Contacts of the helix formed by residues 130 - 139 (chain C) in PDB entry 6Q2J
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 130 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C TRP* 1.3 79.0 - - - +
131C CYS* 1.3 71.0 + - - +
132C LEU* 3.3 4.7 + - - +
133C GLU* 3.4 18.2 + - - +
134C VAL* 3.3 20.3 + - - +
189C CYS* 3.8 1.1 - - - -
190C ASP 3.3 12.1 - - - -
191C CYS* 3.1 22.0 - - - -
195C ASP* 5.3 1.1 + - - -
198C CYS* 3.3 12.5 - - - +
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Residues in contact with CYS 131 (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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130C SER* 1.3 79.4 + - - +
132C LEU* 1.3 57.9 + - - +
133C GLU 3.3 0.2 - - - -
134C VAL* 3.3 3.0 + - - -
135C ALA* 2.9 24.4 + - - +
189C CYS* 2.0 59.9 - - - -
190C ASP* 3.8 4.6 + - - -
191C CYS* 4.6 0.9 - - - -
198C CYS 4.1 15.7 - - - +
201C SER* 4.2 2.6 + - - +
202C LYS* 3.7 30.3 - - + -
205C LEU* 3.4 17.1 - - + +
206C HIS* 4.2 0.4 - - - -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 4.3 18.2 - - + -
285A ILE* 5.7 2.5 - - + -
292A VAL* 4.8 11.0 - - + -
130C SER* 3.3 5.9 + - - +
131C CYS* 1.3 79.5 - - - +
133C GLU* 1.3 64.6 + - + +
135C ALA* 3.3 5.6 + - + +
136C GLU* 2.9 56.4 + - + +
197C PRO* 4.8 20.2 - - + +
198C CYS* 3.7 21.7 - - + +
201C SER* 4.1 14.8 - - - +
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Residues in contact with GLU 133 (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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129C TRP* 4.5 28.4 - - + -
130C SER* 3.4 20.9 + - - +
132C LEU* 1.3 80.6 - - + +
134C VAL* 1.3 60.0 + - - +
136C GLU* 3.4 22.8 + - - +
137C ALA* 2.9 30.7 + - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C TRP* 3.5 21.5 - - + +
130C SER 3.3 14.3 + - - +
131C CYS* 3.3 10.0 + - - +
132C LEU 3.2 0.4 - - - -
133C GLU* 1.3 77.2 - - - +
135C ALA* 1.3 57.3 + - - +
137C ALA* 3.1 5.1 + - - +
138C CYS* 2.9 30.0 + - - +
182C ILE* 5.1 3.0 - - + +
185C MET* 3.4 24.9 - - + +
186C LEU* 3.7 43.5 - - + +
189C CYS* 4.0 8.1 - - + -
205C LEU* 4.1 6.5 - - + -
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Residues in contact with ALA 135 (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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285A ILE* 3.9 21.7 - - + +
294A LEU* 5.0 2.5 - - + -
131C CYS 2.9 16.7 + - - +
132C LEU* 3.3 9.2 + - + +
134C VAL* 1.3 76.6 - - - +
136C GLU* 1.3 61.3 + - - +
137C ALA 3.5 0.5 + - - -
138C CYS* 3.8 1.7 + - - -
139C VAL* 3.3 29.6 + - + +
201C SER* 4.9 9.9 - - - +
205C LEU* 3.7 27.8 - - + +
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Residues in contact with GLU 136 (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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230A LEU* 3.9 29.3 - - + +
231A SER* 3.4 32.2 + - - +
232A PRO* 5.7 0.3 - - - +
233A ARG* 5.8 6.3 - - - -
285A ILE* 5.0 1.8 - - + -
132C LEU* 2.9 37.2 + - + +
133C GLU* 3.8 25.5 - - - +
134C VAL 3.3 0.2 - - - -
135C ALA* 1.3 76.9 - - - +
137C ALA* 1.3 57.3 + - - +
139C VAL 4.5 1.3 - - - -
140C GLY* 4.0 10.9 + - - -
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Residues in contact with ALA 137 (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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129C TRP* 5.4 6.3 - - + -
133C GLU 2.9 17.8 + - - +
134C VAL* 3.1 6.7 + - - +
136C GLU* 1.3 78.5 - - - +
138C CYS* 1.3 63.7 + - - +
139C VAL 3.5 0.2 - - - -
140C GLY* 4.1 4.8 + - - -
141C ASP* 4.1 10.4 + - - +
182C ILE* 4.7 9.9 - - + +
185C MET* 5.2 14.6 - - + -
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Residues in contact with CYS 138 (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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134C VAL 2.9 15.4 + - - +
135C ALA* 3.8 4.7 + - - +
137C ALA* 1.3 77.6 - - - +
139C VAL* 1.3 63.5 + - + +
141C ASP* 2.9 25.9 + - - +
144C CYS* 2.0 62.8 - - - +
145C ASN 3.8 0.4 + - - -
148C LEU* 4.0 20.6 - - + -
174C PHE* 4.6 4.9 - - - -
182C ILE* 4.5 9.8 - - + +
186C LEU* 4.6 9.4 - - + -
205C LEU* 5.8 1.1 - - + -
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Residues in contact with VAL 139 (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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231A SER* 4.3 9.0 - - - +
232A PRO* 3.6 26.5 - - + +
282A MET* 5.4 0.2 - - - +
283A VAL* 3.3 31.2 - - + +
285A ILE* 4.6 11.0 - - + -
294A LEU* 5.6 1.1 - - + -
135C ALA* 3.3 20.5 + - - +
137C ALA 3.5 0.2 - - - -
138C CYS* 1.3 76.5 - - + +
140C GLY* 1.3 62.3 + - - +
141C ASP 3.3 3.7 + - - +
142C VAL* 5.2 0.3 - - - +
145C ASN* 3.5 29.2 + - - +
148C LEU* 3.7 27.8 - - + -
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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