Contacts of the strand formed by residues 111 - 115 (chain D) in PDB entry 2PY2
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 CYS 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D ASP* 3.3 23.6 - - - +
88D TRP 4.1 1.6 - - - +
89D CYS* 2.0 52.0 - - - -
90D ALA 4.9 0.4 - - - -
104D MET 3.7 0.2 - - - -
105D ASN 3.3 5.1 + - - -
106D VAL* 3.0 27.8 + - - +
109D GLY* 3.8 20.6 - - - +
110D LYS* 1.3 74.0 - - - +
112D TRP* 1.3 68.6 + - - +
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Residues in contact with TRP 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 3.8 30.4 - - + +
48D SER* 5.0 4.4 + - - -
64D ILE* 3.8 5.5 - - + +
77D TRP* 3.8 26.2 - + - -
83D MET* 5.3 2.5 - - - -
85D TYR* 3.7 31.4 - + - -
86D ALA* 3.4 23.3 - - + -
87D ASP* 2.8 42.4 + - + +
88D TRP* 3.6 24.6 - + + -
89D CYS* 2.9 27.3 + - - +
92D GLN* 3.7 1.2 - - - +
102D ILE* 4.0 26.9 - - + -
103D GLN 3.3 5.2 - - - +
104D MET* 3.7 27.8 - - + +
105D ASN 5.0 0.2 - - - -
110D LYS 5.6 0.2 - - - -
111D CYS* 1.3 73.8 - - - +
113D ASN* 1.3 62.2 + - - +
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Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TRP* 4.3 3.4 - - - -
89D CYS* 4.6 5.5 - - - +
92D GLN* 3.1 31.3 - - - +
99D GLU* 4.6 0.5 - - - +
103D GLN 3.0 19.8 + - - +
106D VAL* 3.9 31.3 - - + +
111D CYS 4.0 0.2 + - - -
112D TRP* 1.3 75.3 - - - +
114D ASP* 1.3 70.9 + - - +
115D THR* 3.0 24.0 - - + +
904D CA 2.7 22.2 - - - -
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Residues in contact with ASP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASP* 4.6 0.3 - - - +
75D TRP* 3.8 23.9 - - + -
88D TRP* 4.0 5.7 - - + -
92D GLN* 3.0 2.9 + - - +
93D PRO* 3.7 8.7 - - + +
94D ASP* 3.0 16.6 + - - +
95D THR* 2.9 29.5 + - - -
99D GLU* 3.1 32.9 - - - +
100D CYS 4.5 0.7 - - - -
101D CYS 3.2 9.6 - - - +
102D ILE* 4.5 1.6 - - - +
113D ASN* 1.3 75.2 - - - +
115D THR* 1.3 57.8 + - - +
904D CA 2.5 51.9 - - - -
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TRP* 3.1 18.7 - - - -
99D GLU* 3.5 7.6 + - - -
101D CYS* 2.7 28.7 + - - +
103D GLN* 3.0 35.9 + - + +
113D ASN* 3.0 28.5 - - + +
114D ASP* 1.3 75.4 - - - +
116D PRO* 1.3 80.0 + - - +
117D CYS 3.1 3.1 + - - -
119D HIS* 4.3 8.9 - - - +
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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