Contacts of the strand formed by residues 130 - 141 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128G HIS* 3.3 12.6 + - + +
129G PRO* 1.3 77.9 - - - +
131G PHE* 1.3 61.9 + - - +
208G PRO* 4.0 26.2 - - + -
209G CYS 3.5 3.6 - - - +
210G GLU* 3.2 32.6 + - - +
256G PHE* 3.3 9.9 - - - -
257G SER* 2.8 37.6 + - - +
262G ARG* 3.4 53.0 - - - +
501G ADP 3.5 16.9 - + + +
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Residues in contact with PHE 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G MET* 3.7 26.0 - - + -
129G PRO* 4.2 13.2 - - + -
130G TRP* 1.3 74.2 - - - +
132G GLY* 1.3 57.9 + - - +
207G GLY* 3.6 0.2 - - - -
208G PRO* 3.3 2.6 - - - +
209G CYS 2.8 36.7 + - - -
211G GLY* 4.2 4.3 - - - -
214G MET* 3.4 32.3 - - + +
254G THR* 4.0 16.2 - - + -
255G ASN 3.2 5.4 - - - +
256G PHE* 3.2 35.4 - + - -
352G THR* 3.7 32.1 - - + -
355G LEU* 3.6 19.5 - - + -
356G ILE* 3.7 15.3 - - + -
501G ADP 4.0 4.3 - - - -
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Residues in contact with GLY 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G PHE* 1.3 75.5 - - - +
133G MET* 1.3 60.6 + - - -
206G ILE 3.3 9.4 - - - -
207G GLY* 4.0 1.3 - - - -
255G ASN* 2.7 46.7 + - - -
501G ADP 3.6 28.5 + - - -
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Residues in contact with MET 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G GLY* 1.3 79.2 - - - +
134G GLU* 1.3 61.5 + - - +
135G GLN* 3.7 3.2 + - - +
205G GLN* 3.2 4.2 - - - +
206G ILE* 2.9 33.4 + - - +
214G MET* 3.6 39.9 - - + -
218G LEU* 3.5 15.3 - - + -
252G CYS* 3.4 27.8 - - - -
253G HIS 3.4 3.8 - - - +
254G THR* 3.5 28.5 - - + +
346G CYS* 4.0 12.1 - - - -
348G PRO* 3.8 24.5 - - + -
351G VAL* 4.7 3.1 - - + -
352G THR* 4.2 10.1 - - - -
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Residues in contact with GLU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G MET* 1.3 73.0 - - - +
135G GLN* 1.3 60.4 + - - +
136G GLU* 3.1 11.3 + - + +
203G GLU* 3.0 11.5 - - - +
204G PHE 3.6 5.2 - - - -
205G GLN* 3.8 6.3 - - + -
251G GLY 3.7 1.4 - - - +
252G CYS* 3.2 17.7 - - - -
253G HIS* 2.9 27.4 + - + +
255G ASN* 3.2 19.8 + - - +
338G GLU* 3.3 2.8 - - - +
401G MN 3.8 0.7 + - - -
402G MN 2.3 31.3 + - - -
403G MN 2.3 25.6 + - - -
501G ADP 2.7 33.3 + - - +
601G P3S 3.0 2.1 + - - -
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Residues in contact with GLN 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G MET 3.7 1.2 + - - -
134G GLU* 1.3 71.8 - - - +
136G GLU* 1.3 84.8 + - - +
137G TYR* 3.7 4.1 - - + -
203G GLU* 3.3 3.0 - - - -
204G PHE* 2.7 71.3 + - + +
218G LEU* 4.0 11.7 - - + +
222G ARG* 3.0 36.0 + - - +
238G PHE* 3.6 20.9 - - + -
251G GLY 4.4 0.2 + - - -
252G CYS* 3.8 11.1 - - - -
344G ALA* 3.1 23.4 + - - +
