Contacts of the strand formed by residues 314 - 319 (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 LYS 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A SER* 4.3 12.9 - - - -
309A HIS* 2.9 52.2 + - + +
310A GLY* 4.0 0.6 - - - -
312A ASP 4.1 6.3 - - - +
313A GLY* 1.3 80.2 - - - +
315A ILE* 1.3 68.1 + - - +
316A PHE* 3.4 39.7 - - + -
348A THR* 3.9 3.6 - - - +
349A GLN* 3.2 39.2 + - + +
351A SER* 4.1 14.8 + - - +
361A LEU* 4.4 18.4 - - + +
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Residues in contact with ILE 315 (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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306A ILE* 4.7 6.5 - - + -
307A LEU 3.4 8.5 - - - +
308A ASP* 4.0 19.5 - - - +
310A GLY 4.4 2.5 - - - +
314A LYS* 1.3 81.1 - - - +
316A PHE* 1.3 64.4 + - - +
317A VAL* 4.8 4.7 - - + -
335A ALA* 3.9 36.8 - - + +
338A PHE* 4.1 20.4 - - + -
339A ILE* 3.9 12.6 - - + -
344A TYR* 4.5 6.7 - - + -
348A THR* 4.1 13.5 - - + -
349A GLN 2.9 15.5 + - - +
350A VAL* 4.0 11.4 - - + +
351A SER* 3.3 20.6 + - - -
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Residues in contact with PHE 316 (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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305A PHE 3.8 0.2 - - - +
306A ILE* 3.1 7.3 - - - +
307A LEU* 2.7 66.9 + - + +
309A HIS* 4.8 6.1 - + + -
314A LYS* 3.4 42.4 - - + -
315A ILE* 1.3 76.6 - - - +
317A VAL* 1.3 63.1 + - - +
318A TRP 4.0 0.2 - - - -
351A SER* 3.4 22.4 - - - +
353A LEU* 4.4 8.1 - - + -
359A THR* 4.5 7.2 - - - -
361A LEU* 4.2 20.0 - - + -
362A PHE* 3.7 37.7 - + + -
364A GLN* 5.9 0.2 - - - -
365A PHE* 4.1 19.3 - + - -
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Residues in contact with VAL 317 (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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276A VAL* 6.0 1.1 - - + -
304A CYS* 5.3 6.3 - - + -
305A PHE 3.4 7.4 - - - +
306A ILE* 4.3 16.2 - - + -
315A ILE* 4.8 4.3 - - + -
316A PHE* 1.3 76.8 - - - +
318A TRP* 1.3 66.2 + - - +
319A LYS* 4.1 3.7 + - + +
331A ALA* 4.2 27.1 - - + +
334A THR* 5.7 4.7 - - + -
335A ALA* 3.7 31.0 - - + +
350A VAL* 4.6 3.8 - - + -
351A SER 2.8 7.8 + - - +
352A VAL* 3.1 19.0 - - + +
353A LEU* 2.8 28.8 + - - +
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Residues in contact with TRP 318 (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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299A LEU* 3.7 38.3 - - + +
300A ARG 3.5 28.0 - - - -
301A SER* 4.6 0.4 - - - -
303A ASP 4.0 0.4 - - - -
304A CYS* 3.0 10.4 - - - +
305A PHE* 2.6 64.1 + + + +
307A LEU 6.0 0.2 - - - +
316A PHE 4.0 0.2 - - - -
317A VAL* 1.3 71.0 - - - +
319A LYS* 1.3 63.4 + - - +
320A GLY* 3.6 22.2 - - - -
353A LEU* 3.6 11.4 - - + +
355A GLU* 3.7 36.8 - - + +
358A GLU* 3.2 28.3 + - + +
362A PHE* 3.4 36.3 - + + -
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Residues in contact with LYS 319 (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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109A ASP* 3.9 20.0 + - - -
114A GLY* 5.1 3.4 + - - -
116A ALA 5.2 3.0 + - - -
118A GLN* 4.0 13.3 + - - -
304A CYS* 4.0 17.5 - - - -
317A VAL* 4.8 5.6 - - + +
318A TRP* 1.3 78.5 - - - +
320A GLY* 1.3 66.1 + - - +
328A ARG* 3.7 49.1 + - + +
331A ALA* 4.1 16.4 - - + -
352A VAL* 4.3 12.2 - - + +
353A LEU 2.9 22.0 + - - +
354A PRO* 3.8 17.2 - - + +
355A GLU* 2.9 29.5 + - - +
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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