Contacts of the helix formed by residues 59 - 64 (chain A) in PDB entry 5MQI
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU 3.1 1.2 + - - -
56A GLY* 2.9 19.8 + - - +
57A ALA 4.0 5.6 - - - +
58A ALA* 1.3 80.1 - - - +
60A ILE* 1.3 58.9 + - - +
62A GLN* 3.2 37.3 + - + +
63A SER* 2.5 43.8 + - - +
119A ALA* 6.2 0.4 - - - +
120A TYR* 5.6 0.2 - - - -
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Residues in contact with ILE 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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14A CYS* 3.5 39.0 - - + -
17A LEU* 3.8 24.7 - - + -
38A LEU* 4.5 9.6 - - + -
55A LEU* 3.2 27.8 + - + +
58A ALA* 3.8 19.7 - - + +
59A GLN* 1.3 73.8 - - - +
61A LEU* 1.3 68.4 + - - +
63A SER* 5.7 0.2 - - - -
64A ASP* 2.8 39.9 + - - +
65A LEU* 3.0 21.9 + - + -
85A LEU* 5.5 0.4 - - + -
89A LEU* 5.8 1.8 - - + -
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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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55A LEU 4.9 0.8 + - - -
59A GLN 3.4 0.4 - - - -
60A ILE* 1.3 80.6 - - - +
62A GLN* 1.3 61.6 + - + +
65A LEU* 3.8 13.6 - - + +
66A LEU* 2.8 53.0 + - + +
86A MET* 4.0 26.7 - - + -
89A LEU* 4.4 14.3 - - + +
90A THR* 4.3 13.9 - - + -
120A TYR* 3.6 55.5 + - + -
123A ALA* 4.7 1.6 - - + -
124A PHE* 4.0 16.2 - - + -
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Residues in contact with GLN 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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20A LEU* 5.6 0.5 - - - +
56A GLY 5.3 1.4 + - - -
59A GLN* 3.2 49.1 - - + +
61A LEU* 1.3 75.8 - - + +
63A SER* 1.3 65.7 + - - +
66A LEU* 4.3 6.9 - - - +
67A PRO* 3.1 18.4 - - - +
116A TYR* 6.4 0.2 - - - -
119A ALA* 3.9 26.8 + - - +
120A TYR* 3.6 24.1 - - - -
123A ALA* 3.9 25.1 - - + -
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Residues in contact with SER 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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20A LEU* 4.0 13.6 - - - +
25A TYR* 3.7 6.4 - - - -
58A ALA 3.9 4.9 + - - -
59A GLN* 2.5 40.7 + - - +
60A ILE* 5.7 0.2 - - - -
62A GLN* 1.3 73.4 - - - +
64A ASP* 1.3 75.3 + - - +
67A PRO* 3.4 12.3 - - - +
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Residues in contact with ASP 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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14A CYS 4.3 4.0 - - - +
17A LEU* 3.7 26.3 - - + +
18A GLY 3.5 14.0 - - - +
19A TYR* 5.0 0.7 - - - -
25A TYR* 3.1 26.3 + - - +
60A ILE* 2.8 39.6 + - - +
62A GLN 3.3 0.4 - - - -
63A SER* 1.3 87.1 - - - +
65A LEU* 1.3 60.0 + - - +
67A PRO* 3.1 7.1 - - - +
68A ILE* 2.9 32.9 + - - +
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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