Contacts of the strand formed by residues 112 - 122 (chain A) in PDB entry 1QMR
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 SER 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 3.9 1.6 - - - +
11A SER* 3.0 34.2 + - - +
13A ILE 2.9 18.2 + - - -
15A ALA* 3.8 12.8 - - - -
18A LEU* 3.5 20.4 - - - +
104A ILE* 4.0 11.7 - - - +
105A VAL 3.1 13.5 - - - -
107A THR* 3.7 5.5 + - - +
111A GLY* 1.3 76.1 - - - -
113A ILE* 1.3 70.4 + - - +
114A LEU* 4.3 0.5 - - - +
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Residues in contact with ILE 113 (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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8A GLU* 4.1 23.8 - - + +
9A THR 3.6 5.4 - - - +
10A THR* 3.1 34.1 - - + +
103A LYS 3.5 1.4 - - - +
104A ILE* 3.4 2.9 - - - +
105A VAL* 2.7 39.5 + - + +
107A THR* 3.4 22.0 - - + -
112A SER* 1.3 80.9 - - - +
114A LEU* 1.3 74.7 + - - +
115A LYS* 3.9 19.2 + - - +
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Residues in contact with LEU 114 (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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8A GLU* 3.3 6.8 - - - -
9A THR* 2.9 58.3 + - + +
11A SER* 4.1 14.6 - - - -
18A LEU* 3.7 22.7 - - + -
22A PHE* 4.0 32.8 - - + -
102A ILE* 4.4 8.7 - - + -
103A LYS 3.4 4.5 - - - +
104A ILE* 3.9 21.3 - - + -
112A SER* 4.3 1.8 - - - +
113A ILE* 1.3 78.3 - - - +
115A LYS* 1.3 62.0 + - - +
116A ILE* 3.6 11.4 + - + +
144A LEU* 4.3 11.2 - - + -
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Residues in contact with LYS 115 (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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7A THR 3.8 4.3 - - - -
8A GLU* 4.0 24.8 + - + +
101A GLU* 3.6 2.3 - - - +
102A ILE* 3.5 3.6 - - - -
103A LYS* 2.8 63.5 + - + +
105A VAL* 3.6 29.3 - - - +
113A ILE* 4.2 13.3 - - + +
114A LEU* 1.3 72.5 - - - +
116A ILE* 1.3 59.8 + - - +
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Residues in contact with ILE 116 (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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5A TYR 4.1 0.4 - - - +
6A GLU* 3.2 5.7 - - - +
7A THR* 2.8 61.4 + - + +
9A THR* 3.9 25.6 - - + -
100A ASN* 5.9 0.9 - - + -
101A GLU 3.5 5.8 - - - +
102A ILE* 4.6 20.4 - - + -
114A LEU* 4.0 15.0 - - + +
115A LYS* 1.3 78.0 - - - +
117A SER* 1.3 64.7 + - - +
118A ASN* 3.9 22.4 - - - +
137A LYS* 6.4 1.3 - - - -
140A GLY* 5.8 10.1 - - - -
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Residues in contact with SER 117 (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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4A ASN* 2.7 34.0 + - - -
5A TYR 3.6 3.6 - - - -
6A GLU* 4.0 12.6 + - - +
99A SER 3.8 0.3 - - - +
100A ASN* 3.2 5.9 - - - +
101A GLU* 2.9 46.0 + - - +
115A LYS 4.3 0.2 + - - -
116A ILE* 1.3 75.3 - - - +
118A ASN* 1.3 63.4 + - - +
119A LYS* 4.2 5.1 + - - -
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Residues in contact with ASN 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PHE 3.5 2.3 - - - +
4A ASN* 3.5 2.7 - - - -
5A TYR* 2.9 40.2 + - + +
7A THR* 5.4 0.6 - - - +
83A TYR* 5.4 0.3 + - - -
98A ILE* 4.4 1.1 - - + -
100A ASN* 2.7 32.8 + - - +
116A ILE* 3.9 19.0 - - - +
117A SER* 1.3 77.1 + - - +
119A LYS* 1.3 61.5 + - - +
120A TYR* 3.8 22.8 + - + +
133A VAL* 5.4 1.2 + - - +
136A SER* 3.9 24.0 + - - -
137A LYS* 4.2 19.0 - - - +
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Residues in contact with LYS 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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2A VAL* 3.3 34.1 - - + -
3A PHE 3.3 6.7 - - - +
4A ASN* 3.8 21.3 - - - +
97A LYS* 3.8 0.9 - - - +
98A ILE* 3.3 4.8 - - - -
99A SER* 2.7 56.2 + - - +
100A ASN* 4.3 0.2 - - - +
117A SER* 4.2 4.4 + - - -
118A ASN* 1.3 72.1 - - - +
120A TYR* 1.3 62.2 + - - +
121A HIS* 4.0 1.0 + - + -
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Residues in contact with TYR 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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1A GLY 3.5 1.7 - - - +
2A VAL* 3.3 6.4 - - - +
3A PHE* 2.8 45.8 + - + +
5A TYR* 3.8 22.4 - + + -
95A LEU* 3.9 11.0 - - + -
97A LYS 3.8 2.9 - - - -
98A ILE* 3.5 37.1 - - + +
118A ASN* 3.8 25.5 + - + +
119A LYS* 1.3 77.2 - - - +
121A HIS* 1.3 60.2 + - - +
122A THR* 3.7 3.2 + - + +
128A VAL* 3.8 30.5 - - + -
132A GLN* 3.4 31.6 + - + -
133A VAL* 4.0 16.7 - - + -
136A SER* 4.0 16.5 + - - -
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Residues in contact with HIS 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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1A GLY 3.5 11.9 + - - -
2A VAL* 4.5 13.2 - - + +
95A LEU* 3.2 4.8 - - - +
96A GLU* 2.5 70.1 + - + +
97A LYS* 3.0 25.3 + - + +
119A LYS* 4.0 1.0 + - + -
120A TYR* 1.3 70.9 - - - +
122A THR* 1.3 77.6 + - - +
123A LYS* 5.5 0.6 - - - -
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Residues in contact with THR 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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1A GLY 2.7 38.6 + - - -
3A PHE* 3.4 15.2 - - + -
94A THR 3.1 11.9 - - - +
95A LEU* 3.9 8.1 - - + -
96A GLU* 5.5 0.9 - - - -
120A TYR 4.3 2.7 - - - +
121A HIS* 1.3 92.8 + - - +
123A LYS* 1.3 58.4 + - - +
124A GLY 3.6 0.7 + - - -
126A HIS* 2.7 31.0 + - - +
127A GLU 4.8 0.7 - - - +
128A VAL* 3.7 30.1 - - + -
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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