Contacts of the strand formed by residues 237 - 250 (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 TYR 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PHE* 3.2 20.6 - - - +
193A GLN* 4.1 10.8 - - + +
194A GLU* 4.0 3.1 - - - +
230A CYS* 6.1 1.0 - - - +
235A ALA* 3.6 8.3 - - - +
236A GLU* 1.3 93.6 + - + +
238A GLY* 1.3 62.6 + - - +
239A LEU* 4.0 34.8 - - + -
240A TYR* 5.2 1.0 + - - -
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Residues in contact with GLY 238 (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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191A ARG* 3.3 5.2 - - - -
192A PHE* 2.8 43.2 + - - +
237A TYR* 1.3 77.3 - - - +
239A LEU* 1.3 66.3 - - - +
240A TYR* 3.4 26.2 - - - -
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Residues in contact with LEU 239 (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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189A TYR* 3.4 28.0 - - + +
190A PHE 3.7 3.1 - - - -
191A ARG* 4.1 16.4 - - + -
237A TYR* 4.0 28.9 - - + -
238A GLY* 1.3 83.6 - - - +
240A TYR* 1.3 71.2 + - - +
241A SER 4.0 2.2 + - - -
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Residues in contact with TYR 240 (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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189A TYR* 4.0 1.2 - - - -
190A PHE* 2.8 41.6 + - + +
192A PHE* 3.7 15.2 - + - -
206A MET* 3.6 35.4 - - + -
227A ARG* 3.8 33.4 - - + -
228A ASN 3.8 14.4 - - - -
229A SER* 3.5 6.9 - - - -
230A CYS* 3.0 31.5 + - - +
237A TYR 5.2 0.9 + - - -
238A GLY* 3.4 28.9 - - - -
239A LEU* 1.3 82.0 - - - +
241A SER* 1.3 63.7 + - - +
242A ILE* 3.6 3.2 + - + +
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Residues in contact with SER 241 (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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187A GLN* 4.2 22.9 + - - -
188A THR 3.7 5.6 - - - -
189A TYR* 3.2 27.3 - - - +
227A ARG* 5.9 1.0 - - - +
239A LEU 4.0 1.2 - - - -
240A TYR* 1.3 73.5 - - - +
242A ILE* 1.3 61.2 + - - +
243A TYR 4.2 0.9 + - - -
272A ALA* 5.2 1.0 + - - +
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Residues in contact with ILE 242 (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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187A GLN* 3.1 2.9 - - - -
188A THR* 2.8 42.6 + - - +
190A PHE* 3.7 21.3 - - + -
206A MET* 3.5 28.9 - - + +
207A VAL 4.7 0.2 - - - +
208A GLN* 3.0 16.7 + - + +
225A SER* 2.8 42.8 - - - +
226A ALA 4.6 0.7 - - - -
227A ARG* 4.3 24.2 - - + +
240A TYR* 4.1 8.7 - - + +
241A SER* 1.3 77.4 - - - +
243A TYR* 1.3 62.8 + - - +
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Residues in contact with TYR 243 (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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183A TYR* 2.7 30.2 + - - -
185A TYR* 3.2 38.1 - + + +
186A SER 3.3 11.7 - - - -
187A GLN* 3.8 28.3 - - + +
225A SER* 5.0 1.9 - - - -
241A SER 4.1 2.2 + - - -
242A ILE* 1.3 79.0 - - - +
244A GLN* 1.3 76.6 + - - +
245A GLY 3.9 1.1 - - - -
274A PHE* 4.6 7.0 - + - -
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Residues in contact with GLN 244 (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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185A TYR* 3.2 4.2 - - - +
186A SER 3.0 29.5 + - - +
208A GLN* 2.9 48.4 + - - +
210A ILE* 3.8 12.2 - - + +
223A MET* 3.4 26.9 + - + +
224A LYS 3.1 26.9 + - - +
225A SER* 3.3 15.8 + - - +
243A TYR* 1.3 86.4 - - - +
245A GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 245 (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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183A TYR* 3.6 19.6 + - - -
184A ILE 2.9 14.8 - - - -
185A TYR* 3.9 0.7 - - - -
223A MET* 3.3 14.5 - - - +
243A TYR* 3.9 3.8 - - - -
244A GLN* 1.3 78.5 - - - +
246A GLY* 1.3 58.8 + - - -
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Residues in contact with GLY 246 (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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182A TYR 3.5 1.2 - - - +
183A TYR* 3.5 15.0 - - - -
184A ILE 2.9 28.7 + - - +
223A MET* 3.4 8.9 - - - -
245A GLY* 1.3 74.5 - - - -
247A ILE* 1.3 62.4 + - - -
248A PHE* 3.5 13.1 - - - -
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Residues in contact with ILE 247 (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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181A PHE* 3.9 29.2 - - + -
182A TYR 3.2 13.0 - - - +
183A TYR* 4.1 19.1 - - + -
246A GLY* 1.3 73.5 - - - -
248A PHE* 1.3 76.3 + - - +
280A VAL* 4.2 15.5 - - + -
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Residues in contact with PHE 248 (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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181A PHE* 4.4 3.4 - - - -
182A TYR* 2.8 31.1 + - - +
184A ILE* 4.0 24.0 - - + -
222A LEU* 3.6 42.8 - - + -
223A MET* 3.5 42.0 - - + -
246A GLY* 3.5 22.7 - - - -
247A ILE* 1.3 79.2 - - - +
249A GLU* 1.3 65.3 + - - +
250A LEU* 3.5 11.6 + - + +
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Residues in contact with GLU 249 (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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180A GLY* 3.6 18.0 - - - +
181A PHE* 3.2 41.1 - - + -
212A LYS* 4.2 12.6 + - - -
248A PHE* 1.3 72.3 - - - +
250A LEU* 1.3 75.4 + - - +
251A LYS* 5.7 7.5 - - + +
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Residues in contact with LEU 250 (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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176A ILE* 3.7 37.9 - - + -
179A LYS* 3.3 4.1 - - - +
180A GLY 2.8 32.8 + - - -
182A TYR* 3.7 28.5 - - + -
184A ILE* 4.0 10.3 - - + -
212A LYS* 3.8 17.9 - - + +
222A LEU* 4.9 0.9 - - + -
248A PHE* 3.9 19.7 - - + +
249A GLU* 1.3 87.8 - - - +
251A LYS* 1.3 64.2 + - - +
254A ASP* 3.6 4.5 - - + +
256A ILE* 3.7 28.3 - - + -
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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