Contacts of the strand formed by residues 204 - 213 (chain A) in PDB entry 2ANL
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 THR 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A PHE* 3.0 30.3 + - + +
203A LYS* 1.3 78.2 - - - +
205A SER* 1.3 61.8 + - - +
226A PHE* 3.3 19.0 + - + +
229A LYS* 3.5 33.0 - - - +
230A PHE* 3.4 40.8 - - + +
233A ASP* 4.5 6.5 - - - +
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Residues in contact with SER 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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199A VAL 2.2 29.8 + - - -
200A ASN* 2.3 28.4 + - - -
203A LYS 3.6 6.4 + - - -
204A THR* 1.3 78.2 + - - +
206A MET* 1.3 60.6 + - - +
226A PHE* 3.6 8.0 - - - -
229A LYS* 5.0 7.3 + - - -
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Residues in contact with MET 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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199A VAL* 3.1 29.8 + - - +
205A SER* 1.3 80.3 + - - +
207A GLU* 1.3 73.9 + - - +
208A LYS 4.0 1.1 + - - +
209A ALA* 4.1 17.1 + - + -
223A PRO* 5.6 2.0 - - - -
226A PHE* 4.0 21.3 - - + -
296A LYS* 3.6 15.3 - - + +
297A ASN* 3.4 35.0 - - + -
299A PHE* 4.8 10.5 - - + -
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Residues in contact with GLU 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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198A ASP* 2.6 32.9 - - - +
206A MET* 1.3 85.0 - - - +
208A LYS* 1.3 80.4 + - + +
209A ALA 3.3 2.6 + - - -
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Residues in contact with LYS 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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196A ASP* 4.0 31.3 + - + +
197A LEU 3.8 7.9 + - - +
198A ASP* 2.6 17.5 + - - +
206A MET* 5.0 0.9 - - - +
207A GLU* 1.3 87.0 - - + +
209A ALA* 1.3 67.6 + - - +
297A ASN* 4.9 6.9 + - - +
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Residues in contact with ALA 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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196A ASP* 3.6 8.4 - - - +
197A LEU 2.9 32.2 + - - +
199A VAL* 4.7 7.4 - - + -
206A MET* 4.1 20.4 - - + -
207A GLU 3.3 1.7 - - - -
208A LYS* 1.3 83.1 - - - +
210A ASN* 1.3 61.5 + - - +
211A VAL* 3.9 3.4 - - + -
297A ASN* 3.5 19.1 - - - +
299A PHE* 4.4 20.6 - - + -
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Residues in contact with ASN 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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188A ASN* 3.3 25.1 - - - +
189A HIS* 5.6 1.0 + - - -
194A GLN* 3.1 38.3 + - - +
195A VAL 4.0 1.6 - - - -
196A ASP* 5.2 0.9 - - - +
209A ALA* 1.3 72.2 - - - +
211A VAL* 1.3 66.3 + - - +
212A ILE* 3.9 2.0 - - - +
295A ASP* 4.8 4.0 - - - +
297A ASN* 2.5 31.2 + - - +
298A THR* 3.1 17.9 + - - +
299A PHE 2.8 26.9 + - - +
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Residues in contact with VAL 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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193A TRP 3.9 0.2 - - - +
194A GLN* 3.3 0.2 - - - -
195A VAL* 3.0 40.4 + - + +
197A LEU* 4.3 28.5 - - + -
199A VAL* 4.4 14.8 - - + -
209A ALA* 4.8 1.8 - - + -
210A ASN* 1.3 79.2 - - - +
212A ILE* 1.3 75.8 - - - +
213A VAL* 4.7 4.5 - - + -
259A PHE* 4.6 4.7 - - + -
299A PHE* 3.7 31.4 - - + +
301A LEU* 4.1 23.8 - - + -
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Residues in contact with ILE 212 (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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192A PHE* 3.7 38.8 - - + -
193A TRP 3.8 8.1 - - - +
194A GLN* 3.9 10.8 - - + +
210A ASN* 3.9 14.6 - - - +
211A VAL* 1.3 89.0 - - - +
213A VAL* 1.3 66.8 + - - +
214A ASP* 3.7 3.7 + - + -
298A THR* 4.5 10.8 - - + -
299A PHE 3.3 17.2 + - - +
300A ILE* 4.1 22.0 - - + -
301A LEU* 2.4 35.5 + - - +
3151A JE2 4.8 5.8 - - + -
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Residues in contact with VAL 213 (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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35A THR* 2.5 31.0 + - - +
193A TRP* 3.7 18.5 + - + +
195A VAL* 5.5 2.9 - - + -
211A VAL* 4.7 8.3 - - + +
212A ILE* 1.3 88.4 - - - +
214A ASP* 1.3 52.7 + - - +
215A SER 3.9 0.2 - - - -
301A LEU* 3.4 15.5 - - + +
305A PHE* 5.1 5.8 - - + -
306A MET* 4.6 11.2 - - - -
311A THR* 4.9 7.0 - - + -
313A PHE* 3.8 31.4 - - + -
320A ILE* 4.1 16.8 - - + -
322A PHE* 5.0 9.9 - - + -
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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