Contacts of the strand formed by residues 193 - 204 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D LYS* 2.8 30.7 + - - +
183D LEU* 4.1 11.2 - - + +
186D MET* 3.6 17.5 - - + +
187D LYS* 3.4 33.1 - - + +
190D VAL 3.5 11.7 + - - +
191D PRO 3.3 4.0 + - - -
192D GLY* 1.3 75.2 - - - +
194D VAL* 1.3 62.0 + - - +
195D GLY 3.7 5.6 - - - +
196D TRP* 3.3 38.8 - - + -
257D ILE* 3.5 27.8 - - + -
258D GLU 3.9 2.5 - - - +
259D TRP* 3.6 23.3 - - + -
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PRO* 3.4 15.2 - - + +
151D LYS* 3.4 16.0 - - + +
152D VAL 3.8 17.3 - - - +
153D ALA* 3.5 35.7 - - + +
158D ARG* 4.6 5.2 - - + -
187D LYS* 3.3 15.2 - - - -
192D GLY 3.7 13.2 - - - +
193D MET* 1.3 73.5 - - - +
195D GLY* 1.3 56.7 + - - +
258D GLU* 2.8 29.5 + - + +
259D TRP 3.8 17.0 - - - +
260D GLU* 3.8 6.7 - - + +
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Residues in contact with GLY 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ASP 3.1 13.9 - - - -
126D LEU* 3.9 7.9 - - - -
127D PRO* 4.0 7.6 - - - -
187D LYS* 3.9 8.3 - - - -
193D MET* 3.7 2.9 - - - +
194D VAL* 1.3 82.8 - - - +
196D TRP* 1.3 66.5 + - - +
257D ILE* 3.5 5.4 - - - +
258D GLU* 2.9 24.4 + - - +
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Residues in contact with TRP 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS* 3.5 46.2 - - + -
124D SER* 3.5 4.4 - - - -
125D ASP* 2.8 60.1 + - + +
126D LEU* 3.5 8.0 - - - +
180D THR* 4.3 13.0 - - + -
183D LEU* 3.6 46.8 + - + -
184D GLU* 3.7 26.8 - - + +
187D LYS* 3.9 15.7 - - + +
193D MET* 3.3 27.8 - - + -
195D GLY* 1.3 75.1 - - - +
197D MET* 1.3 70.6 + - - +
198D ILE* 4.0 14.8 - - + -
256D HIS 3.1 12.6 - - - +
257D ILE* 4.5 1.3 - - + -
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Residues in contact with MET 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 4.0 15.0 - - + -
79D TYR* 4.2 3.6 - - + -
121D VAL* 3.9 26.7 - - + -
123D LYS 3.5 6.3 - - - -
124D SER* 4.1 4.0 - - - -
126D LEU* 3.6 27.1 - - + -
183D LEU* 5.2 0.2 - - - -
196D TRP* 1.3 80.4 - - - +
198D ILE* 1.3 65.6 + - - +
199D MET* 3.8 25.5 + - + -
254D LEU 3.8 0.9 - - - +
255D VAL* 3.7 2.4 - - - +
256D HIS* 2.8 61.7 + - + +
308D TRP* 3.9 21.5 - - + -
312D LEU* 5.0 0.9 - - - -
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Residues in contact with ILE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 3.6 4.0 - - - +
122D VAL* 2.7 45.0 + - + -
123D LYS* 2.8 19.4 + - + +
175D PHE* 4.5 9.2 - - + -
176D GLU* 4.1 6.5 - - + +
179D ALA* 3.8 12.1 - - + -
180D THR* 3.5 39.3 - - - +
183D LEU* 3.7 23.8 - - + -
196D TRP* 4.0 9.0 - - + -
197D MET* 1.3 71.7 - - - +
199D MET* 1.3 57.4 + - - +
253D TYR* 4.0 24.5 - - + -
254D LEU 3.9 4.5 - - - +
255D VAL* 4.7 6.7 - - + +
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Residues in contact with MET 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.9 16.8 - - + -
10D ILE* 3.8 22.0 - - + -
79D TYR* 3.5 24.7 - - - +
119D PHE* 3.8 21.3 - - + -
120D GLU 3.1 6.5 - - - +
121D VAL* 4.8 2.5 - - + -
162D ILE* 5.2 1.6 - - + -
197D MET* 3.8 31.4 - - + +
198D ILE* 1.3 76.5 - - - +
200D LYS* 1.3 60.4 + - - +
201D GLN 4.2 0.2 + - - -
253D TYR* 3.3 9.8 - - - -
254D LEU* 2.9 56.2 + - + +
256D HIS* 3.9 15.3 - - + -
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Residues in contact with LYS 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PHE* 3.3 3.6 - - - -
120D GLU* 2.8 52.5 + - + +
122D VAL* 3.6 13.0 - - + +
172D GLU* 4.6 10.4 - - - +
176D GLU* 3.9 10.0 + - - +
199D MET* 1.3 72.5 - - - +
201D GLN* 1.3 71.2 + - - +
202D PHE* 3.4 8.1 + - + -
251D THR* 3.9 21.3 - - + -
252D GLN 3.8 2.9 - - - -
253D TYR* 3.4 41.8 + - + +
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Residues in contact with GLN 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TRP* 5.3 3.2 + - - +
117D PRO* 3.8 20.4 - - + +
118D TYR 3.3 12.8 - - - +
119D PHE* 3.5 16.7 - - + -
200D LYS* 1.3 81.2 - - - +
202D PHE* 1.3 62.4 + - - +
203D GLY 3.9 9.0 - - - +
204D VAL* 3.8 12.8 - - - +
247D GLY* 3.6 7.7 - - - -
248D GLN* 3.1 41.9 + - - +
251D THR* 4.1 10.9 - - - +
252D GLN* 2.8 54.6 + - + +
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Residues in contact with PHE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 4.1 17.5 - - + -
85D VAL* 3.8 22.9 - - + -
118D TYR* 3.1 23.4 + - + -
119D PHE 3.5 23.6 - - - -
120D GLU* 3.6 24.2 - - + +
200D LYS* 3.7 7.9 - - + +
201D GLN* 1.3 73.1 - - - +
203D GLY* 1.3 56.9 + - - +
243D PRO* 3.6 29.4 - - + +
246D PRO* 5.0 1.2 - - - +
247D GLY* 3.6 15.1 + - - -
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Residues in contact with GLY 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D PRO* 3.3 6.2 - - - +
118D TYR* 2.6 32.7 + - - +
201D GLN* 3.8 1.5 - - - +
202D PHE* 1.3 80.1 - - - +
204D VAL* 1.3 61.8 + - - +
243D PRO* 3.6 15.0 - - - -
245D ILE 3.3 12.6 - - - -
247D GLY* 3.4 10.8 - - - -
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D TRP* 3.6 39.5 - - + +
116D GLU 3.4 15.9 - - - +
117D PRO* 4.1 4.9 - - + -
118D TYR* 3.9 5.4 - - - -
201D GLN* 3.8 17.0 - - - +
203D GLY* 1.3 80.4 - - - +
205D SER* 1.3 67.7 + - - +
209D SER* 3.4 18.4 - - - +
243D PRO* 3.6 1.5 - - - +
244D PRO* 3.3 7.8 - - - +
245D ILE* 2.9 47.4 + - + +
246D PRO 4.1 4.5 - - - +
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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