Contacts of the strand formed by residues 55 - 62 (chain A) in PDB entry 1Q8R
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 VAL 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.5 15.7 - - + -
53A MET* 3.6 11.9 - - - +
54A PRO* 1.3 79.6 - - - +
56A LYS* 1.3 61.9 + - - +
57A ILE* 5.5 0.2 - - + -
88A TRP* 3.9 32.1 - - + -
93A GLN* 3.0 20.4 + - + +
94A VAL* 3.5 11.4 - - + -
95A VAL* 3.0 26.7 + - - +
96A ASP 3.9 0.5 + - - +
114A ILE* 3.9 18.8 - - + -
115A THR 3.3 11.9 - - - +
116A GLU* 4.2 8.5 - - - -
117A MET* 3.9 6.3 - - - -
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Residues in contact with LYS 56 (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 VAL* 1.3 73.6 - - - +
57A ILE* 1.3 68.6 + - - +
96A ASP* 3.2 26.0 - - + +
113A THR 3.8 0.6 - - - +
114A ILE* 3.3 5.2 - - - +
115A THR* 2.9 56.9 + - - +
117A MET* 3.7 29.2 - - + +
98B ARG* 3.7 26.2 - - - +
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Residues in contact with ILE 57 (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 VAL* 5.5 0.4 - - + -
56A LYS* 1.3 80.9 - - - +
58A ARG* 1.3 70.5 + - - +
59A ILE* 3.9 17.7 - - + -
78A ALA* 6.1 0.4 - - + -
79A PHE* 4.0 19.3 - - + -
82A LEU* 4.4 2.0 - - + -
88A TRP* 4.3 13.0 - - + -
94A VAL* 3.7 20.0 - - + -
96A ASP* 2.9 8.4 + - - +
97A TYR* 3.2 27.4 - - + -
98A ARG* 3.0 24.8 + - - +
112A LEU* 4.2 19.1 - - + -
113A THR 3.2 10.8 - - - +
114A ILE* 3.9 22.7 - - + -
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Residues in contact with ARG 58 (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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56A LYS* 5.3 0.2 - - - +
57A ILE* 1.3 75.3 - - - +
59A ILE* 1.3 67.2 + - - +
60A GLU* 3.1 35.2 + - + +
98A ARG* 3.4 42.4 - - + +
100A VAL* 3.8 32.4 - - + +
102A MET* 4.9 3.4 - - - +
111A GLU 3.6 1.6 - - - +
112A LEU* 3.3 6.6 - - - -
113A THR* 2.9 46.4 + - - +
96B ASP* 5.7 0.2 + - - -
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Residues in contact with ILE 59 (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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57A ILE* 3.9 17.5 - - + -
58A ARG* 1.3 77.8 - - - +
60A GLU* 1.3 63.4 + - - +
61A CYS* 3.7 18.5 + - - -
74A LEU 5.1 4.5 - - - +
75A GLN* 3.9 21.3 - - + -
78A ALA* 5.3 4.3 - - + -
79A PHE* 3.6 32.8 - - + -
97A TYR* 5.0 2.2 - - + -
98A ARG 2.7 12.5 + - - +
99A VAL* 3.3 15.3 - - + +
100A VAL 2.9 26.2 + - - -
110A LEU* 4.3 24.9 - - + -
111A GLU 3.8 2.5 - - - -
112A LEU* 4.6 8.1 - - + -
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Residues in contact with GLU 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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58A ARG* 3.1 44.4 + - - +
59A ILE* 1.3 72.3 - - - +
61A CYS* 1.3 61.0 + - - +
62A HIS* 3.2 25.1 + - + +
100A VAL* 3.5 6.1 - - + -
102A MET* 3.7 29.2 - - + +
110A LEU* 3.3 8.1 - - - +
111A GLU* 2.9 48.8 + - + +
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Residues in contact with CYS 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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10A TRP* 4.1 6.7 - - + -
59A ILE* 4.1 6.7 - - - -
60A GLU* 1.3 71.2 - - - +
62A HIS* 1.3 60.9 + - - +
63A MET* 3.3 25.5 + - - +
71A LEU* 3.9 6.5 - - + -
74A LEU* 3.8 22.0 - - + -
99A VAL* 3.7 30.3 - - - -
100A VAL 2.8 12.3 + - - +
102A MET* 2.8 26.0 + - - +
109A ARG 4.0 3.4 - - - -
110A LEU* 4.0 14.6 - - - -
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Residues in contact with HIS 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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10A TRP* 3.6 3.0 - - - -
60A GLU* 3.2 40.8 + - + +
61A CYS* 1.3 69.2 - - - +
63A MET* 1.4 60.8 + - - +
102A MET* 3.6 23.3 - - + +
103A PRO* 3.7 14.0 + - + +
105A THR* 3.7 19.4 - - + +
108A GLY* 3.1 9.4 - - - -
109A ARG* 2.9 57.9 + - + +
111A GLU* 3.4 32.3 + - + -
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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