Contacts of the strand formed by residues 203 - 209 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.2 8.1 - - + -
164A VAL 3.4 11.4 - - - +
165A PRO* 4.3 0.7 - - - -
191A TYR* 4.5 0.9 - - - -
192A LEU* 3.0 9.4 + - + +
193A GLY* 2.8 39.4 + - - +
195A VAL* 4.1 8.3 - - + -
196A PHE* 3.7 32.8 - - + -
201A VAL* 4.8 2.0 - - + +
202A SER* 1.3 73.4 - - - +
204A VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE 3.9 0.3 - - - +
163A VAL* 3.5 4.8 - - - +
164A VAL* 2.8 42.5 + - + +
165A PRO 3.6 7.0 - - - +
166A ALA* 3.7 20.0 - - + -
168A TRP* 3.5 30.7 - - + +
169A LEU* 4.4 7.6 - - + -
189A VAL* 4.2 19.7 - - + -
190A TYR 3.3 6.3 - - - +
191A TYR* 3.8 24.9 - - + -
192A LEU* 4.2 1.6 - - - +
203A ALA* 1.3 78.6 - - - +
205A VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 4.2 8.7 - - + -
31A MET* 3.8 25.1 - - + -
34A LEU* 4.0 10.5 - - + -
161A VAL* 4.0 23.3 - - + -
162A PHE 3.4 10.3 - - - +
163A VAL* 4.4 2.7 - - + -
189A VAL* 3.4 4.6 - - - +
190A TYR* 2.7 63.3 + - + +
192A LEU* 3.6 26.5 - - + -
204A VAL* 1.3 74.1 - - - +
206A ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.8 18.8 - - + -
160A LEU* 3.5 3.5 - - + +
161A VAL* 3.3 6.1 - - - +
162A PHE* 3.0 52.8 + - + +
164A VAL* 4.3 12.3 - - + -
168A TRP* 3.8 30.1 - - + -
181A LEU* 3.9 24.2 - - + -
187A THR* 3.7 29.8 - - + -
188A SER 3.4 2.9 - - - +
189A VAL* 4.7 0.9 - - + +
204A VAL* 4.0 0.8 - - + -
205A VAL* 1.3 74.4 - - - +
207A ARG* 1.3 66.8 + - - +
208A PHE* 4.4 7.4 - - + +
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.1 29.6 + - + +
36A GLU* 4.1 21.8 + - - +
159A VAL* 3.6 29.5 - - + +
160A LEU 3.3 8.1 - - - +
161A VAL* 4.2 15.5 - - + +
186A LYS* 3.8 5.2 - - - +
187A THR* 3.5 2.1 - - - -
188A SER* 2.7 44.2 + - - +
190A TYR* 3.8 31.6 - - + -
205A VAL 4.0 1.0 + - - -
206A ILE* 1.3 73.0 - - - +
208A PHE* 1.3 59.9 + - - +
209A GLN* 4.0 31.7 + - - +
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.7 28.3 - - + -
154A LEU* 3.8 14.6 - - + -
159A VAL* 3.3 3.3 - - - +
160A LEU* 2.6 57.9 + - + +
181A LEU* 3.3 39.0 - - + -
184A GLU* 3.5 17.3 - - + -
185A GLY* 3.5 28.3 - - - -
186A LYS 3.5 9.6 - - - -
187A THR* 3.7 12.1 - - + +
206A ILE* 3.9 10.2 - - + -
207A ARG* 1.3 77.2 - - - +
209A GLN* 1.3 61.1 + - - +
210A LYS* 3.7 20.9 - - + -
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU* 5.2 4.4 + - - -
157A GLY* 3.2 26.1 + - - +
158A GLY 3.2 3.6 - - - +
159A VAL* 3.9 15.1 - - + +
185A GLY* 3.3 2.6 - - - -
186A LYS* 2.8 62.1 + - + +
207A ARG* 4.0 23.0 + - - +
208A PHE* 1.3 78.7 - - - +
210A LYS* 1.3 55.7 + - - +
211A SER* 2.7 33.6 + - - +
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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