Contacts of the strand formed by residues 130 - 140 (chain C) in PDB entry 2QC8
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 TRP 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C HIS* 3.3 9.8 + - - +
129C PRO* 1.3 77.3 - - - +
131C PHE* 1.3 62.7 + - - +
208C PRO* 3.9 28.3 - - + -
209C CYS 3.5 4.5 - - - +
210C GLU* 3.1 34.3 + - + +
256C PHE* 3.5 8.0 - - - -
257C SER 2.9 29.4 + - - +
262C ARG* 3.5 50.2 - - - +
501C ADP 3.5 23.4 - - - +
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Residues in contact with PHE 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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121C MET* 3.7 24.9 - - + -
129C PRO* 4.1 15.5 - - + -
130C TRP* 1.3 74.0 - - - +
132C GLY* 1.3 57.0 + - - +
207C GLY* 3.6 0.2 - - - -
208C PRO* 3.0 5.9 - - - +
209C CYS 2.7 38.4 + - - -
211C GLY 4.0 10.5 - - - -
214C MET* 3.4 26.1 - - + +
254C THR* 4.1 17.7 - - + -
255C ASN 3.3 6.1 - - - +
256C PHE* 3.5 24.9 - + - -
352C THR* 3.6 34.8 - - + -
355C LEU* 3.8 14.4 - - + -
356C ILE* 3.9 18.8 - - + -
501C ADP 3.9 4.7 - - - -
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Residues in contact with GLY 132 (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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131C PHE* 1.3 74.4 - - - +
133C MET* 1.3 60.9 + - - -
206C ILE 3.4 8.5 - - - -
207C GLY* 4.1 0.9 - - - -
253C HIS 3.4 0.3 - - - +
254C THR* 3.5 0.2 - - - -
255C ASN* 2.6 49.2 + - - -
501C ADP 3.5 28.1 + - - -
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Residues in contact with MET 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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132C GLY* 1.3 75.8 - - - +
134C GLU* 1.3 61.8 + - - +
135C GLN* 3.6 3.7 + - - +
204C PHE 3.6 0.5 - - - +
205C GLN* 3.4 2.8 - - - -
206C ILE* 2.9 34.4 + - - +
214C MET* 3.6 38.1 - - + -
218C LEU* 3.7 26.8 - - + +
252C CYS* 3.7 23.3 - - - -
253C HIS 3.4 2.2 - - - -
254C THR* 3.4 31.4 - - + +
346C CYS* 3.9 13.5 - - - -
348C PRO* 3.8 19.7 - - + -
351C VAL* 4.3 6.1 - - + -
352C THR* 4.5 7.0 - - - -
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Residues in contact with GLU 134 (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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133C MET* 1.3 71.6 - - - +
135C GLN* 1.3 59.2 + - - +
136C GLU* 3.2 8.8 + - + +
203C GLU* 2.9 14.1 - - - +
204C PHE 3.6 5.8 - - - -
205C GLN* 4.0 4.0 - - + +
251C GLY 3.3 2.1 - - - +
252C CYS* 3.2 22.4 - - - -
253C HIS* 2.9 26.1 + - + +
255C ASN* 3.3 15.6 + - - +
338C GLU* 2.9 5.2 - - - +
402C MN 2.3 30.8 + - - -
403C MN 2.0 34.5 + - - -
501C ADP 2.7 33.0 + - - +
601C P3S 3.0 1.6 + - - -
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Residues in contact with GLN 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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133C MET 3.6 2.0 + - - -
134C GLU* 1.3 69.7 - - - +
136C GLU* 1.3 82.8 + - - +
137C TYR* 3.9 3.3 - - + -
203C GLU* 3.2 2.5 - - - -
204C PHE* 2.8 73.8 + - + +
218C LEU* 3.8 12.7 - - + +
222C ARG* 2.9 36.0 + - - +
238C PHE* 3.5 20.6 - - + -
251C GLY 4.5 0.2 + - - -
252C CYS* 3.9 7.3 - - - -
344C ALA* 2.9 26.2 + - - +
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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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134C GLU* 3.2 6.9 + - + +
135C GLN* 1.3 91.8 + - - +
137C TYR* 1.3 61.9 + - - +
196C GLU* 3.0 20.0 - - + -
201C GLN* 4.9 3.8 - - + +
202C TRP 3.2 7.2 - - - +
203C GLU* 3.7 12.1 - - + +
238C PHE* 4.1 0.3 - - - -
249C GLY 4.9 0.2 - - - -
250C ALA* 3.8 8.0 - - + -
251C GLY* 3.0 31.6 + - - +
253C HIS* 4.7 3.8 - - - -
344C ALA* 3.5 11.8 - - - +
401C MN 2.1 39.0 + - - +
601C P3S 2.7 34.8 + - - +
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Residues in contact with TYR 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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135C GLN* 3.9 7.2 - - + -
136C GLU* 1.3 78.8 - - - +
138C THR* 1.3 66.4 + - - +
139C LEU* 3.8 32.3 - - + -
175C ILE* 4.7 1.0 - - + +
176C VAL* 3.4 29.5 - - - +
179C HIS* 5.3 1.4 + - - -
201C GLN* 3.3 6.0 - - - +
202C TRP* 2.8 60.7 + + + +
203C GLU 3.9 4.3 + - - -
204C PHE* 3.7 27.1 - + - +
225C LEU* 3.8 34.1 - - + +
236C ALA* 4.3 3.4 - - + -
237C THR 3.5 15.0 - - - +
238C PHE* 3.7 15.3 - - + -
250C ALA* 4.8 3.8 - - - -
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Residues in contact with THR 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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137C TYR* 1.3 80.1 - - - +
139C LEU* 1.3 74.8 + - - +
140C MET* 3.6 12.2 + - - -
146C PRO* 4.5 1.1 - - + -
198C MET* 3.1 34.0 - - + +
200C ALA* 3.6 10.1 - - + +
201C GLN* 3.6 17.5 + - - +
236C ALA* 3.6 1.9 - - - -
237C THR* 3.0 45.6 + - - +
242C PRO* 3.8 14.0 - - + +
250C ALA* 5.0 1.9 - - - +
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Residues in contact with LEU 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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137C TYR* 3.8 24.2 - - + -
138C THR* 1.3 73.6 - - - +
140C MET* 1.3 55.0 + - - +
146C PRO* 3.5 5.4 - - - +
147C PHE* 2.7 39.2 + - + +
171C TYR 4.1 1.6 - - - +
172C GLY* 3.7 35.7 - - - +
175C ILE* 4.2 15.3 - - + -
176C VAL* 5.2 0.7 - - + -
200C ALA* 2.9 22.0 + - + +
202C TRP* 4.0 14.8 - - + -
229C CYS* 3.6 31.4 - - - -
234C VAL* 4.3 7.0 - - + -
235C ILE 3.4 5.4 - - - +
236C ALA* 4.6 1.1 - - - -
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Residues in contact with MET 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C THR* 3.8 9.9 - - - +
139C LEU* 1.3 77.8 - - - +
141C GLY* 1.3 70.4 + - - +
144C GLY* 2.7 35.0 - - - +
145C HIS 4.2 0.4 - - - +
146C PRO* 3.8 22.0 - - + -
147C PHE* 3.7 6.1 - - - +
234C VAL* 3.6 8.1 - - - +
235C ILE* 2.8 44.6 + - + +
237C THR* 3.8 33.9 - - + -
242C PRO* 5.2 9.0 - - + +
243C ILE* 5.1 7.4 - - + -
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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