Contacts of the strand formed by residues 130 - 140 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B HIS* 3.3 10.7 + - + +
129B PRO* 1.3 76.9 - - - +
131B PHE* 1.3 62.5 + - - +
208B PRO* 3.9 30.3 - - + -
209B CYS 3.5 3.1 - - - +
210B GLU* 3.1 35.2 + - + +
256B PHE* 3.4 8.5 - - - -
257B SER 2.9 32.5 + - - -
262B ARG* 3.4 50.5 - - - +
501B ADP 3.5 19.0 - - - +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B MET* 3.8 25.1 - - + -
129B PRO* 4.2 13.2 - - + -
130B TRP* 1.3 76.0 - - - +
132B GLY* 1.3 59.4 + - - +
207B GLY* 3.6 0.3 - - - -
208B PRO* 3.1 4.9 - - - +
209B CYS 2.8 35.8 + - - -
211B GLY 4.0 9.4 - - - -
214B MET* 3.3 25.8 - - + +
254B THR* 4.0 13.0 - - + -
255B ASN 3.2 9.4 - - - +
256B PHE* 3.3 27.1 - + - -
352B THR* 3.8 31.6 - - + -
355B LEU* 3.8 17.5 - - + -
356B ILE* 3.7 24.2 - - + -
501B ADP 3.9 4.5 - - - -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 1.3 75.9 - - - +
133B MET* 1.3 63.2 + - - -
206B ILE 3.2 9.4 - - - -
207B GLY* 4.2 0.4 - - - -
253B HIS 3.5 0.2 - - - +
254B THR* 3.6 0.2 - - - -
255B ASN* 2.8 44.9 + - - -
501B ADP 3.4 27.2 + - - -
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLY* 1.3 77.7 - - - +
134B GLU* 1.3 62.5 + - - +
135B GLN* 3.6 3.3 + - - +
204B PHE 3.8 0.2 - - - +
205B GLN* 3.2 3.0 - - - -
206B ILE* 2.7 38.7 + - - +
214B MET* 3.6 41.3 - - + +
218B LEU* 3.9 15.0 - - + -
252B CYS* 3.7 26.2 - - - -
253B HIS 3.4 1.6 - - - -
254B THR* 3.3 36.1 - - + +
346B CYS* 4.0 9.4 - - - -
348B PRO* 3.9 25.8 - - + -
351B VAL* 4.3 6.1 - - + -
352B THR* 4.4 4.7 - - - -
501B ADP 4.8 0.7 - - - -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 1.3 73.2 - - - +
135B GLN* 1.3 61.6 + - - +
136B GLU* 3.1 11.3 + - + +
203B GLU* 3.6 12.3 - - - +
204B PHE 3.8 5.2 - - - -
205B GLN* 4.0 4.3 - - + -
251B GLY 3.3 1.9 - - - +
252B CYS* 3.2 20.2 - - - -
253B HIS* 3.0 23.3 + - + +
255B ASN* 3.2 19.5 + - - +
338B GLU* 3.1 4.7 - - - +
402B MN 2.2 37.0 + - - -
403B MN 2.3 21.0 + - - -
501B ADP 2.8 33.2 + - - +
601B P3S 3.0 2.1 + - - -
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET 3.6 2.2 + - - -
134B GLU* 1.3 71.9 - - - +
136B GLU* 1.3 84.3 + - - +
137B TYR* 3.7 3.7 - - + -
203B GLU* 3.3 3.7 - - - -
204B PHE* 2.9 69.1 + - + +
218B LEU* 3.8 12.7 - - + +
222B ARG* 2.9 35.6 + - - +
238B PHE* 3.6 18.9 - - + -
251B GLY 4.3 0.2 + - - -
252B CYS* 3.9 8.5 - - - -
344B ALA* 2.9 26.4 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU* 3.1 6.5 + - + +
135B GLN* 1.3 94.3 + - - +
137B TYR* 1.3 62.7 + - - +
196B GLU* 2.8 20.7 - - + +
201B GLN* 4.9 4.5 - - - +
202B TRP 3.4 5.6 - - - +
203B GLU* 3.8 11.7 - - + +
238B PHE* 4.0 0.5 - - - -
249B GLY 3.8 0.2 - - - +
250B ALA* 4.1 8.1 - - + -
251B GLY* 3.0 32.8 + - - +
253B HIS* 4.5 4.7 + - - -
344B ALA* 3.5 9.7 - - - +
401B MN 2.1 39.2 + - - +
601B P3S 2.7 36.8 + - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLN* 3.7 11.4 - - + -
136B GLU* 1.3 76.4 - - - +
138B THR* 1.3 65.9 + - - +
139B LEU* 3.6 32.3 - - + -
175B ILE* 4.6 1.0 - - - +
176B VAL* 3.5 30.8 - - - +
179B HIS* 5.3 1.4 + - - -
201B GLN* 3.2 6.4 - - - +
202B TRP* 2.9 58.2 + - + +
203B GLU* 3.9 4.6 + - - -
204B PHE* 3.6 27.0 - + - +
225B LEU* 3.8 32.7 - - + +
236B ALA* 4.3 4.3 - - + -
237B THR 3.5 14.6 - - - +
238B PHE* 3.6 15.3 - - + -
250B ALA* 4.8 4.0 - - - -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR* 1.3 79.4 + - - +
139B LEU* 1.3 72.0 + - - +
140B MET* 3.8 15.3 + - - -
146B PRO* 4.6 1.8 - - + -
198B MET* 2.9 39.0 - - + +
200B ALA* 3.6 11.4 - - + +
201B GLN* 3.6 13.9 + - - +
236B ALA* 3.6 0.7 - - - -
237B THR* 2.9 44.7 + - - +
242B PRO* 3.8 10.3 - - + +
250B ALA* 5.0 1.9 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR* 3.6 28.7 - - + -
138B THR* 1.3 78.5 - - - +
140B MET* 1.3 59.3 + - - +
146B PRO* 3.6 5.5 - - - +
147B PHE* 3.0 33.0 + - + +
171B TYR 4.0 7.4 - - - +
172B GLY* 3.8 36.1 - - - +
175B ILE* 4.1 17.7 - - + -
176B VAL* 5.3 0.4 - - + -
200B ALA* 3.1 15.2 + - + +
202B TRP* 4.0 10.8 - - + -
229B CYS* 3.8 27.1 - - - -
234B VAL* 4.6 5.4 - - + -
235B ILE 3.3 6.5 - - - +
236B ALA* 4.5 1.1 - - + -
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 3.9 15.9 - - - +
139B LEU* 1.3 77.9 - - - +
141B GLY* 1.3 70.8 + - - +
144B GLY* 2.8 35.7 - - - +
145B HIS 3.5 4.9 - - - -
146B PRO* 3.9 20.4 - - + -
147B PHE* 3.9 5.2 - - - +
234B VAL* 3.6 8.0 - - - +
235B ILE* 2.7 44.6 + - + +
237B THR* 3.9 28.0 - - + -
242B PRO* 5.0 9.9 - - + +
243B ILE* 5.2 5.4 - - + -
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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