Contacts of the strand formed by residues 206 - 211 (chain A) in PDB entry 3GSB
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 ILE 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 3.0 26.7 + - - +
142A LYS* 3.8 16.4 - - + +
144A ILE* 3.6 24.5 - - + -
185A LEU* 3.3 34.1 - - + -
198A LEU 4.5 3.4 - - - +
199A PHE* 3.4 45.5 - - + -
202A ASN* 4.0 21.1 + - + +
204A GLY 4.9 0.2 - - - +
205A GLU* 1.3 77.6 - - - +
207A ALA* 1.3 60.8 + - - +
208A GLY 3.8 13.7 - - - +
240A ALA* 4.0 4.2 - - - +
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Residues in contact with ALA 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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134A MET* 3.8 15.9 - - + +
135A ARG* 4.6 1.3 - - + +
138A THR* 3.2 31.9 - - - +
140A ARG* 3.8 15.5 - - + +
142A LYS 3.1 18.4 + - - +
143A ILE* 4.4 7.9 - - + -
205A GLU 3.4 2.0 + - - -
206A ILE* 1.3 71.9 - - - +
208A GLY* 1.3 59.3 + - - +
240A ALA* 3.6 3.4 - - - -
241A LEU* 2.8 28.0 + - - +
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Residues in contact with GLY 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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134A MET* 3.1 13.9 - - - +
143A ILE* 3.2 5.9 - - - +
144A ILE* 2.9 32.4 + - - +
206A ILE* 3.5 8.5 - - - +
207A ALA* 1.3 83.8 - - - +
209A VAL* 1.3 59.9 + - - -
240A ALA* 4.4 3.8 - - - -
241A LEU 3.0 14.1 - - - -
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Residues in contact with VAL 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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134A MET* 5.0 0.7 - - - -
144A ILE* 3.3 31.4 - - + +
146A PHE* 3.6 33.2 - - + -
195A VAL* 4.7 7.6 - - + -
199A PHE* 4.4 6.7 - - + -
208A GLY* 1.3 77.2 - - - +
210A ILE* 1.3 64.8 + - - +
211A LEU* 4.5 7.2 - - + -
231A LEU* 4.4 10.3 - - + -
235A THR* 3.9 24.7 - - + -
241A LEU 2.9 7.3 + - - +
242A LEU* 3.8 5.4 - - + +
243A VAL* 2.9 28.8 + - - +
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Residues in contact with ILE 210 (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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127A CYS* 5.0 4.3 - - - -
130A VAL* 4.5 18.6 - - + -
134A MET* 5.2 7.4 - - - -
143A ILE* 4.8 6.7 - - + +
144A ILE 3.0 20.1 + - - +
145A LYS* 3.9 14.6 - - + -
146A PHE* 3.9 10.0 + - - -
151A HIS* 3.9 39.3 - - + +
157A PHE* 4.2 25.1 - - + -
208A GLY 4.3 0.2 - - - -
209A VAL* 1.3 75.0 - - - +
211A LEU* 1.3 70.8 + - - +
243A VAL* 3.2 25.1 - - + +
245A ASP* 4.6 8.1 - - + +
270A THR* 5.8 0.9 - - + -
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Residues in contact with LEU 211 (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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146A PHE* 3.9 15.7 - - + -
149A CYS* 4.7 2.5 - - - -
151A HIS* 4.0 9.9 - - - -
189A TYR* 4.2 8.1 - - + +
209A VAL* 4.5 4.7 - - + -
210A ILE* 1.3 80.0 - - - +
212A GLU* 1.3 72.5 + - - +
213A PRO* 3.1 7.7 - - + +
227A PHE* 4.1 11.4 - - + -
228A LEU* 3.9 19.1 - - + -
231A LEU* 3.5 31.9 - - + -
242A LEU* 4.2 8.1 - - + -
243A VAL 3.1 11.8 + - - +
244A PHE* 3.4 34.6 - - + -
245A ASP 2.9 22.2 + - - -
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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