Contacts of the strand formed by residues 193 - 204 (chain B) in PDB entry 6QPA
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 MET 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B LYS* 2.6 30.1 + - - +
183B LEU* 4.5 5.2 - - + +
186B MET* 3.3 49.8 - - + +
187B LYS* 3.3 34.4 - - + +
190B VAL 3.6 12.7 + - - +
191B PRO 3.2 2.4 - - - -
192B GLY* 1.3 74.5 - - - +
194B VAL* 1.3 61.1 + - - +
195B GLY 3.9 16.6 - - - +
196B TRP* 4.6 4.0 - - - -
257B ILE* 3.8 22.7 - - + -
258B GLU 4.0 0.2 - - - -
259B TRP* 3.5 22.9 - - + -
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Residues in contact with VAL 194 (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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127B PRO* 3.4 14.9 - - + +
151B LYS* 3.4 15.0 - - + +
152B VAL 3.8 16.8 - - - +
153B ALA* 3.5 34.3 - - + +
158B ARG* 4.6 4.0 - - + -
187B LYS* 3.4 15.2 - - - -
192B GLY 3.8 13.2 - - - +
193B MET* 1.3 73.3 - - - +
195B GLY* 1.3 60.4 + - - +
258B GLU* 2.8 27.4 + - + +
259B TRP 3.8 15.9 - - - +
260B GLU* 3.8 7.6 - - + +
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Residues in contact with GLY 195 (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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125B ASP 3.1 14.6 - - - -
126B LEU* 4.2 6.3 - - - -
127B PRO* 4.1 6.5 - - - -
187B LYS* 4.1 9.0 - - - -
193B MET* 3.6 4.1 - - - -
194B VAL* 1.3 81.9 - - - +
196B TRP* 1.3 66.1 + - - +
257B ILE* 3.4 6.6 - - - +
258B GLU* 2.8 25.9 + - - +
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Residues in contact with TRP 196 (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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123B LYS* 3.4 45.5 - - + -
124B SER* 3.4 4.9 - - - -
125B ASP* 2.8 59.7 + - + +
126B LEU* 3.7 8.5 - - - +
180B THR* 4.3 12.1 - - + -
183B LEU* 3.5 59.6 + - + +
184B GLU* 3.9 26.8 - - + +
187B LYS* 4.0 13.6 - - + +
193B MET* 4.6 3.1 - - - -
195B GLY* 1.3 78.9 - - - +
197B MET* 1.3 72.0 + - - +
198B ILE* 3.8 17.3 - - + -
256B HIS 3.0 12.8 - - - +
257B ILE* 4.5 4.5 - - + -
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.8 25.1 - - + -
79B TYR* 3.9 4.7 - - + -
121B VAL* 4.0 24.0 - - + -
123B LYS 3.5 7.2 - - - +
124B SER* 4.1 5.4 - - - -
126B LEU* 3.8 19.7 - - + -
196B TRP* 1.3 79.1 - - - +
198B ILE* 1.3 65.6 + - - +
199B MET* 3.7 32.1 - - + +
254B LEU 3.8 0.5 - - - +
255B VAL* 3.7 2.8 - - - +
256B HIS* 2.8 58.1 + - + +
308B TRP* 3.9 18.6 - - + -
312B LEU* 5.1 0.4 - - - -
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Residues in contact with ILE 198 (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 VAL* 3.6 3.6 - - - -
122B VAL* 2.8 51.4 + - + -
123B LYS* 2.8 15.4 + - + +
175B PHE* 4.6 9.2 - - + -
176B GLU* 4.1 5.4 - - + +
179B ALA* 3.6 13.0 - - + -
180B THR* 3.4 40.8 - - - +
183B LEU* 3.6 24.0 - - + -
196B TRP* 3.8 9.4 - - + -
197B MET* 1.3 71.8 - - - +
199B MET* 1.3 58.0 + - - +
253B TYR* 4.1 20.9 - - + -
254B LEU 3.9 3.8 - - - +
255B VAL* 4.7 6.3 - - + +
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Residues in contact with MET 199 (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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8B ILE* 4.1 14.4 - - + -
10B ILE* 3.8 20.6 - - + -
79B TYR* 3.5 23.8 - - - +
119B PHE* 3.7 22.4 - - + -
120B GLU 3.2 6.5 - - - +
121B VAL* 5.0 2.0 - - + -
162B ILE* 5.2 1.6 - - + -
197B MET* 3.7 33.4 - - + -
198B ILE* 1.3 78.1 - - - +
200B LYS* 1.3 60.6 + - - +
253B TYR* 3.1 9.8 - - - +
254B LEU* 2.9 59.8 + - + +
256B HIS* 3.8 15.7 - - + -
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Residues in contact with LYS 200 (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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119B PHE* 3.2 3.7 - - - -
120B GLU* 2.8 54.5 + - + +
122B VAL* 3.7 11.4 - - + -
172B GLU* 4.5 10.7 - - - +
176B GLU* 3.8 9.6 + - - +
199B MET* 1.3 72.6 - - - +
201B GLN* 1.3 70.8 + - - +
202B PHE* 3.4 7.4 + - + -
251B THR* 4.0 19.5 - - + -
252B GLN 3.8 2.9 - - - -
253B TYR* 3.3 41.8 + - + +
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Residues in contact with GLN 201 (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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115B TRP* 5.3 2.5 + - - +
117B PRO* 3.9 21.9 - - + +
118B TYR 3.3 12.3 - - - +
119B PHE* 3.4 17.1 - - + -
200B LYS* 1.3 80.0 - - - +
202B PHE* 1.3 61.2 + - - +
203B GLY 3.9 10.3 - - - +
204B VAL* 3.8 11.8 - - - +
247B GLY* 3.6 7.9 - - - -
248B GLN* 3.0 48.5 + - - +
251B THR* 4.2 10.4 - - - +
252B GLN* 2.7 52.0 + - + +
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Residues in contact with PHE 202 (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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7B ILE* 4.1 15.5 - - + -
85B VAL* 3.7 22.2 - - + -
118B TYR* 3.0 21.3 + - + -
119B PHE 3.6 22.0 - - - -
120B GLU* 3.5 30.5 - - + +
200B LYS* 3.8 7.2 - - + +
201B GLN* 1.3 73.7 - - - +
203B GLY* 1.3 57.3 + - - +
243B PRO* 3.6 30.0 - - + +
246B PRO* 4.9 1.0 - - - +
247B GLY* 3.6 13.9 + - - -
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Residues in contact with GLY 203 (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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117B PRO* 3.2 7.1 - - - +
118B TYR* 2.7 32.5 + - - +
201B GLN* 3.7 1.6 - - - +
202B PHE* 1.3 80.4 - - - +
204B VAL* 1.3 62.0 + - - +
243B PRO* 3.5 12.6 - - - -
245B ILE 3.3 14.1 - - - -
247B GLY* 3.5 11.4 - - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TRP* 3.6 37.9 - - + +
116B GLU 3.4 13.7 - - - +
117B PRO* 3.9 6.5 - - + -
118B TYR* 3.9 5.2 - - - -
201B GLN* 3.8 17.0 - - - +
203B GLY* 1.3 80.2 - - - +
205B SER* 1.3 67.6 + - - +
209B SER* 3.3 22.9 - - - +
243B PRO* 3.6 1.2 - - - +
244B PRO* 3.2 20.6 - - - +
245B ILE* 2.9 36.1 + - + +
246B PRO 4.3 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