Contacts of the helix formed by residues 54 - 65 (chain A) in PDB entry 5D71
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 CYS 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.3 15.7 - - + -
53A THR* 1.3 82.1 - - - +
55A LEU* 1.3 62.9 + - - +
57A THR* 3.3 1.3 + - - -
58A ARG* 3.0 31.6 + - - +
91A THR* 3.5 0.8 + - - -
92A PRO 2.7 17.0 + - - -
93A GLU* 3.3 15.9 - - - -
95A SER 3.3 12.1 - - - -
96A CYS* 2.1 49.4 - - + -
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Residues in contact with LEU 55 (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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47A PHE* 4.3 9.2 - - + -
53A THR 3.2 4.2 + - - -
54A CYS* 1.3 78.0 - - - +
56A GLN* 1.3 70.9 + - + +
58A ARG* 3.2 13.4 + - - +
59A LEU* 3.2 24.3 + - + +
84A TYR* 3.7 24.2 - - + +
91A THR* 3.0 22.6 + - + +
93A GLU* 4.1 0.2 - - - +
113A PHE* 3.9 19.7 - - + -
117A ILE* 3.7 24.7 - - + -
122A TRP* 3.4 34.3 - - + -
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Residues in contact with GLN 56 (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* 1.3 83.1 - - + +
57A THR* 1.3 62.2 + - - +
59A LEU* 3.5 4.3 + - - +
60A GLU* 3.0 25.9 + - - +
81A ALA* 3.0 45.3 + - - +
84A TYR* 4.4 8.1 - - - +
85A LYS* 3.8 31.1 - - + +
93A GLU* 2.9 24.2 + - + +
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Residues in contact with THR 57 (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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43A ILE* 3.9 18.8 - - + -
54A CYS* 3.7 5.2 - - - -
55A LEU 3.2 0.4 - - - -
56A GLN* 1.3 77.2 - - - +
58A ARG* 1.3 56.1 + - - +
60A GLU* 3.5 5.9 + - + +
61A LEU* 3.0 39.3 + - + +
93A GLU* 2.8 29.7 + - - +
96A CYS* 4.1 20.3 - - + -
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Residues in contact with ARG 58 (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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43A ILE* 3.5 38.8 + - + +
45A GLU* 3.0 30.5 + - - +
46A MET* 4.1 3.2 + - - +
47A PHE* 3.4 41.9 - - - +
53A THR* 3.1 36.5 + - - -
54A CYS* 3.0 18.9 + - - +
55A LEU* 3.2 8.9 + - - +
57A THR* 1.3 73.9 - - - +
59A LEU* 1.3 56.4 + - + +
61A LEU* 3.2 5.2 + - - +
62A TYR* 2.7 59.7 + - + -
109A ASN* 5.9 1.6 - - - +
113A PHE* 4.4 14.4 - - + -
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Residues in contact with LEU 59 (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* 3.2 34.3 + - + +
56A GLN* 4.0 7.0 - - - +
58A ARG* 1.3 79.1 - - - +
60A GLU* 1.3 56.6 + - - +
62A TYR* 3.5 8.7 - - + +
63A LYS* 3.0 38.7 + - - +
77A LEU* 4.1 31.4 - - + +
80A MET* 4.4 7.6 - - + -
81A ALA* 3.6 39.7 - - + +
84A TYR* 5.2 4.0 - - + -
113A PHE* 3.9 30.1 - - + -
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Residues in contact with GLU 60 (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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56A GLN 3.0 18.8 + - - +
57A THR* 3.7 7.0 - - + +
59A LEU* 1.3 77.4 - - - +
61A LEU* 1.3 58.5 + - + +
63A LYS* 3.5 22.1 + - - +
64A GLN* 2.7 57.9 + - - +
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Residues in contact with LEU 61 (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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40A VAL* 4.6 2.6 - - - +
41A GLU* 3.6 44.4 - - + +
42A VAL* 3.9 7.0 - - + -
43A ILE* 3.9 31.9 - - + +
57A THR* 3.0 31.9 + - + +
58A ARG* 3.7 3.4 - - - +
60A GLU* 1.3 74.6 - - + +
62A TYR* 1.3 67.3 + - - +
64A GLN* 3.1 27.0 + - + +
65A GLY* 3.5 4.0 + - - -
98A THR* 3.7 19.5 - - - +
106A PHE* 5.2 0.2 - - - -
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Residues in contact with TYR 62 (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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42A VAL* 4.5 11.9 - - + -
43A ILE 6.2 0.2 - - - -
58A ARG* 2.7 42.6 + - + +
59A LEU* 3.5 18.4 - - + +
60A GLU 3.4 0.2 - - - -
61A LEU* 1.3 70.0 - - - +
63A LYS* 1.3 56.0 + - - +
65A GLY* 2.9 23.0 + - - -
66A LEU* 3.6 14.1 - - - +
77A LEU* 4.0 13.7 - - + -
106A PHE* 3.6 25.7 - + + -
109A ASN* 2.6 34.8 + - - -
110A LEU* 3.8 28.7 - - + -
113A PHE* 3.3 45.7 - + - +
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Residues in contact with LYS 63 (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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59A LEU 3.0 21.4 + - - +
60A GLU* 3.5 26.6 + - - +
61A LEU 3.3 0.2 - - - -
62A TYR* 1.3 75.3 - - - +
64A GLN* 1.3 66.7 + - - +
66A LEU* 3.3 29.2 + - + +
67A ARG* 5.2 3.1 - - - +
74A LYS* 4.9 11.7 - - + +
77A LEU* 3.9 18.6 - - + +
78A THR* 3.5 49.5 + - - +
81A ALA* 3.8 17.1 - - - +
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Residues in contact with GLN 64 (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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40A VAL* 5.3 2.2 - - + -
41A GLU 5.8 1.1 - - - +
60A GLU* 2.7 51.2 + - - +
61A LEU* 3.1 22.1 + - + +
62A TYR 3.1 1.0 - - - -
63A LYS* 1.3 84.0 - - - +
65A GLY* 1.3 55.6 + - - +
66A LEU 3.3 4.2 + - - -
67A ARG* 3.9 39.1 + - - +
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Residues in contact with GLY 65 (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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40A VAL* 4.2 22.6 - - - +
61A LEU 3.5 4.2 + - - -
62A TYR 2.9 12.2 + - - -
64A GLN* 1.3 75.2 - - - +
66A LEU* 1.3 57.2 + - - +
67A ARG 3.7 2.5 - - - -
70A LEU* 4.4 0.7 - - - +
103A PHE* 3.5 17.4 - - - -
106A PHE* 3.3 27.4 - - - -
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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