Contacts of the strand formed by residues 205 - 213 (chain A) in PDB entry 1DG6
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 GLN 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ASP* 4.2 8.2 + - - +
204A LYS* 1.3 73.0 - - - +
206A MET* 1.3 52.7 + - - +
207A VAL* 3.9 13.7 - - + +
227A ARG 3.7 4.9 - - - -
228A ASN* 4.8 3.8 - - + +
261A THR* 2.7 27.4 + - + +
262A ASN* 2.9 16.3 + - - +
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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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190A PHE* 3.6 46.2 - - + -
192A PHE* 4.0 11.0 - - - -
204A LYS* 4.1 10.8 - - + +
205A GLN* 1.3 73.4 - - - +
207A VAL* 1.3 59.4 + - - +
226A ALA* 3.3 2.3 - - - -
227A ARG* 2.8 42.6 + - + +
228A ASN 3.6 6.7 - - - -
229A SER* 3.4 36.3 - - - +
240A TYR* 3.6 42.4 - - + -
242A ILE* 3.5 10.5 - - + +
261A THR* 3.5 3.4 - - - -
262A ASN* 4.6 5.2 - - + +
265A LEU* 5.2 2.0 - - + -
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Residues in contact with VAL 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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190A PHE* 4.0 5.1 - - - -
205A GLN* 4.2 17.9 - - + +
206A MET* 1.3 79.5 - - - +
208A GLN* 1.3 67.3 + - - +
209A TYR* 3.5 38.2 + - + +
224A LYS* 4.6 7.9 - - + -
225A SER 3.3 16.2 - - - +
226A ALA* 3.9 16.4 - - + -
260A VAL* 3.2 9.2 - - - +
261A THR* 3.0 45.2 + - + +
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Residues in contact with GLN 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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186A SER* 3.2 24.0 + - - -
188A THR* 3.1 29.6 + - + +
190A PHE* 5.2 0.2 - - + -
207A VAL* 1.3 74.1 - - - +
209A TYR* 1.3 63.4 + - - +
210A ILE* 3.4 13.7 - - - +
224A LYS* 3.2 4.2 - - - +
225A SER* 2.9 42.2 + - - +
242A ILE* 3.0 33.8 + - + +
244A GLN* 2.9 34.9 + - - +
258A VAL* 3.8 17.5 - - + -
259A SER 3.6 3.6 - - - +
260A VAL* 4.2 1.3 - - + -
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Residues in contact with TYR 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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147A LEU* 3.6 45.8 - - + +
148A GLY* 4.0 4.0 - - - -
207A VAL* 3.5 36.3 - - + +
208A GLN* 1.3 72.8 - - - +
210A ILE* 1.3 63.6 + - - +
211A TYR* 3.5 14.6 - + + -
221A LEU* 3.8 18.2 - - + -
223A MET 3.5 3.1 - - - -
224A LYS* 4.0 22.0 - - + -
257A PHE 3.9 0.2 - - - +
258A VAL* 3.3 7.3 - - - +
259A SER* 2.8 63.3 + - - +
261A THR* 4.0 18.9 - - + +
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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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184A ILE* 4.0 11.9 - - + -
185A TYR* 4.2 5.4 - - - -
186A SER* 4.0 18.8 - - - +
208A GLN* 3.4 23.1 - - - +
209A TYR* 1.3 77.7 - - - +
211A TYR* 1.3 57.3 + - - +
221A LEU* 3.5 2.4 - - - +
222A LEU* 2.8 36.8 + - + +
223A MET* 2.9 42.2 + - + +
244A GLN* 3.8 14.1 - - + +
256A ILE* 3.8 25.6 - - + -
257A PHE 3.4 4.9 - - - +
258A VAL* 4.4 10.8 - - + -
275A PHE* 4.7 2.9 - - + -
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Residues in contact with TYR 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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144A GLU* 5.5 6.5 + - - -
145A LYS 4.5 1.3 + - - -
146A ALA* 3.5 22.3 - - + -
147A LEU* 2.9 35.6 + - - +
209A TYR* 3.5 26.0 - - + -
210A ILE* 1.3 75.1 - - - +
212A LYS* 1.3 58.9 + - - +
219A PRO* 3.9 17.5 - - + -
220A ILE 3.4 6.3 - - - -
221A LEU* 3.5 41.0 - - + +
222A LEU* 4.5 2.2 - - - -
256A ILE* 3.2 10.8 - - - +
257A PHE* 2.9 65.1 + + + -
259A SER* 3.6 17.5 - - - -
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Residues in contact with LYS 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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211A TYR* 1.3 74.7 - - - +
213A TYR* 1.3 75.5 - - - +
214A THR* 3.9 24.1 + - - +
219A PRO* 3.5 3.8 - - - +
220A ILE* 2.8 60.4 + - - +
222A LEU* 4.1 22.0 - - + +
249A GLU 4.2 13.7 + - - -
250A LEU* 3.8 14.6 - - + -
254A ASP* 3.7 19.8 + - + +
255A ARG 3.3 4.0 - - - -
256A ILE* 3.8 16.6 - - + -
257A PHE* 5.1 0.2 - - - -
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Residues in contact with TYR 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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145A LYS* 6.2 0.3 - - - -
150A LYS* 5.3 1.8 - - - -
173A GLU* 4.0 5.2 - - - -
212A LYS* 1.3 73.4 - - - +
214A THR* 1.3 63.7 + - - +
216A TYR 4.7 7.0 - - - -
217A PRO 4.2 7.9 - - - -
218A ALA 4.1 5.4 - - - -
219A PRO* 3.7 40.1 - - + +
253A ASN 4.5 0.7 - - - +
254A ASP* 3.3 8.1 - - - +
255A ARG* 2.7 87.2 + - + +
257A PHE* 3.6 34.4 - + - -
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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