Contacts of the strand formed by residues 314 - 319 (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 LYS 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B SER* 5.4 6.5 - - - -
309B HIS* 2.8 49.2 + - + +
312B ASP* 4.4 5.4 - - - +
313B GLY* 1.3 79.9 - - - +
315B ILE* 1.3 73.2 + - - +
316B PHE* 3.7 35.3 - - + -
348B THR* 3.9 2.0 - - - +
349B GLN* 3.1 43.5 + - + +
350B VAL 4.5 0.9 - - - -
351B SER* 3.3 37.2 + - - +
361B LEU* 5.0 11.1 - - - +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ILE* 4.7 7.6 - - + -
307B LEU 3.4 10.8 - - - +
308B ASP* 3.9 19.7 - - - +
309B HIS 4.2 0.7 - - - +
310B GLY* 4.4 2.7 - - - +
314B LYS* 1.3 85.1 - - - +
316B PHE* 1.3 65.0 + - - +
317B VAL* 5.1 2.5 - - + -
335B ALA* 3.9 17.3 - - + +
338B PHE* 4.0 21.1 - - + -
339B ILE* 3.7 27.6 - - + -
344B TYR* 4.8 4.5 - - + -
348B THR* 4.3 10.8 - - + -
349B GLN 3.0 9.6 + - - +
350B VAL* 3.7 23.3 - - + +
351B SER 3.2 19.9 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE 3.8 0.2 - - - +
306B ILE* 3.3 6.3 - - - +
307B LEU* 2.8 47.7 + - + +
309B HIS* 4.6 5.6 - - + -
314B LYS* 3.7 44.0 - - + -
315B ILE* 1.3 76.9 - - - +
317B VAL* 1.3 63.7 + - - +
351B SER* 3.2 10.1 - - - +
353B LEU* 4.3 15.0 - - + -
359B THR* 5.0 3.4 - - - -
361B LEU* 4.0 22.9 - - + -
362B PHE* 3.9 46.4 - + + -
364B GLN* 5.8 0.2 - - - -
365B PHE* 3.9 21.8 - + - -
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B CYS* 6.1 2.7 - - + -
305B PHE 3.2 8.1 - - - +
306B ILE* 4.5 13.2 - - + -
315B ILE* 5.1 3.8 - - + -
316B PHE* 1.3 78.0 - - - +
318B TRP* 1.3 59.7 + - - +
319B LYS* 4.4 6.5 - - + -
331B ALA* 4.0 20.2 - - + +
334B THR* 5.7 3.4 - - + -
335B ALA* 3.9 31.4 - - + +
350B VAL* 4.4 6.5 - - + -
351B SER 2.9 10.2 + - - +
352B VAL* 3.3 26.2 - - + -
353B LEU* 2.9 24.0 + - - +
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Residues in contact with TRP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.6 44.8 - - + +
300B ARG 3.7 21.8 - - - -
304B CYS* 3.2 8.3 - - - +
305B PHE* 2.7 63.1 + + + +
307B LEU 6.1 0.2 - - - +
316B PHE 4.0 0.6 - - - -
317B VAL* 1.3 73.5 - - - +
319B LYS* 1.3 62.7 + - - +
320B GLY* 3.9 10.1 - - - -
353B LEU* 3.6 13.0 - - + -
354B PRO 4.8 0.2 - - - -
355B GLU* 3.3 51.3 - - + +
358B GLU* 3.1 28.3 + - + +
362B PHE* 3.7 36.6 - + + -
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Residues in contact with LYS 319 (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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109B ASP* 3.7 22.4 + - - -
114B GLY* 5.1 3.4 + - - -
116B ALA 5.7 1.8 + - - -
118B GLN* 4.4 4.8 + - - -
304B CYS* 4.2 16.2 - - - -
317B VAL* 4.4 6.3 - - + -
318B TRP* 1.3 80.0 - - - +
320B GLY* 1.3 66.0 + - - +
328B ARG* 4.1 40.6 + - + +
331B ALA* 4.1 13.9 - - + -
352B VAL* 3.9 30.7 - - + +
353B LEU 3.0 23.8 + - - +
354B PRO* 3.9 11.4 - - + +
355B 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
------------------------------------------------------------
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