Contacts of the strand formed by residues 113 - 121 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PRO 5.4 5.1 + - - -
6B ARG* 4.9 14.8 - - - +
55B GLN* 3.5 27.9 + - - +
109B TYR* 3.2 5.5 - - - -
110B LYS* 2.8 47.1 + - + +
111B GLY 3.3 0.2 - - - -
112B LYS* 1.3 77.1 - - - +
114B LYS* 1.3 68.8 + - - +
115B ILE* 3.5 15.9 + - + +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 5.1 1.9 + - - -
55B GLN* 4.5 1.0 - - - +
104B ASP* 5.1 3.8 + - - -
106B CYS* 5.4 3.1 - - - -
108B GLY 4.7 0.4 - - - +
109B TYR* 3.6 38.1 - - + +
112B LYS 3.6 4.9 + - - +
113B ARG* 1.3 84.2 + - - +
115B ILE* 1.3 64.5 + - - +
116B HIS* 3.7 47.4 + - + +
1E G 4.8 12.9 + - - +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU 5.3 1.3 - - - +
55B GLN* 3.5 36.8 - - + +
106B CYS* 3.9 1.2 - - - -
107B LEU* 2.9 42.9 + - + -
108B GLY 2.8 27.2 + - - +
109B TYR 4.5 0.2 - - - -
110B LYS* 3.9 40.2 - - + +
113B ARG* 3.6 32.3 - - - +
114B LYS* 1.3 70.2 - - - +
116B HIS* 1.3 62.5 + - - +
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 2.9 40.7 + - - +
55B GLN* 3.4 17.5 + - - +
104B ASP* 2.7 28.5 + - - +
105B ILE 3.0 20.2 - - - +
106B CYS* 4.1 4.7 - - + -
107B LEU* 4.4 4.5 - - - -
114B LYS* 3.7 46.2 + - + +
115B ILE* 1.3 77.7 - - - +
117B THR* 1.3 59.5 + - - +
118B VAL* 3.3 23.2 - - + +
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 2.7 43.2 + - + +
52B LEU* 4.7 3.4 + - - -
54B VAL* 4.3 2.7 - - + -
55B GLN 3.3 18.0 + - - -
56B ALA 3.3 19.1 - - - +
58B LEU* 3.8 25.8 - - + -
103B ILE 3.9 1.4 - - - +
104B ASP* 3.8 0.3 - - - -
105B ILE* 2.8 38.8 + - - +
107B LEU* 4.7 1.8 - - - +
116B HIS* 1.3 71.7 - - - +
118B VAL* 1.3 63.3 + - - +
119B ILE* 4.6 2.0 - - + -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 4.1 5.4 - - - +
56B ALA 3.1 5.3 + - - +
57B ASP* 3.3 15.0 - - - +
58B LEU* 2.8 31.9 + - - +
102B MET* 3.6 27.1 - - + -
103B ILE 3.5 3.4 - - - +
104B ASP* 3.5 10.5 - - + +
116B HIS* 3.3 37.9 - - + +
117B THR* 1.3 72.9 - - - +
119B ILE* 1.3 57.7 - - - +
120B TYR* 3.3 34.7 - - + +
2E G 5.3 0.7 - - - +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 6.1 0.2 - - + -
51B VAL* 4.7 5.6 - - + -
58B LEU* 3.3 27.1 - - + +
60B PHE* 3.6 31.0 - - + -
63B LEU* 3.7 18.5 - - + +
70B ILE* 3.8 27.6 - - + -
102B MET* 3.2 8.0 - - - +
103B ILE* 2.8 47.4 + - + +
105B ILE* 3.9 26.2 - - + -
117B THR* 4.6 2.7 - - + -
118B VAL* 1.3 78.7 - - - +
120B TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASP* 4.0 26.4 + - + -
58B LEU 2.7 11.1 + - - -
59B TYR* 3.4 42.7 - + + -
60B PHE* 3.1 24.4 + - - +
63B LEU* 3.8 8.8 - - - +
101B TYR 3.6 16.6 - - - -
102B MET* 4.0 9.0 - - + -
118B VAL* 3.3 32.7 - - + +
119B ILE* 1.3 78.0 - - - +
121B ASP* 1.3 61.8 + - - +
122B SER 3.9 0.2 - - - -
188B MET* 4.2 31.2 - - + -
2E G 3.4 17.0 + - - -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 4.4 2.8 - - - -
60B PHE 3.2 3.0 - - - +
62B ASN* 2.9 30.3 + - - +
63B LEU* 3.1 26.1 + - + +
64B LYS 4.9 1.4 + - - -
100B TRP* 3.5 14.1 - - - +
101B TYR 3.9 4.7 + - - +
120B TYR* 1.3 75.1 - - - +
122B SER* 1.3 62.9 + - - +
123B LEU* 3.0 16.1 + - - +
124B LYS* 2.8 50.6 + - + +
125B LYS* 3.9 6.4 + - - +
188B MET 4.7 1.0 - - - +
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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