Contacts of the helix formed by residues 52 - 62 (chain D) in PDB entry 5H7R
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 THR 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU 3.6 1.2 + - - -
40D ASP* 2.6 40.6 + - - +
42D LEU* 3.3 25.9 - - + +
50D TYR 3.5 0.8 + - - -
51D CYS* 1.3 71.2 - - - +
53D LEU* 1.3 58.7 + - - +
55D LEU* 3.5 1.0 + - - +
56D THR* 2.7 45.1 + - - +
79D LYS* 2.9 27.7 + - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU 4.8 4.5 - - - +
14D GLU* 3.4 31.0 - - - +
15D GLU* 3.6 20.4 - - - +
16D ASN* 3.5 34.3 + - - +
39D LEU 5.2 0.2 + - - -
40D ASP* 5.7 0.2 - - - +
51D CYS* 3.3 1.0 - - - +
52D THR* 1.3 81.8 - - - +
54D CYS* 1.3 60.4 + - - +
56D THR* 3.7 4.0 - - - -
57D ASN* 3.0 51.9 + - - +
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Residues in contact with CYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ASN* 3.3 20.6 - - - -
31D CYS* 4.1 0.9 - - - -
33D ILE* 3.8 25.2 - - + +
34D CYS* 3.6 14.8 - - - -
51D CYS* 3.1 8.8 + - + +
53D LEU* 1.3 82.9 - - - +
55D LEU* 1.3 57.6 + - - +
57D ASN* 3.5 4.1 + - - +
58D PHE* 2.9 29.3 + - - +
202D ZN 2.3 36.1 - - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 3.9 12.0 - - + +
42D LEU* 4.2 21.3 - - + -
44D THR* 4.1 12.6 - - + -
50D TYR* 3.9 28.7 - - + -
51D CYS 2.9 15.4 + - - +
52D THR 4.1 2.0 - - - +
54D CYS* 1.3 73.6 - - - +
56D THR* 1.3 66.4 + - - +
58D PHE* 3.6 4.2 - - + +
59D LEU* 3.0 36.4 + - + +
66D PRO* 4.6 5.2 - - + -
72D LEU* 3.9 20.0 - - + -
74D LEU* 4.5 2.7 - - + -
77D CYS* 3.7 30.3 - - + -
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Residues in contact with THR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D THR* 2.7 31.8 + - - +
53D LEU* 3.7 6.5 - - - -
55D LEU* 1.3 78.1 - - - +
57D ASN* 1.3 67.3 - - - +
59D LEU* 3.5 3.2 + - - +
60D VAL* 3.4 25.1 + - + +
74D LEU* 3.9 35.1 - - + +
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 4.0 9.8 + - - +
53D LEU* 3.0 39.8 + - - +
54D CYS* 4.0 4.2 - - - +
56D THR* 1.3 80.5 - - - +
58D PHE* 1.3 66.8 + - - +
60D VAL* 3.3 20.9 + - - +
61D GLU* 4.0 5.0 + - - +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 4.0 29.6 - - + -
54D CYS 2.9 18.6 + - - +
55D LEU* 3.6 7.0 - - + +
57D ASN* 1.3 79.3 - - - +
59D LEU* 1.3 65.4 + - + +
60D VAL 3.3 0.2 + - - -
61D GLU* 3.4 1.9 + - - +
62D LYS* 3.0 75.7 + - + +
64D PHE* 3.3 39.7 - + - -
66D PRO* 3.7 29.6 - - + -
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 3.0 38.8 + - + +
56D THR* 3.5 4.9 + - - +
57D ASN 3.3 0.4 - - - -
58D PHE* 1.3 77.6 - - + +
60D VAL* 1.3 63.0 + - - +
62D LYS 2.9 23.1 - - - +
63D ASP* 4.1 3.4 - - - +
64D PHE 4.0 20.4 - - - +
72D LEU* 3.9 28.7 - - + +
73D VAL* 3.9 5.8 - - - -
74D LEU* 3.6 41.5 - - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D THR* 3.4 20.3 + - + +
57D ASN* 3.3 13.9 + - - +
58D PHE 3.2 1.2 - - - -
59D LEU* 1.3 78.6 - - - +
61D GLU* 1.3 70.1 + - + +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ASN 4.0 3.7 + - - +
58D PHE 3.4 4.6 + - - +
60D VAL* 1.3 88.5 - - + +
62D LYS* 1.3 72.7 + - + +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PHE* 3.0 58.7 + - + +
59D LEU* 2.9 29.1 - - - +
60D VAL 3.7 0.2 - - - -
61D GLU* 1.3 88.5 - - + +
63D ASP* 1.3 62.0 + - - +
64D PHE* 3.8 17.7 - - + -
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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