Contacts of the helix formed by residues 60 - 69 (chain A) in PDB entry 1H5R
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 ASP 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 5.2 1.2 - - - +
13A SER 5.6 1.7 - - - +
24A VAL 4.9 0.9 - - - -
25A SER* 2.7 41.0 + - - +
27A GLN* 5.9 0.7 - - - +
56A SER* 3.4 11.4 - - - +
57A THR* 2.8 30.2 + - - +
59A GLN* 1.3 82.8 - - - +
61A THR* 1.3 66.0 + - - +
62A PRO* 3.2 2.9 - - - -
63A ARG* 3.0 21.9 + - - +
64A PHE* 3.3 15.6 + - + -
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Residues in contact with THR 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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54A ILE* 4.5 1.1 - - + +
55A ILE 5.3 0.2 - - - -
56A SER* 2.9 32.5 + - - +
57A THR 2.7 21.2 + - - -
60A ASP* 1.3 73.9 - - - +
62A PRO* 1.3 71.7 - - + +
64A PHE* 3.0 16.8 + - + +
65A GLN* 3.1 12.0 + - - +
80A TYR* 3.9 28.9 - - + -
81A LYS 3.8 20.7 + - - +
82A VAL* 3.9 11.1 - - + +
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Residues in contact with PRO 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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58A PRO 3.4 17.9 - - - +
59A GLN 3.2 13.2 - - - +
60A ASP 3.2 5.2 - - - -
61A THR* 1.3 95.8 - - + +
63A ARG* 1.3 67.1 + - - +
65A GLN* 3.4 11.7 + - + +
66A GLN* 2.9 39.5 + - + +
82A VAL* 5.8 0.9 - - + -
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Residues in contact with ARG 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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25A SER* 4.5 5.6 - - - +
28A LEU* 4.2 22.6 - - + +
59A GLN* 3.8 22.7 + - - +
60A ASP* 3.0 19.5 + - - +
62A PRO* 1.3 84.6 - - - +
64A PHE* 1.3 64.4 + - - +
66A GLN* 3.4 35.9 + - - +
67A LEU* 3.1 22.0 + - - +
63B ARG* 3.2 38.0 - - - +
66B GLN* 4.8 6.9 + - - -
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Residues in contact with PHE 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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10A ALA* 3.9 6.3 - - + -
25A SER* 4.2 4.3 - - - -
27A GLN* 3.7 32.8 - - + -
28A LEU* 3.5 36.1 - - + -
37A ILE* 3.9 27.4 - - + -
54A ILE* 4.3 11.2 - - + -
56A SER* 3.4 34.8 - - - -
60A ASP* 3.3 29.4 + - + -
61A THR* 3.0 7.1 + - - +
63A ARG* 1.3 76.4 - - + +
65A GLN* 1.3 57.5 + - - +
67A LEU* 3.1 5.7 + - - +
68A LEU* 2.8 39.4 + - + +
80A TYR* 3.9 15.3 - - + -
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Residues in contact with GLN 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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61A THR* 3.1 13.2 + - - +
62A PRO* 3.7 13.0 - - + +
64A PHE* 1.3 72.5 - - - +
66A GLN* 1.3 65.4 + - + +
69A GLY* 2.9 29.2 + - - -
80A TYR* 3.6 48.5 - - + +
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Residues in contact with GLN 66 (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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62A PRO* 2.9 29.8 + - + +
63A ARG* 3.4 41.1 + - - +
64A PHE 3.3 0.2 - - - -
65A GLN* 1.3 79.1 - - + +
67A LEU* 1.3 61.3 + - - +
69A GLY 4.6 0.9 + - - -
59B GLN* 6.0 1.8 - - - +
63B ARG* 4.2 11.6 + - - +
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Residues in contact with LEU 67 (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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28A LEU* 3.6 29.2 - - + -
35A PRO* 4.5 4.7 - - + -
37A ILE* 4.9 2.9 - - + -
38A TYR* 4.4 19.5 - - + +
63A ARG 3.1 15.1 + - - +
64A PHE* 3.7 4.9 - - - +
66A GLN* 1.3 80.2 - - - +
68A LEU* 1.3 82.1 + - + +
73A GLN* 5.1 2.1 + - - -
19B PRO 5.0 2.0 - - - +
22B MET* 4.0 50.4 - - + +
23B ALA* 4.1 12.6 - - + +
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Residues in contact with LEU 68 (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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37A ILE* 4.5 18.4 - - + -
38A TYR* 4.0 19.3 - - + +
41A LEU* 4.9 7.0 - - + -
54A ILE* 3.6 30.1 - - + -
64A PHE* 2.8 22.8 + - + +
67A LEU* 1.3 86.9 - - + +
69A GLY* 1.3 64.8 + - - +
70A ASP 3.5 0.2 + - - -
71A GLY* 3.4 6.1 + - - -
73A GLN* 2.9 27.6 + - - +
74A TRP* 3.8 33.7 - - + -
78A LEU* 3.7 11.0 - - + -
80A TYR* 3.4 11.2 - - - +
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Residues in contact with GLY 69 (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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65A GLN* 2.9 23.3 + - - -
66A GLN 4.6 1.0 + - - -
67A LEU 3.7 0.8 - - - -
68A LEU* 1.3 78.4 - - - +
70A ASP* 1.3 61.0 + - - -
71A GLY 3.2 0.2 - - - -
73A GLN* 5.2 0.2 - - - -
78A LEU* 3.6 2.3 - - - +
80A TYR* 2.7 33.4 + - - -
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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