Contacts of the helix formed by residues 271 - 280 (chain A) 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 HIS 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLU* 3.0 15.1 + - - +
269A ILE* 3.4 21.5 - - + +
270A GLY* 1.3 85.6 + - - +
272A LEU* 1.3 63.8 + - - +
273A GLU* 3.8 14.5 + - + +
274A THR* 3.1 18.9 + - + +
275A MET* 3.1 12.2 + - - +
296A PRO* 5.0 1.3 - - - -
401A ZN 2.2 36.3 - - - -
504A ACT 4.0 8.4 + - - -
1377A NAD 3.6 12.0 + - - -
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Residues in contact with LEU 272 (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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270A GLY 4.3 0.6 + - - -
271A HIS* 1.3 71.6 - - - +
273A GLU* 1.3 74.7 + - - +
275A MET* 3.0 23.0 + - - +
276A ILE* 3.1 20.4 + - + +
295A PRO* 3.9 28.5 - - + -
296A PRO* 4.3 14.2 - - + +
299A LYS* 3.9 22.7 - - + +
300A MET 3.3 28.3 - - - +
301A LEU* 4.0 16.4 - - + +
305B PRO* 3.9 17.9 - - + -
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Residues in contact with GLU 273 (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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271A HIS* 3.8 13.3 + - + +
272A LEU* 1.3 95.0 + - - +
274A THR* 1.3 59.5 + - + +
276A ILE* 3.4 12.6 + - + +
277A ASP* 3.0 35.2 + - - +
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Residues in contact with THR 274 (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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198A PHE* 4.7 9.6 - - + -
267A GLU* 2.6 30.5 + - - +
269A ILE* 3.9 18.4 - - + +
271A HIS* 3.1 17.6 + - + +
273A GLU* 1.3 78.2 - - + +
275A MET* 1.3 59.6 + - - +
277A ASP* 3.6 15.3 - - + +
278A ALA* 2.7 31.4 + - - +
1377A NAD 4.0 26.2 - - - +
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Residues in contact with MET 275 (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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267A GLU* 3.6 22.0 - - + +
270A GLY 4.1 7.6 - - - -
271A HIS 3.1 24.5 + - - +
272A LEU* 3.0 18.5 + - - +
274A THR* 1.3 76.6 - - - +
276A ILE* 1.3 56.7 + - - +
278A ALA* 3.2 3.8 + - - +
279A LEU* 3.0 26.7 + - - +
289A SER* 4.5 1.7 + - - -
291A VAL* 3.8 25.5 - - + +
293A GLY 3.5 24.5 - - - +
295A PRO* 3.6 34.1 - - + -
301A LEU* 4.6 13.5 - - + -
314A TRP* 4.5 12.1 + - + -
305B PRO* 5.2 3.8 - - - -
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Residues in contact with ILE 276 (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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272A LEU 3.1 14.5 + - - +
273A GLU* 3.6 10.5 - - - +
275A MET* 1.3 74.5 - - - +
277A ASP* 1.3 62.5 + - - +
279A LEU* 3.0 9.3 + - + +
280A ALA* 2.9 32.0 + - + +
301A LEU* 3.3 35.0 - - + -
302A THR 3.4 16.4 - - - +
303A TYR* 4.3 17.0 - - + -
307A LEU* 4.8 13.5 - - + -
314A TRP* 5.3 1.8 - - + -
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Residues in contact with ASP 277 (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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198A PHE* 3.9 8.3 - - + -
250A ILE* 3.9 24.8 + - + +
251A SER* 4.9 1.0 - - - -
273A GLU* 3.0 28.2 + - - +
274A THR* 3.3 16.7 + - + +
276A ILE* 1.3 78.9 - - - +
278A ALA* 1.3 56.2 + - - +
280A ALA* 4.1 4.7 - - - +
281A SER* 2.6 34.7 + - - -
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Residues in contact with ALA 278 (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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198A PHE* 3.9 26.0 - - + -
265A THR* 2.8 29.7 + - - +
267A GLU* 4.2 18.6 - - + +
274A THR 2.7 20.9 + - - +
275A MET 3.5 5.8 - - - +
277A ASP* 1.3 72.9 - - - +
279A LEU* 1.3 66.0 + - - +
281A SER 3.2 5.9 + - - -
289A SER* 3.4 11.9 - - - +
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Residues in contact with LEU 279 (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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275A MET 3.0 13.6 + - - +
276A ILE* 3.3 9.6 - - - +
278A ALA* 1.3 72.0 - - - +
280A ALA* 1.3 55.0 + - - +
281A SER 2.8 14.1 + - - -
282A CYS* 2.9 25.5 + - - -
289A SER* 3.4 13.4 + - - +
303A TYR* 3.9 31.6 - - + -
307A LEU* 4.2 15.0 - - + +
308A LEU* 4.7 4.3 - - + +
312A ARG* 3.1 32.4 + - + -
313A THR 5.0 0.2 - - - +
314A TRP* 3.8 52.3 - - + -
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Residues in contact with ALA 280 (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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251A SER* 3.4 24.2 - - - +
276A ILE* 2.9 19.9 + - + +
277A ASP* 4.5 3.4 - - - +
279A LEU* 1.3 73.0 - - - +
281A SER* 1.3 57.8 + - - +
282A CYS 3.5 0.2 - - - -
307A LEU* 3.8 25.6 - - + -
312A ARG* 3.2 26.8 + - - +
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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