Contacts of the strand formed by residues 315 - 321 (chain A) in PDB entry 3BDP
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 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ALA* 3.1 5.1 - - - +
314A ASP* 1.3 83.0 - - + +
316A ALA* 1.3 68.1 + - - +
339A ASN* 3.3 17.0 - - - +
340A GLU 4.7 0.3 + - - -
367A LYS* 3.2 18.3 - - + +
369A SER* 3.9 7.6 + - - -
391A SER* 4.2 13.3 + - - -
455A TRP* 3.7 28.4 - - + -
458A GLU* 3.2 38.6 + - - -
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Residues in contact with ALA 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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311A MET 5.7 0.2 - - - +
313A ALA* 5.0 2.2 - - + +
315A LYS* 1.3 80.3 - - - +
317A ALA* 1.3 63.3 + - - +
337A VAL* 3.9 18.6 - - + -
338A VAL 3.3 12.8 - - - +
339A ASN* 3.8 9.4 - - + +
360A TRP* 4.1 20.0 - - + -
367A LYS 3.1 5.7 + - - +
368A LYS* 3.3 7.2 - - - -
369A SER* 2.9 24.5 + - - -
455A TRP* 3.5 8.3 - - - -
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Residues in contact with ALA 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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316A ALA* 1.3 74.5 - - - +
318A LEU* 1.3 59.2 + - - +
336A ALA 3.8 0.5 - - - +
337A VAL* 3.4 5.4 - - - -
338A VAL* 2.8 33.0 + - + +
369A SER* 3.4 9.2 - - - +
451A ALA* 3.1 33.8 - - - +
454A ILE* 4.1 8.1 - - + -
455A TRP* 3.6 27.6 - - + +
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Residues in contact with LEU 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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316A ALA 3.8 0.8 + - - -
317A ALA* 1.3 74.6 - - - +
319A VAL* 1.3 74.8 + - - +
320A VAL* 3.7 24.7 - - + -
335A ILE* 4.1 7.4 - - + -
336A ALA 3.5 10.8 - - - +
337A VAL* 3.9 17.0 - - + -
357A PHE* 4.4 2.9 - - + -
360A TRP* 4.2 13.0 - - + -
361A LEU* 3.7 25.8 - - + -
368A LYS* 4.1 25.4 - - + -
369A SER 2.9 12.2 + - - +
370A MET* 3.5 43.9 - - + +
371A PHE 4.9 0.3 + - - -
387A LEU* 4.3 4.5 - - + -
454A ILE* 4.8 1.7 - - - +
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Residues in contact with VAL 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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318A LEU* 1.3 78.3 - - - +
320A VAL* 1.3 62.9 + - - +
321A GLU* 3.6 28.7 - - - +
335A ILE* 3.3 10.6 - - - +
336A ALA* 2.9 40.7 + - + +
370A MET* 5.1 0.2 - - - -
447A LEU* 3.7 37.2 - - + +
450A LYS* 4.3 10.3 - - + -
451A ALA* 3.7 22.0 - - + +
454A ILE* 4.4 8.3 - - + -
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Residues in contact with VAL 320 (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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318A LEU* 3.7 32.4 + - + -
319A VAL* 1.3 77.2 - - - +
321A GLU* 1.3 62.0 + - - +
322A VAL* 3.4 9.5 + - - +
332A ILE* 3.7 37.2 - - + -
334A GLY 4.1 2.9 - - - -
335A ILE* 4.3 11.9 - - + -
352A LEU* 6.0 0.4 - - + -
357A PHE* 6.0 0.7 - - + -
361A LEU* 5.0 4.3 - - + -
370A MET* 4.3 8.5 - - + +
375A ARG* 5.5 2.3 - - - +
376A ALA* 3.8 27.7 - - + +
380A LEU* 4.4 16.6 - - + -
387A LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 321 (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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319A VAL* 3.6 8.4 - - - +
320A VAL* 1.3 71.2 - - - +
322A VAL* 1.3 63.5 + - - +
323A VAL* 3.7 14.5 - - + +
332A ILE* 3.3 4.4 - - - -
333A VAL* 2.7 36.6 + - + +
334A GLY 3.2 14.0 + - - +
425A ASP* 4.8 0.2 - - - -
429A TYR* 2.7 34.1 + - - +
447A LEU* 3.4 32.6 - - + +
450A LYS* 2.7 36.6 + - - -
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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