Contacts of the strand formed by residues 203 - 209 (chain D) in PDB entry 2IBS
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 ALA 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D VAL* 4.2 11.0 - - + -
164D VAL 3.4 10.8 - - - +
165D PRO* 4.4 0.4 - - + -
191D TYR* 4.3 1.6 - - - -
192D LEU* 3.0 9.9 + - + -
193D GLY* 2.8 40.2 + - - +
195D VAL* 4.4 7.0 - - + -
196D PHE* 3.7 30.7 - - + -
201D VAL* 3.8 1.3 + - + -
202D SER* 1.3 74.3 + - - +
204D VAL* 1.3 66.5 + - - +
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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
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163D VAL* 3.5 5.0 - - - +
164D VAL* 2.8 43.5 + - + +
165D PRO 3.8 4.5 - - - +
166D ALA* 3.7 19.7 - - + -
168D TRP* 3.5 32.1 - - + +
169D LEU* 4.3 7.0 - - + -
189D VAL* 4.0 20.6 - - + -
190D TYR 3.3 6.7 - - - +
191D TYR* 3.9 21.8 - - + -
192D LEU* 4.3 1.3 - - - +
203D ALA* 1.3 79.5 - - - +
205D VAL* 1.3 65.2 + - - +
206D ILE 5.1 0.2 - - - +
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Residues in contact with VAL 205 (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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27D VAL* 4.8 0.2 - - + -
30D PHE* 3.9 13.9 - - + -
31D MET* 4.0 17.7 - - + -
34D LEU* 3.8 26.5 - - + -
161D VAL* 3.9 17.5 - - + -
162D PHE 3.4 9.4 - - - +
163D VAL* 4.4 7.2 - - + -
189D VAL* 3.5 2.4 - - - -
190D TYR* 2.7 54.2 + - + -
192D LEU* 3.6 27.1 - - + +
204D VAL* 1.3 74.5 - - - +
206D ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 206 (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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147D LEU* 3.9 22.2 - - + -
160D LEU* 3.3 9.2 - - + +
161D VAL* 3.3 2.4 - - - +
162D PHE* 2.9 51.2 + - + +
164D VAL* 4.1 13.2 - - + -
168D TRP* 3.9 21.1 - - + -
181D LEU* 3.8 33.0 - - + -
187D THR* 3.9 23.8 - - + -
188D SER 3.4 3.4 - - - +
189D VAL* 4.8 0.4 - - + +
204D VAL* 4.0 0.6 - - + -
205D VAL* 1.3 74.2 - - - +
207D ARG* 1.3 66.1 + - - +
208D PHE* 4.4 6.3 - - + +
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Residues in contact with ARG 207 (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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34D LEU* 3.5 25.9 + - + +
36D GLU* 3.3 25.3 + - - +
159D VAL* 3.7 26.8 - - + +
160D LEU 3.2 7.9 - - - +
161D VAL* 4.1 14.1 - - + +
186D LYS* 3.9 7.2 - - - +
187D THR* 3.6 1.2 - - - -
188D SER* 2.8 46.6 + - - -
190D TYR* 3.8 32.7 - - + -
205D VAL 4.0 0.8 + - - -
206D ILE* 1.3 72.8 - - - +
208D PHE* 1.3 58.9 - - - +
209D GLN* 4.0 32.8 + - - +
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Residues in contact with PHE 208 (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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151D VAL* 3.7 26.9 - - + -
154D LEU* 4.0 13.0 - - + -
159D VAL* 3.3 5.6 - - - +
160D LEU* 2.6 55.0 + - + +
181D LEU* 3.3 39.9 - - + -
184D GLU* 3.6 15.9 - - + -
185D GLY* 3.5 29.8 - - - -
186D LYS 3.4 5.8 - - - -
187D THR* 3.4 17.7 - - - +
206D ILE* 3.9 9.3 - - + -
207D ARG* 1.3 74.9 - - - +
209D GLN* 1.3 60.3 + - - +
210D LYS* 3.8 20.2 - - + -
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Residues in contact with GLN 209 (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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157D GLY* 3.3 26.0 + - - +
158D GLY 3.3 3.8 - - - +
159D VAL* 4.2 13.6 - - + +
185D GLY* 3.3 2.3 - - - -
186D LYS* 2.8 63.3 + - + +
207D ARG* 4.0 21.9 + - - +
208D PHE* 1.3 78.0 - - - +
210D LYS* 1.3 60.3 + - - +
211D SER* 2.8 27.6 + - - +
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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