Contacts of the strand formed by residues 130 - 140 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128I HIS* 3.2 11.9 + - - +
129I PRO* 1.3 79.2 - - - +
131I PHE* 1.3 61.3 + - - +
208I PRO* 4.1 27.6 - - + -
209I CYS 3.4 5.2 - - - +
210I GLU* 3.5 32.2 + - + +
256I PHE* 3.4 9.9 - - - -
257I SER 2.9 29.2 + - - -
262I ARG* 3.5 51.1 - - - +
501I ADP 3.9 17.9 - - + +
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Residues in contact with PHE 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I MET* 4.1 19.3 - - - -
129I PRO* 4.1 13.0 - - + -
130I TRP* 1.3 74.0 - - - +
132I GLY* 1.3 59.2 + - - +
207I GLY* 4.0 0.3 - - - -
208I PRO* 3.3 1.4 - - - +
209I CYS 2.7 42.4 + - - -
211I GLY 4.1 4.9 - - - -
214I MET* 3.4 35.5 - - + +
254I THR* 4.1 17.5 - - + -
255I ASN 3.3 7.4 - - - +
256I PHE* 3.4 36.3 - + - -
352I THR* 3.9 31.0 - - + -
355I LEU* 4.0 15.7 - - + -
356I ILE* 3.8 16.2 - - + -
501I ADP 3.9 5.8 - - - -
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Residues in contact with GLY 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I PHE* 1.3 72.8 - - - +
133I MET* 1.3 62.9 + - - -
206I ILE 3.2 11.7 - - - -
207I GLY* 4.3 1.6 - - - -
254I THR* 3.5 0.9 - - - -
255I ASN* 2.7 43.7 + - - +
501I ADP 3.5 28.9 + - - -
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Residues in contact with MET 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I GLY* 1.3 79.5 - - - +
134I GLU* 1.3 63.8 + - - +
135I GLN 3.6 2.7 + - - -
204I PHE 3.7 0.2 - - - +
205I GLN* 3.3 3.3 - - - -
206I ILE* 3.0 33.5 + - - +
214I MET* 3.6 39.7 - - + -
218I LEU* 3.9 10.4 - - + +
252I CYS* 3.6 25.1 - - - -
253I HIS 3.2 4.7 - - - +
254I THR* 3.5 30.1 - - + +
346I CYS* 4.0 12.6 - - - -
348I PRO* 3.9 29.4 - - + -
351I VAL* 4.6 4.3 - - + -
352I THR* 4.3 7.9 - - - -
501I ADP 4.8 0.4 - - - -
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Residues in contact with GLU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I MET* 1.3 71.8 - - - +
135I GLN* 1.3 60.6 + - - +
136I GLU* 3.0 10.9 + - + +
203I GLU* 2.8 14.5 - - - +
204I PHE 3.6 5.4 - - - -
205I GLN* 3.8 6.5 - - + +
251I GLY 3.2 12.6 - - - +
252I CYS* 3.3 10.3 - - - -
253I HIS* 2.9 21.8 + - + +
255I ASN* 3.2 21.6 + - - +
338I GLU* 3.3 1.7 - - - +
402I MN 2.3 31.2 + - - -
403I MN 2.1 34.4 + - - -
501I ADP 2.8 28.1 + - - +
601I P3S 2.6 2.9 + - - -
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Residues in contact with GLN 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I MET 3.6 2.4 + - - -
134I GLU* 1.3 70.8 - - - +
136I GLU* 1.3 82.7 + - - +
137I TYR* 3.7 4.4 - - + -
203I GLU* 3.3 3.2 - - - -
204I PHE* 2.8 66.9 + - + +
218I LEU* 3.9 12.4 - - + +
222I ARG* 3.0 34.3 + - + +
238I PHE* 3.6 21.9 - - + -
251I GLY 4.4 0.8 + - - -
252I CYS* 3.9 8.0 - - - -
344I ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I GLU* 3.0 9.1 + - + +
135I GLN* 1.3 95.3 + - - +
137I TYR* 1.3 61.5 + - - +
196I GLU* 3.2 14.2 - - + +
201I GLN* 5.0 4.3 - - + +
202I TRP 3.3 9.0 - - - +
203I GLU* 3.8 15.5 - - + +
238I PHE* 4.0 0.2 - - - -
249I GLY 4.9 0.2 - - - -
250I ALA* 3.7 7.5 - - + -
251I GLY* 2.8 34.3 + - - +
253I HIS* 4.8 3.6 - - - -
344I ALA* 3.6 9.0 - - - +
401I MN 2.3 32.2 + - - +
601I P3S 2.7 35.1 + - - +
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Residues in contact with TYR 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I GLN* 3.7 7.9 - - + -
136I GLU* 1.3 79.0 - - - +
138I THR* 1.3 63.4 + - - +
139I LEU* 3.7 33.4 - - + -
175I ILE* 4.4 1.0 - - - +
176I VAL* 3.5 22.3 - - - +
179I HIS* 5.6 0.9 + - - -
201I GLN* 3.4 5.3 - - - +
202I TRP* 2.9 65.3 + - + +
203I GLU 3.8 4.9 + - - -
204I PHE* 3.9 24.9 - + - -
225I LEU* 3.8 33.8 - - + +
236I ALA* 4.2 4.7 - - + -
237I THR 3.5 15.5 - - - +
238I PHE* 3.6 15.7 - - + +
250I ALA* 4.6 6.4 - - - +
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Residues in contact with THR 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I TYR* 1.3 78.8 - - - +
139I LEU* 1.3 77.7 - - - +
140I MET* 4.0 11.9 - - - -
146I PRO* 4.3 2.7 - - + -
198I MET* 3.5 35.1 - - + +
200I ALA 3.4 10.8 - - - +
201I GLN* 3.7 14.2 + - - +
236I ALA* 3.5 2.3 - - - -
237I THR* 2.9 45.4 + - - +
242I PRO* 3.9 13.3 - - + +
250I ALA* 5.5 0.9 - - - +
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Residues in contact with LEU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I TYR* 3.7 28.3 - - + -
138I THR* 1.3 85.1 - - - +
140I MET* 1.3 59.3 + - - +
146I PRO* 3.5 0.5 - - - +
147I PHE* 3.0 32.2 + - + +
171I TYR 3.9 16.4 - - - +
172I GLY* 3.8 26.7 - - - +
175I ILE* 3.9 18.6 - - + -
176I VAL* 5.3 0.4 - - + -
200I ALA* 2.9 14.3 + - + +
202I TRP* 4.1 9.4 - - + -
229I CYS* 3.8 26.7 - - - -
234I VAL* 4.5 8.1 - - + -
235I ILE 3.3 6.1 - - - +
236I ALA* 4.7 0.7 - - - -
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Residues in contact with MET 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I THR* 4.0 13.7 - - - +
139I LEU* 1.3 76.7 - - - +
141I GLY* 1.3 68.9 + - - +
144I GLY* 3.3 27.4 - - - +
145I HIS 3.6 5.8 - - - +
146I PRO* 3.8 24.9 - - + -
147I PHE* 3.7 5.4 - - - +
234I VAL* 3.4 7.1 - - - +
235I ILE* 2.8 44.6 + - + +
237I THR* 4.0 31.0 - - + +
242I PRO* 4.7 17.7 - - + +
243I ILE* 5.2 2.7 - - + -
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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