Contacts of the helix formed by residues 54 - 61 (chain D) in PDB entry 7A62
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 GLN 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D LEU* 2.8 25.0 + - + +
52D SER* 2.5 37.3 + - - +
53D GLY* 1.3 76.6 - - - +
55D LEU* 1.3 65.0 + - - +
56D ARG 3.4 2.0 - - - -
57D GLU* 3.4 23.1 + - - +
58D ARG* 3.1 42.7 + - - +
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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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42D ILE* 3.6 23.6 - - + -
46D LEU* 3.6 28.3 - - + -
49D LEU* 3.2 30.5 + - + +
50D ILE* 4.2 11.7 - - + -
53D GLY 3.5 1.6 - - - -
54D GLN* 1.3 78.0 - - - +
56D ARG* 1.3 67.0 + - + +
58D ARG* 3.0 6.3 + - - +
59D VAL* 3.0 25.5 + - + +
86D ILE 4.7 1.3 - - - +
89D ALA* 3.4 42.2 - - + +
90D TYR* 3.5 12.8 - - + +
93D GLY* 5.5 1.1 - - - -
502D CL 4.2 4.6 - - + +
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Residues in contact with ARG 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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53D GLY 5.2 0.8 + - - +
54D GLN 3.4 0.2 - - - -
55D LEU* 1.3 79.4 - - + +
57D GLU* 1.3 58.9 + - - +
59D VAL* 3.2 2.1 + - - +
60D GLU* 2.8 42.9 + - - +
90D TYR* 3.0 43.4 + - + +
91D VAL 2.9 23.6 + - - -
93D GLY* 3.2 19.9 - - - +
94D LYS 5.3 0.8 - - - +
98D ASP* 2.8 49.3 + - - -
99D VAL* 3.6 4.6 - - - +
100D ARG* 3.2 32.7 - - - +
502D CL 4.3 14.8 - - + +
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Residues in contact with GLU 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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53D GLY 5.6 1.0 + - - +
54D GLN* 3.4 22.1 + - - +
55D LEU 3.2 0.2 - - - -
56D ARG* 1.3 77.2 - - - +
58D ARG* 1.3 80.0 + - - +
60D GLU* 3.1 10.8 + - - +
61D LYS* 3.0 60.9 + - + +
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Residues in contact with ARG 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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41D PHE* 4.5 20.3 - - - -
42D ILE* 3.8 26.5 - - + +
49D LEU* 4.3 22.2 - - + +
54D GLN* 3.1 36.6 + - - +
55D LEU* 3.0 10.6 + - - +
57D GLU* 1.3 94.1 + - - +
59D VAL* 1.3 61.8 + - - +
61D LYS* 3.4 5.9 + - - +
62D LEU* 3.3 22.9 + - - +
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Residues in contact with VAL 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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42D ILE* 4.5 6.3 - - + -
55D LEU* 3.0 30.2 + - + +
56D ARG 3.7 5.8 - - - +
58D ARG* 1.3 76.3 - - - +
60D GLU* 1.3 64.5 + - - +
61D LYS 3.2 1.0 + - - -
62D LEU* 3.2 23.1 + - + +
86D ILE* 3.8 24.5 - - + -
90D TYR* 3.8 31.0 - - + -
103D LEU* 5.6 0.9 - - + -
104D PRO* 4.3 16.5 - - + +
106D ASN* 5.5 2.4 - - - +
107D ILE* 4.0 23.9 - - + +
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Residues in contact with GLU 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 ARG* 2.8 30.8 + - - +
57D GLU* 3.7 8.4 + - - +
59D VAL* 1.3 76.2 - - - +
61D LYS* 1.3 64.6 + - + +
62D LEU 3.4 4.6 + - - +
90D TYR* 2.6 36.3 + - + +
100D ARG* 4.8 5.4 + - - -
104D PRO* 4.3 14.0 - - + +
106D ASN* 5.5 0.9 + - - -
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Residues in contact with LYS 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 GLU* 3.0 51.4 + - + +
58D ARG* 3.4 6.5 + - - +
59D VAL 3.1 0.2 - - - -
60D GLU* 1.3 82.6 - - + +
62D LEU* 1.3 63.6 + - - +
63D ASN* 3.6 8.2 + - - +
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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