Contacts of the helix formed by residues 116 - 121 (chain A) in PDB entry 2ZPB
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 ALA 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLN 3.3 10.3 - - - +
94A ILE* 4.4 4.0 - - + -
115A THR* 1.3 72.1 - - - +
117A TRP* 1.3 65.4 + - - +
118A PRO* 3.2 4.7 - - + -
119A ILE* 3.2 22.5 + - + -
120A LEU* 2.9 24.8 + - + +
167A ARG* 3.8 19.9 - - + +
168A TYR 3.6 25.8 + - - +
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Residues in contact with TRP 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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47A PHE* 4.1 7.4 - + - -
51A PHE* 3.3 29.4 - + + +
89A PRO* 3.8 9.9 - - + +
90A GLN* 3.3 29.7 + - + +
113A SER* 5.2 1.2 + - - -
115A THR* 2.8 26.4 + - + +
116A ALA* 1.3 71.8 - - - +
118A PRO* 1.4 66.9 - - + +
121A GLY* 2.8 34.7 + - - -
122A LEU* 3.4 19.7 - - + -
123A PRO* 3.6 27.3 - - + +
301A NO 5.1 9.0 + - - -
37B TYR* 3.4 42.0 + + - -
40B MET* 4.4 5.4 - - + -
41B PHE* 3.6 37.2 - + - -
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Residues in contact with PRO 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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51A PHE* 3.6 20.6 - - + -
52A SER 3.4 9.6 + - - -
55A ARG* 3.0 35.5 + - - +
86A TYR 3.3 21.3 - - - +
87A LEU 4.5 0.2 - - - -
88A GLY* 3.7 24.9 - - - +
89A PRO 3.4 23.3 - - - +
90A GLN 3.8 6.1 - - - +
91A GLY* 3.8 7.2 - - - -
116A ALA* 3.4 5.6 - - + -
117A TRP* 1.4 88.3 - - - +
119A ILE* 1.3 58.8 + - + +
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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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52A SER 3.1 12.8 - - - +
53A PRO* 3.4 3.5 - - - +
55A ARG* 4.1 6.3 - - + -
56A GLY* 3.0 32.8 + - - +
59A LEU* 3.9 16.2 - - + -
81A VAL* 4.1 6.3 - - + -
86A TYR* 3.8 32.3 - - + +
94A ILE* 4.2 22.7 - - + -
116A ALA* 3.7 24.9 - - + +
118A PRO* 1.3 80.1 - - + +
120A LEU* 1.3 64.9 + - + +
169A MET* 3.9 37.0 - - + -
195A LEU* 3.9 0.3 - - - +
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Residues in contact with LEU 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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53A PRO* 3.4 21.7 - - - +
56A GLY* 5.3 0.4 - - - -
107A ILE* 4.9 3.8 - - + -
115A THR* 4.2 14.4 - - + -
116A ALA* 2.9 15.0 + - + +
119A ILE* 1.3 91.1 - - + +
121A GLY* 1.3 63.4 + - - +
168A TYR 4.1 15.3 - - - +
169A MET* 3.9 22.7 - - + -
192A LYS* 2.8 24.1 + - + +
195A LEU* 3.8 33.9 - - + +
196A ILE* 3.8 29.6 - - + -
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Residues in contact with GLY 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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51A PHE 3.8 20.0 - - - -
52A SER* 3.8 6.3 - - - -
53A PRO* 4.2 2.2 - - - -
115A THR* 3.4 18.2 - - - +
117A TRP* 2.8 19.7 + - - +
119A ILE 3.7 1.0 - - - -
120A LEU* 1.3 81.1 - - - +
122A LEU* 1.3 69.9 + - - +
192A LYS* 3.7 4.0 + - - -
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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