Contacts of the strand formed by residues 130 - 140 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A HIS* 3.3 9.4 + - - +
129A PRO* 1.3 77.2 - - - +
131A PHE* 1.3 62.1 + - - +
208A PRO* 3.9 27.1 - - + -
209A CYS 3.6 2.9 - - - +
210A GLU* 3.2 35.4 + - + +
256A PHE* 3.4 7.8 - - - -
257A SER 2.7 34.0 + - - -
262A ARG* 3.4 50.6 - - - +
501A ADP 3.4 23.9 - - + +
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 4.0 11.4 - - + -
129A PRO* 4.2 16.8 - - + -
130A TRP* 1.3 75.0 - - - +
132A GLY* 1.3 59.5 + - - +
207A GLY* 3.5 0.5 - - - -
208A PRO* 3.1 5.0 - - - +
209A CYS 2.8 40.9 + - - -
211A GLY 4.1 6.5 - - - -
214A MET* 3.4 32.8 - - + +
254A THR* 4.0 15.9 - - + -
255A ASN 3.1 5.4 - - - +
256A PHE* 3.5 28.3 - + - -
352A THR* 3.6 46.9 - - + -
355A LEU* 3.8 17.0 - - + -
356A ILE* 4.0 13.0 - - + -
501A ADP 3.9 4.5 - - - -
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE* 1.3 74.3 - - - +
133A MET* 1.3 60.1 + - - -
206A ILE 3.3 9.2 - - - -
207A GLY* 4.1 0.9 - - - -
254A THR* 3.5 0.5 - - - -
255A ASN* 2.6 46.9 + - - -
501A ADP 3.6 29.2 + - - -
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY* 1.3 76.9 - - - +
134A GLU* 1.3 63.2 + - - +
135A GLN* 3.7 3.5 + - - +
204A PHE 3.7 0.2 - - - +
205A GLN* 3.2 3.1 - - - -
206A ILE* 2.9 35.5 + - - +
214A MET* 3.6 37.5 - - + +
218A LEU* 3.6 22.1 - - + +
252A CYS* 3.5 26.0 - - - -
253A HIS 3.3 3.8 - - - +
254A THR* 3.5 36.6 - - + +
346A CYS* 4.1 8.7 - - - -
348A PRO* 3.9 23.3 - - + -
351A VAL* 4.7 4.0 - - + -
352A THR* 4.4 4.0 - - - -
501A ADP 4.1 0.6 + - - -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A MET* 1.3 72.8 - - - +
135A GLN* 1.3 60.4 + - - +
136A GLU* 3.0 11.7 + - + +
203A GLU* 3.6 12.7 - - - +
204A PHE 3.5 6.3 - - - -
205A GLN* 4.0 3.6 - - + +
251A GLY 3.4 1.9 - - - +
252A CYS* 3.3 18.8 - - - -
253A HIS* 3.0 21.8 + - + +
255A ASN* 3.1 22.4 + - - +
338A GLU* 2.9 6.2 - - - +
402A MN 2.3 30.5 + - - -
403A MN 2.1 29.6 + - - -
501A ADP 2.6 34.5 + - - +
601A P3S 2.8 1.6 + - - -
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A MET 3.7 2.0 + - - +
134A GLU* 1.3 70.9 - - - +
136A GLU* 1.3 82.4 + - - +
137A TYR* 3.6 4.4 - - + -
203A GLU* 3.3 2.3 - - - -
204A PHE* 2.7 70.5 + - + -
218A LEU* 3.8 12.4 - - + +
222A ARG* 2.9 35.3 + - + -
238A PHE* 3.6 21.1 - - + -
251A GLY 4.5 0.2 + - - -
252A CYS* 4.0 8.7 - - - +
344A ALA* 2.9 25.6 + - - +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLU 3.0 9.7 + - - +
135A GLN* 1.3 91.0 + - - +
137A TYR* 1.3 62.9 + - - +
196A GLU* 2.8 17.9 - - + +
201A GLN* 4.9 3.8 - - - +
202A TRP 3.3 5.4 - - - +
203A GLU* 3.8 14.8 - - + +
238A PHE* 4.0 0.3 - - - -
249A GLY 4.7 0.2 - - - -
250A ALA* 3.8 8.0 - - + -
251A GLY* 3.1 31.1 + - - +
253A HIS* 4.8 4.0 - - - -
344A ALA* 3.3 11.4 - - - +
401A MN 2.1 38.8 + - - +
601A P3S 2.7 36.0 + - - +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 3.6 10.8 - - + -
136A GLU* 1.3 77.0 - - - +
138A THR* 1.3 73.0 + - - +
139A LEU* 3.9 28.0 - - + -
175A ILE* 4.5 1.4 - - - +
176A VAL* 3.5 31.4 - - - +
179A HIS* 5.7 0.7 + - - +
201A GLN* 3.3 6.2 - - - +
202A TRP* 2.9 57.7 + - + +
203A GLU 3.8 3.7 + - - -
204A PHE* 3.7 25.3 - + - -
225A LEU* 3.8 35.0 - - + +
236A ALA* 4.4 3.6 - - + -
237A THR 3.4 14.8 - - - +
238A PHE* 3.5 14.6 - - + -
250A ALA* 4.5 5.3 - - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR* 1.3 82.6 + - - +
139A LEU* 1.3 73.7 + - - +
140A MET* 3.7 12.5 + - - -
146A PRO* 4.5 1.3 - - + -
198A MET* 3.0 37.4 - - + +
200A ALA* 3.6 11.7 - - + +
201A GLN* 3.7 12.8 + - - +
236A ALA* 3.7 0.7 - - - -
237A THR* 2.9 45.3 + - - +
242A PRO* 3.7 14.7 - - + +
250A ALA* 5.1 1.6 - - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR* 3.9 22.7 - - + -
138A THR* 1.3 73.7 - - - +
140A MET* 1.3 54.9 + - - +
146A PRO* 3.5 4.9 - - - +
147A PHE* 2.7 41.2 + - + +
171A TYR 4.1 1.3 - - - +
172A GLY* 3.9 34.8 - - - +
175A ILE* 4.1 15.7 - - + -
176A VAL* 5.2 0.7 - - + -
200A ALA* 3.0 19.7 + - + +
202A TRP* 4.0 16.2 - - + +
229A CYS* 3.6 30.7 - - - -
234A VAL* 4.1 8.5 - - + -
235A ILE 3.4 7.2 - - - +
236A ALA* 4.4 1.1 - - - -
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 4.0 7.2 - - - +
139A LEU* 1.3 74.3 - - - +
141A GLY* 1.3 71.6 + - - +
144A GLY* 2.9 32.5 - - - +
145A HIS 3.5 6.3 - - - +
146A PRO* 3.9 26.7 - - + -
147A PHE* 4.1 4.0 - - - -
234A VAL* 3.5 6.3 - - - +
235A ILE* 2.7 51.7 + - + +
237A THR* 3.6 34.1 - - + -
242A PRO* 5.0 11.7 - - + +
243A ILE* 5.2 4.7 - - + -
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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