Contacts of the strand formed by residues 196 - 205 (chain R) in PDB entry 3DLQ
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 GLU 196 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170R GLN 5.0 0.7 - - - +
195R THR* 1.3 81.9 - - - +
197R PHE* 1.3 69.8 + - - +
218R ARG* 3.6 42.1 + - + +
219R VAL 3.4 9.7 - - - +
220R LYS* 3.6 23.2 - - + +
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Residues in contact with PHE 197 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R ILE* 4.6 7.4 - - + -
169R LEU* 3.9 24.7 - - + -
170R GLN 3.7 8.3 - - - +
171R VAL* 3.5 41.7 - - + -
191R LEU* 3.8 26.7 - - + -
192R THR* 3.9 7.0 - - - -
195R THR* 3.3 42.0 - - + -
196R GLU* 1.3 76.8 - - - +
198R LEU* 1.3 61.3 + - - +
199R GLY 4.2 0.4 - - - -
217R CYS 3.8 0.3 - - - +
218R ARG* 3.4 7.7 - - - +
219R VAL* 2.8 35.5 + - + +
221R THR* 3.6 29.4 - - + -
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Residues in contact with LEU 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168R GLU 3.8 0.9 - - - +
169R LEU* 3.6 3.3 - - - -
170R GLN* 2.8 50.1 + - + +
197R PHE* 1.3 75.9 - - - +
199R GLY* 1.3 60.6 + - - +
200R THR* 4.6 8.4 - - + +
216R MET* 3.4 39.5 - - + -
217R CYS 3.5 18.8 - - - +
218R ARG* 3.5 42.0 - - + +
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Residues in contact with GLY 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137R MET* 4.0 16.4 - - - -
168R GLU 3.2 8.1 - - - -
169R LEU* 4.0 10.1 - - - +
197R PHE 4.2 0.2 - - - -
198R LEU* 1.3 71.3 - - - +
200R THR* 1.3 65.0 + - - +
201R ILE* 4.0 5.2 - - - -
216R MET* 3.1 5.9 - - - +
217R CYS* 2.8 39.9 + - - -
219R VAL* 5.7 0.4 - - - +
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Residues in contact with THR 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137R MET* 5.4 0.2 - - - +
166R HIS* 3.6 2.3 - - - +
167R LEU* 3.3 4.0 - - - +
168R GLU* 2.9 51.0 + - + +
170R GLN* 6.6 0.2 - - + -
198R LEU* 4.6 9.4 - - + +
199R GLY* 1.3 79.1 - - - +
201R ILE* 1.3 65.0 + - - +
202R MET* 6.0 1.5 - - - +
214R PRO* 4.2 14.8 - - + -
215R TYR 3.3 6.5 - - - -
216R MET* 3.9 25.4 - - + -
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Residues in contact with ILE 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124R PRO* 3.8 12.8 - - + +
126R VAL* 3.8 28.7 - - + -
137R MET* 3.2 34.8 - - + -
139R VAL* 3.9 18.8 - - + -
165R TYR* 4.7 3.6 - - + -
166R HIS 3.4 3.4 - - - +
167R LEU* 3.9 22.4 - - + -
199R GLY 4.0 2.0 - - - +
200R THR* 1.3 85.4 - - - +
202R MET* 1.3 67.0 + - - +
214R PRO* 3.3 2.0 - - - +
215R TYR* 2.8 56.4 + - + +
217R CYS* 4.7 0.4 - - - -
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Residues in contact with MET 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R PRO* 4.5 1.8 - - - -
165R TYR* 3.4 6.4 - - - +
166R HIS* 2.9 67.0 + - + +
200R THR* 6.0 1.1 - - - +
201R ILE* 1.3 78.7 - - - +
203R ILE* 1.3 60.7 + - - +
204R LEU* 3.8 13.5 - - + -
211R GLU* 3.1 48.7 - - + +
212R SER* 3.4 17.7 - - - +
213R ALA 5.5 0.9 - - - -
214R PRO* 4.2 14.6 - - + -
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Residues in contact with ILE 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121R LEU* 3.8 18.2 - - + -
122R LYS 3.8 21.5 - - - +
124R PRO* 4.0 25.8 - - + +
142R THR* 4.1 8.7 - - - +
156R LEU* 4.0 20.0 - - + -
157R GLU* 5.3 1.6 - - - +
163R LEU* 3.6 31.9 - - + -
164R PHE 3.7 3.8 - - - -
165R TYR* 4.2 17.0 - - + -
202R MET* 1.3 74.0 - - - +
204R LEU* 1.3 67.6 + - - +
211R GLU* 3.4 3.5 - - - -
212R SER* 2.9 39.0 + - - +
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Residues in contact with LEU 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163R LEU* 3.4 1.2 - - - +
164R PHE* 2.9 75.0 + - + +
166R HIS* 3.9 22.9 - - + -
202R MET* 3.8 18.8 - - + +
203R ILE* 1.3 83.7 - - - +
205R VAL* 1.3 67.5 + - - +
206R PRO* 3.6 6.0 - - + +
210R LYS 3.6 3.8 - - - +
211R GLU* 3.7 25.4 - - + +
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Residues in contact with VAL 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121R LEU* 3.8 22.4 - - + -
160R PHE* 3.8 33.2 - - + -
162R ASP* 3.2 24.7 - - - +
163R LEU* 3.9 21.8 - - + -
204R LEU* 1.3 78.2 - - - +
206R PRO* 1.3 69.0 - - - +
207R THR 3.2 0.2 - - - -
208R TRP* 3.0 23.2 + - + +
210R LYS* 2.9 32.9 + - + -
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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