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Residues in contact with GLU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G GLU 3.1 9.3 + - - +
135G GLN* 1.3 94.5 + - - +
137G TYR* 1.3 62.5 + - - +
196G GLU* 3.1 16.1 - - + +
201G GLN* 5.0 3.4 - - - +
202G TRP 3.4 11.4 - - - +
203G GLU* 3.8 7.0 - - + +
238G PHE* 4.1 0.3 - - - -
250G ALA* 3.6 8.2 - - + -
251G GLY* 2.9 32.7 + - - +
253G HIS* 4.8 2.5 - - - -
344G ALA* 3.5 9.7 - - - +
401G MN 2.3 38.2 + - - +
601G P3S 2.6 35.2 + - - -
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Residues in contact with TYR 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G GLN* 3.7 7.9 - - + -
136G GLU* 1.3 79.7 - - - +
138G THR* 1.3 65.8 + - - +
139G LEU* 3.7 30.3 - - + -
175G ILE* 4.7 0.7 - - - +
176G VAL* 3.7 21.7 - - - +
179G HIS* 5.5 1.2 + - - -
201G GLN* 3.2 7.3 - - - +
202G TRP* 2.7 64.6 + - + +
203G GLU* 3.8 4.1 + - - -
204G PHE* 3.7 26.0 - + - -
225G LEU* 3.7 35.2 - - + +
236G ALA* 4.4 2.9 - - + -
237G THR 3.6 15.7 - - - +
238G PHE* 3.6 14.8 - - + -
250G ALA* 4.6 4.7 - - - +
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Residues in contact with THR 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G TYR* 1.3 79.7 + - - +
139G LEU* 1.3 73.9 + - - +
140G MET* 4.0 13.5 - - - -
146G PRO* 4.4 4.0 - - + -
198G MET* 3.0 37.9 - - + +
200G ALA 3.5 9.6 - - - +
201G GLN* 3.7 10.6 + - - +
235G ILE 3.6 0.3 - - - +
236G ALA* 3.7 1.2 - - - -
237G THR* 2.9 45.5 + - - +
242G PRO* 3.7 12.3 - - + +
250G ALA* 5.1 2.3 - - - +
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G TYR* 3.7 26.9 - - + -
138G THR* 1.3 76.7 - - - +
140G MET* 1.3 60.4 + - - +
146G PRO* 3.4 5.9 - - - +
147G PHE* 2.8 33.6 + - + +
171G TYR 3.9 2.2 - - - +
172G GLY* 3.7 37.9 - - - +
175G ILE* 3.9 17.0 - - + -
176G VAL* 5.3 0.4 - - + -
200G ALA* 2.9 16.4 + - - +
202G TRP* 3.9 15.7 - - + -
229G CYS* 3.7 30.1 - - - -
234G VAL* 4.5 6.3 - - + -
235G ILE 3.4 4.9 - - - +
236G ALA* 4.7 0.9 - - - -
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Residues in contact with MET 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G THR* 4.0 17.3 - - - -
139G LEU* 1.3 74.1 - - - +
141G GLY* 1.3 68.0 + - - +
144G GLY* 2.9 40.8 - - - +
145G HIS 3.6 2.5 - - - -
146G PRO* 3.8 24.9 - - + -
147G PHE* 4.2 4.9 - - - -
234G VAL* 3.5 7.6 - - - +
235G ILE* 2.8 47.5 + - + +
237G THR* 3.7 28.3 - - + -
242G PRO* 5.0 8.3 - - + +
243G ILE* 5.3 5.4 - - + -
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Residues in contact with GLY 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G MET* 1.3 82.9 - - - +
142G THR* 1.3 60.5 + - - -
143G ASP* 3.0 9.0 - - - -
144G GLY* 2.9 23.2 + - - -
145G HIS 2.7 17.2 + - - -
147G PHE* 4.0 9.8 - - - +
233G GLY 5.3 0.4 - - - -
234G VAL* 5.1 6.1 - - - -
235G ILE* 3.8 5.3 - - - +
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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