Contacts of the strand formed by residues 304 - 309 (chain A) in PDB entry 1D0N
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 CYS 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A LYS* 3.9 0.7 - - - -
276A VAL* 3.0 47.9 + - + +
303A ASP* 1.3 80.8 - - - +
305A PHE* 1.3 67.9 + - - +
317A VAL* 5.3 5.4 - - + -
318A TRP 3.0 12.8 - - - +
319A LYS* 4.0 21.5 - - + -
323A ALA* 4.1 11.0 - - - -
327A GLU* 3.9 32.2 + - - +
328A ARG* 5.2 0.9 - - - -
331A ALA* 6.1 0.7 - - - -
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Residues in contact with PHE 305 (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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273A LEU* 4.2 21.8 - - + -
274A TYR 3.2 19.7 - - - +
275A LYS* 4.1 20.2 - - + -
276A VAL* 4.6 0.2 - - - -
288A VAL* 4.5 11.0 - - + -
298A ALA 3.0 27.8 - - - -
299A LEU* 4.2 8.7 - - + -
300A ARG* 3.4 41.5 - - + -
303A ASP* 3.9 17.7 - - + -
304A CYS* 1.3 76.4 - - - +
306A ILE* 1.3 64.5 + - - +
307A LEU 4.1 0.4 - - - -
317A VAL* 3.4 4.7 - - - +
318A TRP* 2.6 62.3 + + + +
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Residues in contact with ILE 306 (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 LYS 3.8 0.2 - - - +
273A LEU* 3.7 2.6 - - - -
274A TYR* 2.9 41.9 + - + +
276A VAL* 4.5 17.3 - - + -
283A MET* 5.8 0.2 - - - -
285A VAL* 5.8 1.3 - - + -
305A PHE* 1.3 77.1 - - - +
307A LEU* 1.3 71.0 + - - +
308A ASP 3.4 2.6 + - - +
315A ILE* 4.7 6.7 - - + -
316A PHE 3.1 9.9 - - - +
317A VAL* 4.3 17.0 - - + -
334A THR* 4.5 19.5 - - + +
335A ALA* 5.0 0.9 - - - -
338A PHE* 3.7 61.5 - - + -
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Residues in contact with LEU 307 (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 ALA* 4.1 20.6 - - + -
272A LYS 3.8 2.7 - - - -
273A LEU* 4.2 12.0 - - + +
294A PHE* 3.4 31.6 - - + -
305A PHE 4.1 0.8 - - - -
306A ILE* 1.3 68.4 - - - +
308A ASP* 1.3 65.2 + - - +
309A HIS* 3.6 2.8 + - + +
315A ILE* 3.4 6.8 - - - +
316A PHE* 2.7 61.9 + - + +
318A TRP* 6.0 0.2 - - - +
362A PHE* 3.9 21.5 - - + -
365A PHE* 4.0 29.6 - - + -
366A PHE* 4.3 5.6 - - + -
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Residues in contact with ASP 308 (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 ALA* 3.5 4.9 - - - -
272A LYS* 2.7 42.5 + - - +
274A TYR* 3.5 30.3 + - + -
306A ILE* 3.4 1.2 + - - -
307A LEU* 1.3 72.0 - - - +
309A HIS* 1.3 60.3 + - - +
310A GLY* 2.9 17.0 + - - -
315A ILE* 4.0 6.0 - - - +
338A PHE* 3.6 18.9 - - + -
342A MET* 3.8 5.4 - - - +
344A TYR* 2.7 29.5 + - - -
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Residues in contact with HIS 309 (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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268A ARG* 3.9 17.0 + - + -
270A LEU 3.5 23.0 + - - -
271A ALA* 3.8 6.4 - - - +
307A LEU* 3.6 15.0 + - + -
308A ASP* 1.3 73.0 - - - +
310A GLY* 1.3 64.4 + - - +
311A LYS* 3.2 5.1 + - + +
312A ASP* 2.9 50.9 + - + +
314A LYS* 2.9 41.5 + - + +
316A PHE* 4.8 4.3 - + + -
365A PHE* 3.8 27.6 - + + -
708A PRO* 4.3 12.9 - - + +
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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