Contacts of the helix formed by residues 304 - 310 (chain B) 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 ASP 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A MET* 4.0 18.1 - - + +
276B ILE* 5.9 0.2 - - - +
303B TYR* 1.3 87.9 - - - +
305B PRO* 1.3 69.9 - - - +
306B MET* 2.9 38.9 + - - +
307B LEU* 3.0 30.6 + - + +
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Residues in contact with PRO 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 3.9 10.1 - - + -
275A MET* 5.2 4.3 - - - -
295A PRO* 4.2 21.8 - - + -
299A LYS 3.3 25.8 - - - +
300A MET* 4.3 0.2 - - - -
301A LEU* 3.4 33.0 - - + -
303B TYR* 3.3 18.8 - - + +
304B ASP* 1.3 88.4 - - - +
306B MET* 1.3 56.8 + - - +
307B LEU 3.1 0.2 - - - -
308B LEU* 3.0 6.2 + - + +
309B PHE* 2.8 28.0 + - - +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 5.0 25.4 - - + +
294A VAL* 5.1 8.7 - - + -
295A PRO* 4.4 19.7 - - + +
304B ASP* 2.9 19.2 + - - +
305B PRO* 1.3 76.4 - - - +
307B LEU* 1.3 56.5 + - + +
309B PHE* 3.3 39.7 - - + -
310B THR* 2.6 36.1 + - + +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ILE* 4.3 19.3 - - + -
279B LEU* 4.0 27.1 - - + -
280B ALA* 4.1 22.7 - - + -
303B TYR* 4.1 5.8 - - + -
304B ASP* 3.0 33.8 + - + +
306B MET* 1.3 75.9 - - + +
308B LEU* 1.3 64.0 - - - +
310B THR* 3.3 7.8 + - - -
312B ARG* 3.1 52.3 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A VAL* 3.6 22.4 - - + -
314A TRP* 3.4 55.6 - - + +
315A LYS* 3.8 2.7 - - - -
316A GLY* 3.3 12.8 - - - +
279B LEU* 4.9 3.3 - - + +
303B TYR* 3.7 19.7 - - + +
304B ASP 4.1 0.6 + - - -
305B PRO 3.0 8.7 + - - +
307B LEU* 1.3 80.1 - - - +
309B PHE* 1.3 66.2 + - - +
311B GLY 2.9 14.4 + - - -
312B ARG* 3.1 32.9 + - + +
314B TRP* 4.3 15.0 - - + -
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A VAL* 4.6 13.6 - - + +
292A VAL 3.6 11.7 - - - -
293A GLY 3.9 12.8 - - - -
294A VAL* 3.7 22.9 - - + -
295A PRO* 4.0 10.3 - - + -
316A GLY* 3.9 6.3 - - - -
317A CYS 3.3 25.3 + - - -
318A VAL* 3.7 23.8 - - + +
501A ACT 5.5 0.7 - - + -
1377A NAD 3.5 31.6 - - - -
305B PRO 2.8 19.0 + - - +
306B MET* 3.3 36.3 - - + +
307B LEU 3.7 0.2 - - - -
308B LEU* 1.3 71.8 - - - +
310B THR* 1.3 63.1 + - + +
311B GLY 2.8 6.8 + - - -
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Residues in contact with THR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.5 14.2 - - + +
116A ILE* 3.5 19.5 - - + -
318A VAL* 3.9 10.3 - - + +
284B MET* 3.1 51.8 + - + +
285B ASN* 2.9 25.6 + - - +
306B MET* 2.6 26.7 + - + +
307B LEU* 3.3 7.3 + - - -
309B PHE* 1.3 84.1 - - + +
311B GLY* 1.3 54.8 + - - +
312B ARG* 4.2 0.7 + - - -
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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