Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 1MQ0
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 ALA 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 19.7 - - + -
42A LEU* 3.4 6.4 - - - +
43A LEU* 2.8 33.3 + - + +
82A PHE 3.5 2.0 - - - -
83A ARG* 1.3 82.9 - - - +
85A ILE* 1.3 62.0 + - - +
113A TRP* 3.7 6.8 - - - -
114A PRO* 3.4 27.6 - - + +
116A TYR* 4.0 7.2 - - + -
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Residues in contact with ILE 85 (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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18A LEU* 4.4 3.6 - - - -
40A ALA* 4.3 5.4 - - + -
41A ALA 3.2 18.4 - - - +
42A LEU* 4.3 14.4 - - + -
67A GLU* 3.9 40.6 - - + +
70A ALA* 5.0 0.4 - - + -
71A ILE* 4.7 4.9 - - + -
84A ALA* 1.3 79.0 - - - +
86A ALA* 1.3 64.2 + - - +
87A ILE* 5.0 1.1 - - + -
106A MET* 4.0 14.1 - - + -
113A TRP* 3.5 21.3 - - + -
114A PRO 3.2 8.7 + - - +
115A VAL* 4.0 18.9 - - + +
116A TYR* 2.7 31.7 + - - +
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Residues in contact with ALA 86 (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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18A LEU* 3.7 40.6 - - + +
19A LEU 4.7 0.2 - - - +
22A SER* 3.4 7.1 - - - +
40A ALA* 3.2 6.8 - - - +
41A ALA 3.0 30.6 + - - +
85A ILE* 1.3 75.9 - - - +
87A ILE* 1.3 62.0 + - - +
116A TYR* 3.3 20.4 - - + +
118A THR* 4.6 6.5 - - + -
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Residues in contact with ILE 87 (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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22A SER* 4.3 0.7 - - - -
38A VAL* 3.8 23.6 - - + -
39A GLY 3.4 4.9 - - - +
40A ALA* 5.4 0.4 - - + -
67A GLU* 3.7 26.0 - - + +
85A ILE* 5.0 3.4 - - + -
86A ALA* 1.3 77.7 - - - +
88A ALA* 1.3 57.5 + - - +
96A ILE* 2.9 33.4 - - + +
98A PRO* 3.6 45.3 - - + -
106A MET* 4.7 0.7 - - + -
115A VAL* 4.0 15.5 - - + -
116A TYR 2.9 9.4 + - - +
117A MET* 4.8 0.7 - - + -
118A THR* 2.6 32.9 + - - +
148A BRD 4.4 2.2 - - - -
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Residues in contact with ALA 88 (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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22A SER* 3.6 25.8 - - - +
23A GLN* 3.5 31.0 - - - +
26A LYS* 4.5 4.5 - - + -
38A VAL* 3.2 10.4 - - - +
39A GLY 2.9 28.1 + - - +
87A ILE* 1.3 77.5 - - - +
89A SER* 1.3 62.5 + - - +
96A ILE* 3.2 6.3 - - - -
118A THR* 3.7 5.2 - - - +
119A LYS 6.5 0.2 - - - -
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Residues in contact with SER 89 (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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23A GLN* 4.5 0.9 - - - +
26A LYS* 3.4 13.9 + - - -
36A PHE* 4.0 11.9 - - - -
37A PRO 3.6 14.8 - - - -
38A VAL* 4.7 0.4 - - - -
88A ALA* 1.3 76.0 - - - +
90A ASP* 1.3 58.9 + - - +
91A MET* 3.0 27.0 + - - +
96A ILE* 2.8 37.2 - - - +
118A THR* 5.0 1.9 + - - -
119A LYS* 6.2 0.6 - - - +
120A PRO* 3.3 20.3 - - - +
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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