Contacts of the helix formed by residues 230 - 237 (chain D) in PDB entry 3DLX
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 PHE 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D VAL 5.4 0.2 - - - +
62D GLY* 4.6 0.4 - - - -
63D GLY 4.4 11.0 - - - +
64D PHE* 4.8 2.5 - + - -
90D ASN* 3.5 45.5 - - + +
138D GLN* 3.6 28.3 - - + -
141D LEU* 4.1 12.8 - - + -
142D ALA* 3.5 31.2 - - + -
145D ILE* 4.2 17.7 - - + -
229D ASN* 1.3 88.4 + - + +
231D ASN* 1.3 62.7 + - - -
232D LEU 3.3 1.3 + - - -
233D PRO* 3.5 8.3 - - + +
234D MET* 3.3 42.3 + - + +
382D SER* 3.3 29.6 - - - -
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Residues in contact with ASN 231 (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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62D GLY* 3.2 20.5 - - - -
68D GLY 2.9 21.7 + - - +
210D VAL* 3.7 10.7 - - + +
211D LYS 3.1 30.5 + - - +
223D PHE* 3.5 19.1 - - + -
227D ALA 2.9 24.5 + - - -
228D ARG 2.7 12.1 + - - +
229D ASN* 3.7 7.7 + - - -
230D PHE* 1.3 78.4 - - - +
232D LEU* 1.3 58.7 + - - +
235D CYS* 3.3 26.7 + - - -
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Residues in contact with LEU 232 (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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223D PHE* 4.0 10.4 - - + -
228D ARG* 3.4 42.3 + - + +
231D ASN* 1.3 76.1 - - - +
233D PRO* 1.4 78.7 - - + +
234D MET 3.3 0.3 + - - -
235D CYS* 3.3 18.0 + - - +
236D LYS* 3.6 28.3 - - - +
260D HIS* 3.5 30.7 - - + +
261D ILE* 3.6 14.5 - - + +
381D SER* 4.0 13.7 - - - +
383D ASP* 4.4 5.4 - - - +
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Residues in contact with PRO 233 (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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142D ALA* 4.4 10.1 - - - +
145D ILE* 3.4 23.8 - - + +
146D ARG* 4.6 7.8 - - + +
229D ASN 3.5 15.3 - - - +
230D PHE* 3.5 19.5 - - + +
232D LEU* 1.4 100.2 - - + +
234D MET* 1.3 59.6 + - - +
236D LYS* 3.2 20.0 + - + +
237D ALA* 3.7 5.4 + - - +
383D ASP* 3.6 37.9 - - + +
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Residues in contact with MET 234 (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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60D LEU* 3.8 20.4 - - + +
61D VAL 3.6 32.5 - - - +
62D GLY* 3.7 6.5 - - - -
88D VAL* 3.3 30.3 - - + +
89D SER* 4.4 3.8 - - - -
90D ASN 5.0 1.1 - - - +
141D LEU* 6.1 0.4 - - + -
145D ILE* 3.5 39.5 - - + -
208D ALA* 3.3 17.6 - - - +
210D VAL* 4.2 9.0 - - + -
230D PHE* 3.3 33.1 + - + +
231D ASN 4.0 3.1 - - - +
232D LEU 3.2 1.2 - - - -
233D PRO* 1.3 71.8 - - - +
235D CYS* 1.3 65.1 + - - +
236D LYS 3.1 2.6 + - - -
237D ALA 3.5 7.6 + - - -
238D ALA 3.9 1.2 + - - -
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Residues in contact with CYS 235 (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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393C HIS* 5.4 0.3 - - - -
210D VAL* 3.6 23.5 - - - +
221D VAL* 5.7 0.7 - - - -
223D PHE* 4.6 2.2 - - - -
231D ASN 3.3 16.9 + - - -
232D LEU 3.3 10.0 + - - +
234D MET* 1.3 78.0 - - - +
236D LYS* 1.3 59.0 + - - +
238D ALA 4.7 1.6 + - - +
241D THR* 2.8 35.0 + - + -
243D VAL* 4.5 3.8 - - - -
261D ILE* 3.9 35.9 - - + -
265D TYR* 3.3 16.8 - - + +
267D HIS* 5.3 0.9 - - - -
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Residues in contact with LYS 236 (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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384C GLU* 2.8 35.7 + - - +
387C ALA* 6.0 1.8 - - + -
393C HIS* 3.1 19.2 - - - -
146D ARG* 5.9 10.2 - - + +
149D GLY* 3.1 26.5 - - - +
232D LEU* 3.6 30.3 - - - +
233D PRO* 3.2 10.7 + - + +
234D MET 3.1 1.2 - - - -
235D CYS* 1.3 79.0 - - - +
237D ALA* 1.3 60.6 + - - +
238D ALA 3.6 2.3 + - - +
260D HIS 5.3 0.4 - - - -
261D ILE* 3.5 23.6 - - + -
262D PRO* 5.9 0.4 - - - -
265D TYR* 3.6 40.8 - - + +
383D ASP* 5.1 4.8 + - - -
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Residues in contact with ALA 237 (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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60D LEU* 3.7 11.2 - - + -
145D ILE* 3.3 45.3 - - + +
148D GLY 4.7 0.4 - - - -
149D GLY* 3.8 10.3 - - - +
203D ILE 3.9 8.1 - - - +
204D THR* 3.2 14.5 - - - +
205D GLY 3.1 17.2 + - - -
233D PRO 3.9 1.1 - - - +
234D MET 3.5 1.4 + - - -
236D LYS* 1.3 77.9 - - - +
238D ALA* 1.3 59.3 + - - +
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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