Contacts of the helix formed by residues 305 - 310 (chain D) in PDB entry 1D1T
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 PRO 305 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C LEU* 3.7 21.1 - - + -
275C MET* 5.1 4.0 - - - -
295C PRO* 4.1 16.2 - - + -
299C LYS 3.1 26.7 - - - +
301C LEU* 3.3 30.3 - - + +
303D TYR* 3.0 25.8 - - + +
304D ASP* 1.3 84.4 - - - +
306D MET* 1.3 52.0 + - - +
308D LEU* 2.7 33.4 + - - +
309D PHE* 3.2 5.2 + - - +
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Residues in contact with MET 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 5.7 9.2 - - + +
294C VAL* 4.7 8.7 - - + -
295C PRO* 3.8 24.8 - - - +
296C PRO 5.9 1.1 - - - +
297C SER* 6.4 1.6 - - - -
304D ASP* 3.0 24.6 + - - +
305D PRO* 1.3 78.4 - - - +
307D LEU* 1.3 62.1 + - - +
308D LEU 3.3 0.2 + - - -
309D PHE* 3.4 39.7 - - + +
310D THR* 3.3 33.3 + - + +
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Residues in contact with LEU 307 (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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276D ILE* 4.4 16.8 - - + -
279D LEU* 4.2 24.0 - - + -
280D ALA* 3.9 30.5 - - + -
303D TYR* 4.5 0.4 - - + -
304D ASP* 2.9 37.1 + - + +
306D MET* 1.3 77.3 - - - +
308D LEU* 1.3 58.3 + - - +
310D THR* 3.1 15.9 + - - -
312D ARG* 3.1 40.8 + - - +
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Residues in contact with LEU 308 (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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275C MET* 6.4 0.9 - - - -
291C VAL* 3.9 16.2 - - + -
314C TRP* 3.5 57.7 - - + +
315C LYS 4.5 0.7 - - - +
316C GLY* 3.7 13.2 + - - +
279D LEU* 4.9 3.1 - - + +
303D TYR* 3.6 24.6 - - + +
304D ASP 4.2 0.2 + - - -
305D PRO 2.7 11.5 + - - +
307D LEU* 1.3 75.7 - - - +
309D PHE* 1.3 65.6 + - - +
310D THR 3.1 2.5 - - - -
311D GLY 2.8 14.6 + - - -
312D ARG* 3.2 25.9 + - + +
314D TRP* 4.2 22.0 - - + -
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Residues in contact with PHE 309 (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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116C ILE* 6.6 0.4 - - + -
291C VAL* 4.3 13.4 - - + +
292C VAL 3.5 11.2 - - - -
293C GLY 3.9 12.8 - - - -
294C VAL* 3.6 24.0 - - + -
295C PRO* 4.0 13.9 - - + -
316C GLY* 3.9 7.2 - - - -
317C CYS 3.4 22.8 + - - -
318C VAL* 3.7 22.0 - - + +
505C ACT 5.2 0.7 - - - -
3377C NAD 3.0 35.2 - - - -
305D PRO 3.2 5.8 + - - +
306D MET* 3.4 36.5 + - + +
308D LEU* 1.3 78.5 - - - +
310D THR* 1.3 62.6 + - + +
311D GLY 2.8 6.3 + - - -
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Residues in contact with THR 310 (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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110C LEU* 3.5 25.6 - - + +
116C ILE* 4.9 12.1 - - + -
318C VAL* 4.3 5.9 - - + +
284D MET* 3.0 43.1 + - + +
285D ASN* 2.7 34.0 + - - +
306D MET* 3.3 20.5 + - + +
307D LEU 3.1 15.2 + - - -
308D LEU 2.9 2.0 + - - -
309D PHE* 1.3 81.0 - - + +
311D GLY* 1.3 47.9 + - - +
312D ARG* 3.7 1.2 + - - -
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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