Contacts of the helix formed by residues 54 - 62 (chain A) in PDB entry 1A8H
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 GLU 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLY* 1.3 72.2 - - - -
55A THR* 1.3 71.9 + - - +
56A VAL 3.3 0.2 - - - -
57A TYR* 3.5 8.6 - - + +
58A ARG* 2.9 57.6 + - + +
130A CYS 3.9 6.7 - - - +
131A GLU 4.7 2.9 - - - +
132A ARG* 3.5 29.6 + - - +
205A ARG* 4.6 4.3 - - - -
209A ARG 4.1 19.5 - - - +
210A VAL* 3.8 10.6 - - + +
211A PRO* 5.0 3.1 - - + -
225A TYR* 3.1 35.5 + - - -
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Residues in contact with THR 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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13A TYR* 3.3 26.8 + - - +
53A GLY* 4.8 2.4 - - - -
54A GLU* 1.3 92.3 + - - +
56A VAL* 1.3 65.5 + - - +
58A ARG* 3.4 20.9 + - - +
59A ALA* 3.1 23.8 + - - +
132A ARG* 5.3 8.1 - - - +
146A ILE* 5.4 11.9 - - + -
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Residues in contact with VAL 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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13A TYR* 3.4 33.9 - - + +
14A VAL* 3.8 16.4 - - + -
15A ASN* 4.4 5.4 - - + -
51A GLU 3.5 22.4 - - - +
52A HIS 4.3 6.5 - - - +
53A GLY 4.0 6.9 + - - +
55A THR* 1.3 79.2 + - - +
57A TYR* 1.3 63.3 + - - +
59A ALA* 3.3 7.4 + - - +
60A ALA* 3.1 21.6 + - + +
67A PRO* 5.5 2.2 - - + +
70A PHE* 4.1 11.3 - - + -
71A VAL* 3.6 20.6 - - + -
212A TRP* 3.8 6.7 - - - +
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Residues in contact with TYR 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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53A GLY 3.4 16.6 + - - +
54A GLU* 3.3 8.7 + - + +
55A THR 3.2 0.4 - - - -
56A VAL* 1.3 81.9 - - - +
58A ARG* 1.3 61.5 + - + +
60A ALA* 3.2 7.3 + - - +
61A GLN* 3.0 65.8 + - + +
67A PRO* 3.9 29.8 - - + -
211A PRO* 3.6 36.3 - - + +
212A TRP* 3.7 24.9 - + + -
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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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54A GLU* 2.9 39.6 + - + +
55A THR* 3.9 20.8 - - - +
57A TYR* 1.3 77.6 - - + +
59A ALA* 1.3 63.7 + - - +
61A GLN* 3.6 23.7 - - - +
62A ALA* 3.1 22.0 + - - +
129A SER 4.1 11.5 + - - -
130A CYS* 2.9 43.8 + - - +
131A GLU* 4.5 6.7 - - - +
146A ILE* 5.8 2.4 - - - +
147A HIS* 5.1 4.2 + - - -
209A ARG 5.6 0.6 + - - -
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Residues in contact with ALA 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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15A ASN* 3.5 24.0 - - - +
55A THR 3.1 16.2 + - - +
56A VAL 3.5 5.6 - - - +
57A TYR 3.2 0.4 - - - -
58A ARG* 1.3 75.5 - - - +
60A ALA* 1.3 65.7 + - - +
62A ALA* 3.4 7.8 + - - +
63A ALA* 3.3 20.6 + - - +
70A PHE* 3.9 14.8 - - + -
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Residues in contact with ALA 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 VAL* 3.1 12.7 + - + +
57A TYR* 3.2 9.6 + - - +
59A ALA* 1.3 74.3 - - - +
61A GLN* 1.3 64.9 + - + +
63A ALA* 3.3 3.6 + - - +
64A GLY 3.2 4.2 + - - -
65A GLU* 3.1 36.1 + - - +
67A PRO* 3.9 16.8 - - + -
70A PHE* 3.6 36.7 - - + -
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Residues in contact with GLN 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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57A TYR* 3.0 58.1 + - + +
58A ARG* 3.6 25.9 - - - +
59A ALA 3.3 0.2 - - - -
60A ALA* 1.3 78.2 - - + +
62A ALA* 1.3 62.2 + - - +
64A GLY* 3.2 12.7 + - - -
65A GLU 4.7 3.1 - - - +
67A PRO* 6.3 0.7 - - + -
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Residues in contact with ALA 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 ARG 3.1 11.5 + - - +
59A ALA* 3.5 11.9 - - - +
61A GLN* 1.3 77.6 - - - +
63A ALA* 1.3 58.3 + - - +
64A GLY 3.0 9.5 + - - -
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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