Contacts of the strand formed by residues 220 - 227 (chain D) in PDB entry 1DVM
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 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C ALA 4.5 3.7 + - - -
27C SER* 3.9 8.8 + - - -
28C LYS* 3.3 38.8 + - + -
30C ARG* 3.6 28.8 - - + +
212D GLU* 4.0 19.1 - - - +
213D PHE 3.1 5.6 - - - +
214D THR* 3.2 39.7 - - + -
218D GLY* 4.3 17.3 - - - -
219D HIS* 1.3 71.7 - - - +
221D TYR* 1.3 65.8 + - - +
240D PRO* 3.8 14.6 - - - +
241D TYR 4.5 2.8 + - - -
242D GLU* 5.6 5.2 - - - -
245D VAL* 4.4 7.5 - - - +
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Residues in contact with TYR 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D GLU* 3.4 8.5 - - - +
213D PHE* 2.6 41.7 + + + +
215D THR* 4.0 6.3 - - + -
219D HIS* 3.3 39.7 - - + +
220D TYR* 1.3 72.4 - - - +
222D ASP* 1.3 64.4 + - - +
223D ILE* 3.7 19.1 - - + -
238D ALA 4.8 0.9 - - - -
239D ALA 3.7 7.0 - - - +
240D PRO* 3.5 40.4 - - + -
241D TYR 5.3 0.4 - - - +
245D VAL* 4.4 2.5 - - + -
246D PRO 2.5 27.9 + - - -
247D LEU* 4.4 6.7 - - + -
249D ALA* 3.0 17.7 - - - +
250D LEU* 3.6 40.1 + - + -
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Residues in contact with ASP 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D TYR* 2.8 33.5 + - + -
212D GLU* 4.7 4.7 - - - +
221D TYR* 1.3 72.0 - - - +
223D ILE* 1.3 60.4 + - - +
224D LEU* 3.9 2.5 + - + +
237D ILE* 2.9 13.9 - - - +
238D ALA* 3.5 0.5 - - - -
239D ALA* 2.8 38.7 + - + +
241D TYR* 4.3 20.7 - - - +
352D ILE* 4.5 19.1 - - + +
354D ILE* 5.6 1.0 - - + +
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Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ASN 3.9 0.2 - - - +
210D TYR* 3.3 10.0 - - - -
211D THR* 3.0 42.7 + - + +
213D PHE* 3.4 28.0 - - + -
221D TYR* 3.7 22.0 - - + +
222D ASP* 1.3 79.3 - - - +
224D LEU* 1.3 63.8 + - - +
236D PHE* 4.5 4.0 - - + -
237D ILE 3.2 4.9 - - - +
238D ALA* 3.7 18.4 - - + -
262D TRP* 3.5 43.7 - - + +
266D MET* 3.8 15.6 - - + +
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE* 3.9 22.7 - - + -
209D ASN 3.6 15.5 - - - +
210D TYR* 3.8 25.6 - - + -
222D ASP* 5.0 3.4 - - + +
223D ILE* 1.3 74.4 - - - +
225D GLU* 1.3 61.4 + - - +
226D LEU* 4.5 5.6 - - + -
235D MET 3.7 0.7 - - - +
236D PHE* 3.1 9.4 - - - +
237D ILE* 2.7 51.4 + - + +
266D MET* 5.0 0.7 - - - -
273D LEU* 3.6 37.2 - - + -
352D ILE* 4.2 23.3 - - + -
354D ILE* 5.0 6.3 - - + -
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE* 4.7 8.3 - - - -
209D ASN* 3.0 52.8 + - + +
224D LEU* 1.3 75.6 - - - +
226D LEU* 1.3 68.2 + - - +
227D PRO* 3.7 15.4 - - + +
234D SER* 2.8 31.9 + - - +
235D MET 3.6 2.5 - - - +
236D PHE* 3.7 34.4 - - + -
263D LYS* 4.4 8.3 - - - +
266D MET* 4.2 3.4 - - - +
365D ASN* 4.3 5.5 + - - +
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D TRP* 3.4 25.6 - - + -
179D PHE* 4.0 18.6 - - + -
208D PHE* 4.6 9.4 - - + -
224D LEU* 4.2 9.0 - - + +
225D GLU* 1.3 78.0 - - - +
227D PRO* 1.3 66.3 - - - +
228D TYR* 3.8 0.3 + - - -
234D SER* 3.7 1.5 - - - -
235D MET* 2.8 55.0 + - + +
237D ILE* 3.5 31.2 - - + -
273D LEU* 3.4 32.5 - - + -
275D LEU* 4.4 8.1 - - + -
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Residues in contact with PRO 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D TRP* 3.7 7.1 - - - +
176D LYS* 3.0 37.0 + - + +
177D THR 4.6 0.3 + - - -
208D PHE* 6.3 1.1 - - + -
209D ASN* 6.5 0.7 - - + -
225D GLU* 3.7 16.2 - - + +
226D LEU* 1.3 86.4 - - + +
228D TYR* 1.3 61.0 - - - +
231D ASP* 3.6 25.4 - - - +
233D LEU 3.7 7.4 - - - +
234D SER* 3.8 12.8 - - - +
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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