Contacts of the helix formed by residues 122 - 126 (chain C) in PDB entry 2Z9I
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 SER 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C VAL* 5.8 0.3 - - - +
20C VAL 4.2 2.1 + - - -
21C MSE 3.5 35.0 + - - +
32C GLU* 2.7 37.9 - - - +
33C GLY 4.2 0.2 - - - -
34C SER* 3.0 14.8 + - - -
121C GLY* 1.3 74.8 - - - -
123C PRO* 1.4 66.8 - - - +
124C LEU 3.2 0.9 + - - -
125C GLY 3.0 5.8 + - - -
126C LEU 3.3 5.8 - - - -
127C GLU* 3.5 19.1 - - - +
128C GLY 4.0 1.2 + - - -
167C GLY* 3.5 6.7 + - - -
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Residues in contact with PRO 123 (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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204B LEU* 3.8 21.5 - - + -
121C GLY 3.3 10.1 - - - +
122C SER* 1.4 84.2 - - - +
124C LEU* 1.3 61.5 + - + +
126C LEU* 2.8 34.2 + - + +
129C THR* 3.6 24.7 - - + +
163C ALA 5.9 0.4 - - - +
165C ASN* 3.7 16.6 - - + -
166C PRO 3.2 9.0 - - - +
167C GLY* 3.9 3.5 - - - -
168C ASN* 3.1 31.0 - - - +
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Residues in contact with LEU 124 (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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188B ALA* 4.3 17.3 - - + -
189B THR 3.7 28.0 - - - +
190B LEU* 3.8 29.2 - - + -
202B ILE* 4.4 5.6 - - + -
204B LEU* 3.7 17.0 - - + -
32C GLU* 4.3 4.2 + - - -
122C SER 3.2 0.8 + - - -
123C PRO* 1.3 70.8 - - - +
125C GLY* 1.3 58.3 + - - +
126C LEU* 3.0 18.9 + - + +
165C ASN* 3.9 12.8 - - + -
166C PRO* 2.9 25.4 + - + +
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Residues in contact with GLY 125 (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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21C MSE 4.0 16.3 - - - +
32C GLU* 3.5 20.4 + - - -
122C SER 3.0 10.6 + - - -
124C LEU* 1.3 77.6 - - - +
126C LEU* 1.3 60.8 + - - +
127C GLU* 3.2 8.5 + - - +
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Residues in contact with LEU 126 (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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140B ARG* 3.7 38.4 - - + +
141B PRO 5.8 1.1 - - - +
142B VAL* 5.9 0.9 - - + -
159B GLN* 4.0 13.2 - - - +
188B ALA* 4.5 6.5 - - + -
204B LEU* 4.3 20.2 - - + -
206B PHE* 3.9 24.9 - - + -
121C GLY 3.3 0.5 - - - +
122C SER* 3.3 15.6 + - - -
123C PRO* 2.8 16.6 + - - +
124C LEU* 3.0 10.2 - - + +
125C GLY* 1.3 76.5 - - - +
127C GLU* 1.3 65.7 + - - +
129C THR* 3.0 24.3 + - - +
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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