Contacts of the helix formed by residues 329 - 337 (chain A) in PDB entry 1D0L
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 LEU 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLN* 3.6 44.9 - - + +
271A VAL 3.1 17.3 + - - +
273A VAL* 4.3 14.4 - - + -
306A LEU* 4.3 13.7 - - + -
309A HIS* 3.8 38.8 - - + +
311A GLN 4.1 10.3 - - - +
312A ALA* 4.2 7.9 - - + -
327A TYR 4.2 6.7 - - - +
328A GLY* 1.3 81.2 - - - +
330A PRO* 1.4 76.7 - - + +
331A ASN 3.2 0.9 - - - -
332A PHE* 2.9 17.0 + - - +
333A TYR* 3.4 4.7 + - - +
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Residues in contact with PRO 330 (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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264A GLY 5.9 1.1 - - - +
266A VAL* 5.3 7.6 - - + -
269A ASP* 4.8 6.1 - - - +
309A HIS* 3.6 27.1 - - + +
311A GLN 5.2 3.8 - - - +
312A ALA* 6.3 0.2 - - - -
329A LEU* 1.4 89.6 - - + +
331A ASN* 1.3 64.3 + - - +
333A TYR* 3.0 12.5 + - + +
334A THR* 3.0 23.4 + - - -
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Residues in contact with ASN 331 (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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264A GLY 4.2 1.2 - - - +
265A TRP* 3.5 38.0 - - + -
266A VAL* 2.9 50.3 + - - +
269A ASP* 3.2 27.8 + - - +
270A GLN 3.7 14.4 + - - +
271A VAL* 4.0 5.4 - - - -
329A LEU 3.1 1.6 + - - -
330A PRO* 1.3 75.7 - - - +
332A PHE* 1.3 65.4 + - - +
334A THR* 3.3 7.3 + - - -
335A ILE* 3.2 24.9 + - - +
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Residues in contact with PHE 332 (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 VAL* 3.3 37.4 + - + +
272A ALA* 4.1 6.7 - - + -
286A PHE* 4.0 9.0 - - + -
313A SER* 5.0 2.0 - - - -
315A LEU* 3.6 39.9 - - + -
328A GLY* 4.4 2.7 - - - -
329A LEU 2.9 12.9 + - - +
331A ASN* 1.3 76.6 - - - +
333A TYR* 1.3 63.7 + - - +
335A ILE* 3.0 17.7 + - + +
336A THR* 3.2 27.5 + - + +
342A THR* 3.5 28.5 - - + -
345A ALA* 3.6 10.3 - - + -
346A MET* 3.7 37.7 - - + -
349A TRP* 5.4 0.2 - + - -
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Residues in contact with TYR 333 (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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286A PHE* 3.6 33.4 - + - +
287A LYS* 4.9 8.7 - - + +
329A LEU 3.4 4.1 + - - +
330A PRO* 3.0 14.7 + - + +
332A PHE* 1.3 83.6 - - - +
334A THR* 1.3 63.8 + - - +
336A THR* 2.6 30.3 + - - -
337A ARG* 3.2 55.7 + - + -
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Residues in contact with THR 334 (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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259A TYR* 5.4 1.4 - - - -
260A PHE* 3.8 41.0 - - + +
263A HIS* 3.4 27.6 + - + +
264A GLY 3.8 11.6 + - - -
265A TRP* 3.9 8.1 - - + +
330A PRO 3.0 13.3 + - - -
331A ASN* 3.5 14.9 - - - -
332A PHE 3.2 0.2 - - - -
333A TYR* 1.3 77.0 - - - +
335A ILE* 1.3 63.1 + - - +
337A ARG* 3.1 24.7 + - - +
338A TYR* 3.9 2.3 + - - +
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Residues in contact with ILE 335 (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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154A ILE* 4.1 19.1 - - + -
158A ILE* 4.5 0.4 - - + -
260A PHE* 3.8 27.8 - - + -
265A TRP* 4.1 2.5 - - + -
271A VAL* 3.8 28.5 - - + -
331A ASN 3.2 10.9 + - - +
332A PHE* 3.0 10.3 + - + +
334A THR* 1.3 76.6 - - - +
336A THR* 1.3 56.9 + - - +
337A ARG 3.1 0.2 - - - -
338A TYR* 3.0 25.5 + - - +
339A ASN 3.7 3.1 + - - +
344A TYR* 4.2 8.1 - - + -
345A ALA* 3.5 39.5 - - + +
348A VAL* 4.2 16.6 - - + -
349A TRP* 4.2 4.7 - - + +
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Residues in contact with THR 336 (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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286A PHE* 3.6 36.1 - - + -
332A PHE* 3.6 15.5 - - + +
333A TYR* 2.6 21.8 + - - -
335A ILE* 1.3 75.7 - - - +
337A ARG* 1.3 75.8 + - - +
338A TYR 3.1 0.2 - - - -
339A ASN 3.1 20.5 - - - -
340A HIS* 2.9 24.6 - - - -
341A SER 3.8 12.1 - - - +
345A ALA* 3.7 17.7 - - + -
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Residues in contact with ARG 337 (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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259A TYR* 2.7 24.1 + - + -
263A HIS* 3.8 36.6 - - + +
286A PHE* 3.3 24.0 - - - -
287A LYS* 5.7 0.6 - - - +
333A TYR* 3.4 46.8 + - + +
334A THR* 3.1 19.8 + - - +
336A THR* 1.3 106.3 + - - +
338A TYR* 1.3 55.8 + - - +
340A HIS* 3.6 30.0 + - - -
401A BLG 4.1 6.4 - - - +
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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