Contacts of the strand formed by residues 101 - 106 (chain C) 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 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B GLN* 3.8 10.5 - - - -
25C TRP* 3.4 31.2 - - + -
63C TRP* 3.5 22.5 - - + -
66C GLY 3.7 3.6 - - - -
67C THR* 3.8 5.6 - - - -
69C CYS* 4.0 0.4 - - - -
99C GLU 3.7 0.4 - - - -
100C CYS* 1.3 77.6 - - - +
102C ILE* 1.3 64.6 + - - +
103C GLN 3.6 0.2 + - - -
114C ASP* 3.3 2.0 - - - -
115C THR 2.8 32.3 + - - +
117C CYS* 2.0 46.0 - - - -
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Residues in contact with ILE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TRP* 3.4 7.6 - - - -
64C ILE* 3.2 50.9 + - + +
66C GLY* 2.9 25.9 + - - +
75C TRP* 3.7 23.8 - - + -
77C TRP* 4.5 2.9 - - + -
83C MET* 3.8 28.9 - - + -
88C TRP* 3.7 24.0 - - + -
101C CYS* 1.3 70.7 - - - +
103C GLN* 1.3 70.5 + - - +
112C TRP* 4.0 26.7 - - + -
113C ASN 4.2 2.5 - - - -
114C ASP* 4.5 0.9 - - - +
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PRO* 3.1 25.8 - - - +
62C SER 3.4 17.3 - - - +
63C TRP* 3.9 8.7 - - + -
101C CYS 3.6 0.2 + - - -
102C ILE* 1.3 77.0 - - - +
104C MET* 1.3 64.8 + - - +
106C VAL* 3.4 24.2 - - + +
112C TRP* 3.3 4.2 - - - +
113C ASN 3.0 31.0 + - - +
115C THR* 3.0 33.4 + - + +
121C HIS* 3.2 36.7 + - + -
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Residues in contact with MET 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ILE* 4.1 12.6 - - + -
48C SER* 4.9 1.6 - - - +
51C VAL* 3.8 17.7 - - + -
52C LYS* 3.6 36.8 - - + +
55C THR* 4.6 2.2 - - + -
61C PRO* 3.4 1.9 - - - +
62C SER* 2.8 41.9 + - - +
64C ILE* 3.7 27.7 - - + +
102C ILE 4.2 0.4 + - - -
103C GLN* 1.3 73.2 - - - +
105C ASN* 1.3 88.1 + - + +
106C VAL* 3.2 6.5 + - - +
111C CYS 3.8 4.0 - - - -
112C TRP* 3.8 22.0 - - + +
124C ILE* 4.2 12.3 - - - -
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Residues in contact with ASN 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS* 3.5 34.1 - - - +
55C THR* 3.0 30.7 + - - +
59C LEU* 3.5 19.2 - - - +
60C ILE 3.0 22.7 - - - +
61C PRO* 3.4 17.6 - - + +
104C MET* 1.3 85.5 - - - +
106C VAL* 1.3 61.1 + - - +
107C GLY 3.9 0.5 + - - -
110C LYS* 3.6 33.5 + - + +
111C CYS 3.3 5.1 + - - -
112C TRP* 5.0 0.2 - - - -
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PRO* 5.0 3.1 - - + -
89C CYS* 3.9 10.2 - - - -
103C GLN* 3.4 62.1 - - + +
104C MET 3.7 0.9 - - - +
105C ASN* 1.3 74.6 - - - +
107C GLY* 1.3 73.2 + - - +
109C GLY 4.2 0.3 + - - -
110C LYS 3.2 11.6 + - - -
111C CYS* 3.0 16.4 + - - +
113C ASN* 3.8 31.2 - - + +
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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