - +
76A LYS* 3.2 16.5 + - + +
77A ILE* 3.1 29.6 + - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 5.1 0.2 - - + -
46A ILE* 4.7 6.5 - - + -
63A PHE* 5.9 1.8 - - + -
65A VAL* 4.3 24.5 - - + -
69A VAL* 4.1 6.2 - - + +
70A ASN 3.0 12.0 + - - +
71A MET* 3.6 19.3 - - - +
73A GLU* 1.3 75.0 - - - +
75A VAL* 1.3 65.8 + - - +
77A ILE* 3.1 18.8 + - + +
78A ILE* 3.0 40.8 + - + +
92A LEU* 4.1 10.3 - - + -
106A ILE* 4.7 8.3 - - + -
122A MET* 3.6 39.5 - - + -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET 2.8 24.1 + - - +
72A SER 3.7 6.1 - - - +
74A LEU* 1.3 72.3 - - - +
76A LYS* 1.3 64.7 + - + +
78A ILE 3.7 0.4 + - - +
79A ARG* 3.0 30.7 + - - +
90A PHE* 3.8 25.8 - - + +
91A PHE* 6.1 0.2 - - - -
92A LEU* 3.9 33.2 - - + +
99A MET* 4.1 4.7 - - + -
100A VAL* 3.9 43.3 - - + +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER* 3.4 24.8 + - - +
73A GLU* 3.2 17.3 + - + +
74A LEU 3.2 0.2 - - - -
75A VAL* 1.3 80.0 - - + +
77A ILE* 1.3 56.8 + - - +
79A ARG* 3.4 10.9 + - - +
80A ARG* 3.1 50.0 + - - +
100A VAL* 6.2 2.9 - - + +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 6.0 2.7 - - + -
69A VAL* 4.8 13.0 - - + -
73A GLU* 3.3 21.3 - - + +
74A LEU* 3.1 19.2 + - + +
76A LYS* 1.3 73.9 - - - +
78A ILE* 1.3 73.0 + - + +
80A ARG* 3.3 30.4 + - - +
81A ARG* 3.2 26.3 + - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.5 38.4 - - + -
58A LEU* 3.9 24.5 - - + -
63A PHE* 3.8 27.1 - - + -
74A LEU* 3.0 28.5 + - + +
75A VAL 4.3 0.4 - - - +
77A ILE* 1.3 80.0 - - + +
79A ARG* 1.3 61.0 + - - +
81A ARG* 3.5 7.3 + - - +
82A LEU* 3.2 23.9 + - + +
90A PHE* 3.9 25.1 - - + -
92A LEU* 4.1 7.9 - - + -
124A TYR* 4.9 1.6 - - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 3.0 24.8 + - - +
76A LYS* 3.4 11.0 - - - +
77A ILE 3.1 0.2 - - - -
78A ILE* 1.3 74.8 - - - +
80A ARG* 1.3 65.5 + - + +
81A ARG 3.1 1.6 - - - -
82A LEU* 3.3 13.0 + - - +
83A GLN 3.3 7.8 + - - -
84A LEU* 3.6 27.2 + - + +
85A ASN 3.3 20.1 + - - -
86A PRO* 3.6 15.6 + - - +
88A GLN 3.1 20.4 + - - -
90A PHE* 3.1 46.2 - - + +
131C GLY 3.4 9.2 + - - -
132C PHE* 3.8 19.8 + - - +
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.1 33.3 + - - +
77A ILE* 3.3 42.4 + - - +
79A ARG* 1.3 77.7 - - + +
81A ARG* 1.3 57.3 + - - +
83A GLN* 3.1 25.0 + - - +
84A LEU 5.4 0.2 - - - +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.0 14.3 - - + +
59A ASP* 3.0 39.8 + - - +
60A LYS* 3.7 15.2 - - - +
63A PHE* 4.0 31.3 - - - -
77A ILE* 3.2 15.5 + - - +
78A ILE* 3.5 13.7 - - - +
79A ARG 3.1 0.4 - - - -
80A ARG* 1.3 80.9 - - - +
82A LEU* 1.3 59.4 + - - +
83A GLN* 3.2 12.8 + - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 5.1 3.6 - - + -
56A PRO* 3.6 39.8 - - + +
57A VAL 4.3 2.0 - - - +
58A LEU* 3.6 32.1 - - + +
78A ILE* 3.2 14.8 + - + +
79A ARG 3.8 0.7 - - - +
80A ARG 3.3 0.6 - - - -
81A ARG* 1.3 75.8 - - - +
83A GLN* 1.3 71.5 + - - +
84A LEU* 3.3 29.1 + - + +
90A PHE* 3.6 35.9 - - + -
124A TYR* 4.0 15.9 - - + +
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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