Contacts of the strand formed by residues 194 - 203 (chain D) in PDB entry 4R2G
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 TYR 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ASP* 3.3 1.0 - - - -
163D TYR* 2.7 63.2 + - + +
164D PHE* 4.1 24.3 - + - -
165D PRO* 4.6 1.3 - - + -
166D GLU* 4.0 46.4 - - + -
186D ALA* 4.0 5.8 - - + -
187D VAL 3.0 20.9 - - - +
188D LEU* 3.3 37.1 - - + +
192D GLY 4.9 0.2 - - - -
193D LEU* 1.3 72.7 - - - +
195D SER* 1.3 67.5 + - - +
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.4 16.0 + - - -
159D LEU* 5.6 0.2 - - - -
160D VAL 3.3 10.1 - - - -
161D LYS* 3.2 26.6 - - - +
162D ASP 2.9 11.6 + - - -
163D TYR* 3.4 1.3 - - - -
187D VAL* 3.3 32.1 + - - +
189D GLN* 2.7 28.9 + - - -
194D TYR* 1.3 79.0 + - - +
196D LEU* 1.3 59.8 - - - +
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Residues in contact with LEU 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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178C TYR* 3.4 7.8 - - - -
159D LEU* 4.5 1.9 - - - +
160D VAL* 3.0 43.9 + - + +
163D TYR* 3.4 28.7 - - + +
168D VAL* 3.6 30.7 - - + +
170D VAL* 4.5 1.8 - - + -
183D THR* 3.5 25.6 - - + -
184D PHE 3.3 26.0 - - - +
185D PRO 4.1 1.1 - - - +
186D ALA* 3.9 14.6 - - + +
195D SER* 1.3 73.9 - - - +
197D SER* 1.3 65.5 + - - +
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Residues in contact with SER 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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134C VAL* 3.7 18.8 - - - +
136C LEU* 4.2 26.7 - - - -
178C TYR* 3.1 22.5 + - - -
142D LEU* 4.2 8.9 - - - +
158D CYS 3.9 4.9 - - - -
159D LEU* 4.1 7.1 - - - +
182D HIS 4.1 0.2 - - - +
184D PHE* 3.0 33.8 + - - +
196D LEU* 1.3 80.2 + - - +
198D SER* 1.3 60.0 + - - +
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Residues in contact with SER 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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142D LEU* 4.6 0.9 - - - +
157D GLY* 3.3 2.9 - - - -
158D CYS* 2.9 39.1 + - - -
160D VAL* 5.7 0.4 - - - -
170D VAL* 3.5 28.3 - - - +
172D TRP* 3.1 26.0 + - - -
182D HIS 4.0 3.4 - - - -
183D THR* 3.2 22.9 + - - +
197D SER* 1.3 74.8 - - - +
199D VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 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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117C THR* 5.3 3.1 - - + -
119C PHE* 4.0 22.4 - - + -
136C LEU* 3.5 26.0 - - + -
142D LEU* 5.7 0.9 - - + -
155D ALA* 5.8 2.5 - - + -
156D LEU 3.5 10.5 - - - +
157D GLY* 4.4 0.7 - - - -
172D TRP* 3.5 5.2 + - - -
181D VAL* 3.3 7.4 - - - +
182D HIS* 3.1 52.1 + - + +
184D PHE* 4.3 9.4 - - + -
198D SER* 1.3 78.9 + - - +
200D VAL* 1.3 70.8 + - - +
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Residues in contact with VAL 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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154D ALA 3.9 0.3 - - - +
155D ALA* 4.2 1.2 - - - -
156D LEU* 3.2 46.8 + - + +
172D TRP* 3.6 26.2 - - + -
177D LEU* 3.7 27.4 - - + -
180D GLY 3.4 12.3 - - - +
181D VAL* 3.9 8.7 - - + -
199D VAL* 1.3 82.2 - - - +
201D THR* 1.3 77.9 + - - +
202D VAL* 3.8 14.5 + - + -
212D TYR* 6.4 1.1 - - + -
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Residues in contact with THR 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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153D THR* 5.0 16.4 - - - +
154D ALA 3.5 12.8 - - - +
155D ALA* 5.4 3.6 - - + -
177D LEU* 5.4 1.0 - - - +
179D SER 5.1 0.9 - - - +
180D GLY* 3.1 25.7 + - - +
200D VAL* 1.3 82.3 - - - +
202D VAL* 1.3 60.6 + - - +
203D PRO* 4.4 3.0 - - - +
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Residues in contact with VAL 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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153D THR* 4.7 3.4 - - - -
154D ALA* 3.1 33.7 + - + +
156D LEU* 4.9 9.2 - - + -
177D LEU* 4.5 3.6 - - + -
200D VAL* 3.8 23.7 + - + +
201D THR* 1.3 79.0 - - - +
203D PRO* 1.3 86.9 - - + +
206D SER 5.2 4.0 - - - +
207D LEU* 5.1 9.2 - - + -
212D TYR* 3.2 52.3 - - + +
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Residues in contact with PRO 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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152D GLY 4.9 0.9 - - - +
153D THR* 4.5 12.8 - - + -
201D THR 4.4 3.4 - - - +
202D VAL* 1.3 103.0 - - + +
204D SER* 1.3 67.0 + - - +
205D SER 3.2 17.9 + - - +
206D SER 4.3 0.2 + - - -
207D LEU* 4.2 3.3 - - - +
212D TYR* 5.3 1.3 - - - +
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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