Contacts of the strand formed by residues 304 - 309 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B LYS* 3.9 2.8 - - - +
276B VAL* 2.9 50.2 + - + +
303B ASP* 1.3 78.6 - - - +
305B PHE* 1.3 64.7 + - - +
317B VAL* 6.1 2.9 - - + -
318B TRP 3.2 12.6 - - - +
319B LYS* 4.2 17.9 - - - -
323B ALA* 4.1 18.4 - - - -
327B GLU* 4.3 30.8 + - - +
328B ARG* 5.0 0.7 - - - -
331B ALA* 6.0 1.8 - - - -
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Residues in contact with PHE 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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273B LEU* 3.7 23.3 - - + -
274B TYR 3.2 16.8 - - - +
275B LYS* 3.9 27.8 - - + -
276B VAL* 4.5 0.6 - - - +
288B VAL* 4.6 9.0 - - + -
298B ALA 3.1 26.9 - - - -
299B LEU* 4.0 5.4 - - + -
300B ARG* 3.3 43.3 - - + -
303B ASP* 4.0 12.6 - - + -
304B CYS* 1.3 77.0 - - - +
306B ILE* 1.3 64.2 + - - +
307B LEU 4.1 0.6 + - - -
317B VAL* 3.2 5.4 - - - +
318B TRP* 2.7 63.8 + + + +
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Residues in contact with ILE 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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272B LYS 3.7 0.2 - - - +
273B LEU* 3.9 2.7 - - - -
274B TYR* 2.8 43.0 + - + +
276B VAL* 4.2 19.1 - - + -
283B MET* 5.4 0.4 - - - -
285B VAL* 5.9 0.7 - - + -
305B PHE* 1.3 77.6 - - - +
307B LEU* 1.3 69.4 + - - +
308B ASP 3.3 2.9 + - - -
315B ILE* 4.7 7.0 - - + -
316B PHE 3.3 10.5 - - - +
317B VAL* 4.5 13.0 - - + -
334B THR* 4.3 20.6 - - + +
335B ALA* 5.1 1.1 - - - -
338B PHE* 3.5 61.2 - - + -
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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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271B ALA* 4.0 14.8 - - + -
272B LYS 3.6 8.1 - - - +
273B LEU* 4.0 8.1 - - + +
294B PHE* 3.6 28.9 - - + -
305B PHE 4.1 1.2 - - - -
306B ILE* 1.3 69.5 - - - +
308B ASP* 1.3 63.8 + - - +
309B HIS 3.8 0.6 + - - +
315B ILE* 3.4 6.4 - - - +
316B PHE* 2.8 48.0 + - + +
318B TRP 5.5 0.2 - - - +
362B PHE* 3.7 33.5 - - + -
365B PHE* 4.0 22.4 - - + -
366B PHE* 3.7 19.1 - - + -
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Residues in contact with ASP 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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271B ALA* 3.1 9.2 - - - +
272B LYS* 2.7 42.8 + - + +
274B TYR* 3.9 23.0 + - + -
306B ILE* 3.3 1.4 + - - +
307B LEU* 1.3 73.0 - - - +
309B HIS* 1.3 60.1 + - - +
310B GLY* 2.6 34.9 + - - -
315B ILE* 3.9 5.9 - - - +
338B PHE* 3.7 19.2 - - + -
342B MET* 4.3 4.3 - - - +
344B TYR* 2.7 33.3 + - - -
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Residues in contact with HIS 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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268B ARG* 3.0 24.7 + - + -
269B LYS* 4.8 0.2 - - - -
270B LEU 3.3 22.6 + - - -
271B ALA* 4.2 5.4 - - + -
307B LEU* 3.8 1.5 + - + -
308B ASP* 1.3 74.4 + - - +
310B GLY* 1.3 64.9 + - - +
311B LYS* 3.3 3.8 - - + -
312B ASP* 3.1 43.9 + - + +
313B GLY 3.3 0.2 + - - -
314B LYS* 2.8 39.4 + - - +
316B PHE* 4.6 9.2 - - + -
364B GLN* 5.7 1.1 - - - -
365B PHE* 3.3 32.9 - + + -
708B PRO* 4.1 12.3 - - + +
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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