Contacts of the strand formed by residues 113 - 120 (chain C) in PDB entry 2ZT9
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 ILE 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C THR* 5.1 5.2 - - - +
13C PRO* 3.8 30.3 - - + -
75C VAL* 4.1 9.6 - - + -
76C LEU 3.6 2.0 - - - -
77C MET* 4.0 29.4 - - + +
78C LEU 5.5 0.4 - - - +
105C PRO* 3.5 3.1 - - - +
106C TYR* 3.0 41.7 + - + -
110C LYS* 3.1 39.2 + - + +
112C ASN* 1.3 91.3 - - - +
114C VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA 3.7 1.0 - - - +
75C VAL* 3.4 4.5 - - - -
76C LEU* 2.8 43.1 + - + +
78C LEU* 4.4 10.3 - - + -
84C ILE* 3.6 39.0 - - + -
103C PHE* 4.1 8.5 - - + -
104C GLN 3.6 11.4 - - - +
105C PRO* 5.6 0.9 - - + -
111C ASP 3.6 19.7 - - - +
112C ASN 4.0 7.4 - - - +
113C ILE* 1.3 75.8 - - - +
115C ILE* 1.3 70.0 + - - +
129C PHE* 3.9 18.7 - - + -
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Residues in contact with ILE 115 (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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2C PRO* 3.2 45.1 - - + +
6C GLN* 3.5 24.2 - - - +
74C ALA 3.7 3.1 - - - -
75C VAL* 4.5 8.5 - - + +
102C TYR 4.0 0.3 - - - +
103C PHE* 3.7 0.9 - - - -
104C GLN* 2.9 62.7 + - + +
105C PRO 5.0 1.1 - - - +
106C TYR* 3.5 35.2 - - + -
113C ILE 4.0 2.0 + - - -
114C VAL* 1.3 72.5 - - - +
116C VAL* 1.3 71.4 + - - +
117C GLY* 4.0 3.1 - - - +
301C HEM 5.1 0.4 - - + -
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Residues in contact with VAL 116 (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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2C PRO* 3.4 3.9 - - - +
73C GLY* 3.2 3.3 - - - -
74C ALA 2.8 35.6 + - - +
101C VAL* 3.6 15.7 - - + -
102C TYR 4.4 2.5 - - - +
103C PHE* 3.5 33.2 - - + +
115C ILE* 1.3 81.8 - - - +
117C GLY* 1.3 63.1 + - - +
119C LEU* 3.6 29.8 - - + -
127C ILE* 4.0 18.4 - - + -
129C PHE* 3.9 15.9 - - + -
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Residues in contact with GLY 117 (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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2C PRO* 3.6 15.7 - - - +
3C PHE* 5.6 2.9 - - - -
72C VAL 3.6 4.6 - - - +
102C TYR 4.7 5.5 + - - -
104C GLN* 5.0 4.8 + - - -
115C ILE* 4.0 6.7 - - - +
116C VAL* 1.3 78.9 - - - +
118C PRO* 1.4 78.6 - - - +
119C LEU* 3.4 12.0 + - - +
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Residues in contact with PRO 118 (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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1C TYR* 3.4 36.8 - - + -
2C PRO* 4.3 6.2 - - + -
3C PHE* 4.7 11.9 - - + -
71C ASN* 4.4 19.1 - - + +
72C VAL 3.5 6.7 - - - +
117C GLY* 1.4 83.1 - - - +
119C LEU* 1.3 63.4 + - - +
120C PRO* 4.7 1.4 - - - +
301C HEM 4.4 6.7 - - + -
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Residues in contact with LEU 119 (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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71C ASN* 3.2 6.7 - - - +
72C VAL* 2.8 40.8 + - + +
100C ASP* 4.0 17.7 - - + +
101C VAL* 4.1 12.6 - - + -
102C TYR 5.6 0.9 - - - +
116C VAL* 3.6 29.8 - - + -
117C GLY 3.7 4.7 - - - +
118C PRO* 1.3 78.1 - - - +
120C PRO* 1.3 71.5 - - + +
121C GLY 3.0 0.7 + - - -
124C TYR* 3.8 43.7 - - + -
127C ILE* 3.9 19.1 - - + -
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Residues in contact with PRO 120 (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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70C LEU 4.4 0.2 - - - +
71C ASN* 3.6 10.7 - - - +
118C PRO 4.7 1.3 - - - +
119C LEU* 1.3 85.1 - - + -
121C GLY* 1.3 58.7 + - - +
122C GLU* 2.9 12.0 + - + +
123C GLN* 3.3 38.7 + - - +
124C TYR* 3.3 22.4 + - + +
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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