Contacts of the strand formed by residues 113 - 121 (chain A) in PDB entry 2PY5
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 ARG 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN* 5.0 3.4 - - - +
109A TYR* 3.2 8.9 - - - +
110A LYS* 2.9 39.2 + - + +
111A GLY 3.3 0.2 - - - -
112A LYS* 1.3 104.4 - - - +
114A LYS* 1.3 62.6 + - - +
115A ILE* 3.6 16.4 + - + +
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Residues in contact with LYS 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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6A ARG* 5.1 2.6 + - - -
55A GLN* 4.2 5.4 - - - +
85A GLY* 3.8 11.9 + - - -
104A ASP* 5.8 2.2 - - - -
106A CYS* 2.6 45.1 - - - +
108A GLY 4.0 2.9 - - - +
109A TYR* 3.5 38.2 + - + +
112A LYS 3.9 2.4 + - - -
113A ARG* 1.3 71.6 - - - +
115A ILE* 1.3 64.9 + - - +
116A HIS* 3.7 38.2 + - + +
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Residues in contact with ILE 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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52A LEU 4.6 4.9 - - - +
53A LYS* 6.1 0.2 - - - -
55A GLN* 3.5 42.6 - - + +
106A CYS* 3.8 1.9 - - - -
107A LEU* 2.9 50.3 + - + -
108A GLY 2.8 23.5 + - - +
109A TYR 4.3 0.2 - - - -
110A LYS* 3.8 39.5 - - + +
113A ARG* 3.7 29.4 - - + +
114A LYS* 1.3 69.4 - - - +
116A HIS* 1.3 64.8 + - - +
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Residues in contact with HIS 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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6A ARG* 2.9 44.5 + - - -
55A GLN* 3.3 15.6 + - - +
104A ASP* 2.8 31.1 + - - +
105A ILE 3.1 18.4 - - - +
106A CYS* 4.1 4.5 - - - -
107A LEU* 4.4 4.9 - - - -
114A LYS* 3.7 35.9 + - + +
115A ILE* 1.3 78.6 - - - +
117A THR* 1.3 61.2 + - - +
118A VAL* 3.2 23.7 - - + +
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Residues in contact with THR 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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51A VAL* 2.6 47.8 + - + +
52A LEU* 4.7 2.6 + - - -
54A VAL* 4.4 1.1 - - + -
55A GLN 3.3 20.1 + - - -
56A ALA 3.4 15.7 - - - +
58A LEU* 3.7 24.5 - - + -
103A ILE 3.9 1.2 - - - +
104A ASP* 3.7 0.4 - - - -
105A ILE* 2.9 37.2 + - - +
107A LEU* 4.9 2.1 - - - +
116A HIS* 1.3 71.8 - - - +
118A VAL* 1.3 65.0 + - - +
119A ILE* 4.5 1.8 - - + -
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Residues in contact with VAL 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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6A ARG* 4.2 5.6 - - - +
56A ALA 3.1 6.3 + - - +
57A ASP* 3.4 9.6 - - - +
58A LEU* 2.8 32.4 + - - +
102A MET* 3.5 29.4 - - + -
103A ILE 3.6 2.9 - - - +
104A ASP* 3.3 9.0 - - + +
116A HIS* 3.2 35.4 - - + +
117A THR* 1.3 72.7 - - - +
119A ILE* 1.3 59.0 + - - +
120A TYR* 3.4 38.1 - - + +
2D G 4.9 2.7 - - - +
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Residues in contact with ILE 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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51A VAL* 4.6 5.4 - - + -
58A LEU* 3.3 26.9 - - + +
60A PHE* 3.6 32.3 - - + -
63A LEU* 3.8 16.8 - - + +
70A ILE* 3.8 27.4 - - + -
102A MET* 3.2 7.4 - - - +
103A ILE* 2.7 50.7 + - + +
105A ILE* 3.9 24.2 - - + -
117A THR* 4.5 5.6 - - + +
118A VAL* 1.3 78.7 - - - +
120A TYR* 1.3 64.0 + - - +
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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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57A ASP* 4.1 25.8 + - + -
58A LEU 2.7 12.1 + - - -
59A TYR* 3.4 43.0 - + + -
60A PHE* 3.1 24.9 + - - +
63A LEU* 4.0 7.6 - - - +
101A TYR 3.7 16.2 - - - +
102A MET* 4.1 7.9 - - + -
118A VAL* 3.4 28.9 - - + +
119A ILE* 1.3 80.3 - - - +
121A ASP* 1.3 61.6 + - - +
122A SER 3.9 0.4 - - - -
188A MET* 4.1 34.0 - - + +
2D G 3.3 20.1 + - - -
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Residues in contact with ASP 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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59A TYR* 4.4 2.9 - - - -
60A PHE 3.2 2.6 - - - +
62A ASN* 2.9 30.3 + - - +
63A LEU* 3.0 25.9 + - + -
64A LYS* 4.9 1.6 + - - +
100A TRP* 3.4 14.1 - - - +
101A TYR 3.8 6.1 + - - +
120A TYR* 1.3 74.7 - - - +
122A SER* 1.3 64.1 + - - +
123A LEU* 3.1 20.7 + - - +
124A LYS* 2.8 50.4 + - + +
125A LYS* 3.8 6.6 + - - +
188A MET* 4.7 1.6 - - - +
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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