Contacts of the helix formed by residues 117 - 123 (chain A) in PDB entry 1QMU
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 ASN 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN 3.1 11.0 + - - +
73A MET 2.9 21.7 + - - +
75A GLY* 3.2 12.9 - - - +
115A SER* 3.5 5.1 + - - -
116A MET* 1.3 80.7 - - - +
118A PRO* 1.3 59.8 - - - +
119A ASP* 3.6 5.0 + - - +
120A GLY* 3.0 17.4 + - - -
121A TYR* 3.3 13.5 + - - +
135A ARG 3.1 15.2 + - - -
136A ASN 3.1 26.0 + - - -
137A ASN* 3.9 12.8 - - - +
143A LEU* 3.8 9.3 - - + +
161A GLU* 4.1 6.5 - - - +
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Residues in contact with PRO 118 (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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16A PHE* 3.7 31.0 - - + -
42A SER* 3.9 7.0 - - - -
46A ARG* 3.9 22.0 - - + +
47A GLU 4.4 0.7 - - - +
48A LEU* 3.9 18.8 - - + -
81A ARG* 4.4 2.5 - - - +
115A SER* 3.2 22.6 - - - +
116A MET 3.4 8.5 - - - +
117A ASN* 1.3 87.3 - - - +
119A ASP* 1.3 66.1 + - - +
121A TYR* 3.4 8.4 + - + +
122A GLU* 3.3 26.3 + - - +
161A GLU* 5.1 0.2 - - + -
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Residues in contact with ASP 119 (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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42A SER* 2.6 38.4 + - - -
43A VAL* 3.0 15.4 + - - +
44A GLU* 3.0 43.3 + - + +
46A ARG* 3.0 13.1 + - - +
117A ASN* 3.3 5.3 - - - +
118A PRO* 1.3 76.9 - - - +
120A GLY* 1.3 64.8 + - - +
122A GLU* 3.3 13.0 + - - +
123A LYS* 3.4 20.8 + - - +
138A SER* 3.8 11.5 - - - +
161A GLU* 3.2 6.1 - - - +
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Residues in contact with GLY 120 (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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75A GLY* 3.6 0.2 - - - -
117A ASN* 3.0 22.2 + - - -
119A ASP* 1.3 76.3 - - - +
121A TYR* 1.3 64.7 + - - +
123A LYS* 3.0 14.8 + - - -
124A SER* 2.9 12.8 + - - -
134A GLY* 3.2 31.8 - - - +
136A ASN 3.8 7.2 + - - -
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Residues in contact with TYR 121 (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 HIS* 3.6 26.7 + - - +
14A HIS 3.5 22.7 + - - -
15A HIS* 3.4 27.2 + + - -
72A ASN* 3.6 19.5 - - - +
75A GLY* 3.5 19.8 - - - -
78A VAL* 3.4 26.5 - - + -
81A ARG* 3.5 33.9 - - - +
82A GLU* 3.8 2.6 + - - -
117A ASN 3.3 7.1 + - - +
118A PRO 3.4 9.0 - - - +
119A ASP 3.2 0.4 - - - -
120A GLY* 1.3 75.8 - - - +
122A GLU* 1.3 70.4 + - - +
124A SER* 2.7 32.1 + - - +
278A TYR* 3.6 13.7 + + - -
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Residues in contact with GLU 122 (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 HIS* 2.8 32.2 + - - +
16A PHE* 2.9 36.7 + - - +
46A ARG* 3.7 31.6 - - - +
81A ARG* 4.1 0.5 + - - -
118A PRO 3.3 13.0 + - - +
119A ASP 3.3 7.6 + - - +
120A GLY 3.3 0.8 - - - -
121A TYR* 1.3 90.1 - - - +
123A LYS* 1.3 61.1 + - + +
124A SER 3.2 5.1 + - - +
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Residues in contact with LYS 123 (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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44A GLU* 2.9 39.3 + - - -
46A ARG* 5.3 0.6 - - - +
119A ASP 3.4 16.1 + - - +
120A GLY* 3.0 11.0 + - - +
121A TYR 3.0 0.2 + - - -
122A GLU* 1.3 78.9 - - + +
124A SER* 1.3 62.0 + - - +
125A GLN* 4.4 5.4 - - - +
133A VAL* 3.3 24.5 - - + +
134A GLY* 4.3 10.5 - - - +
136A ASN 5.8 0.7 - - - +
137A ASN 5.1 2.0 - - - -
138A SER* 4.3 22.7 - - - +
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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