Contacts of the strand formed by residues 323 - 328 (chain A) in PDB entry 5N4D
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 LEU 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ASN* 3.2 2.9 - - - -
320A HIS* 2.8 42.0 + - + +
321A GLY 3.3 0.4 - - - -
322A SER* 1.3 76.0 + - - +
324A VAL* 1.3 60.7 + - - +
325A TYR* 3.6 31.0 - - + +
339A THR* 3.7 33.0 - - + +
341A ASP* 3.7 32.5 + - + +
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Residues in contact with VAL 324 (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 TYR* 4.3 5.8 - - + -
274A TYR* 4.0 22.9 - - + +
289A VAL* 6.0 0.9 - - + -
316A ILE* 3.7 30.3 - - + -
318A THR 3.7 9.2 - - - +
319A ASN* 4.1 6.7 - - + -
322A SER 3.9 4.7 - - - +
323A LEU* 1.3 75.5 - - - +
325A TYR* 1.3 64.6 + - - +
326A ILE* 3.7 14.9 - - + +
338A ILE 3.8 0.7 - - - +
339A THR* 3.2 4.4 - - - -
340A ILE* 2.9 36.6 + - + +
342A LEU* 3.7 29.8 - - + -
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Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ILE* 3.9 1.7 - - - +
317A ILE* 2.9 31.3 + - + -
318A THR* 2.8 33.6 + - + +
319A ASN* 4.4 0.9 - - - -
320A HIS* 3.7 29.5 - + - +
323A LEU* 3.6 40.0 - - + +
324A VAL* 1.3 70.8 - - - +
326A ILE* 1.3 65.1 + - - +
337A VAL* 4.5 5.6 - - + -
338A ILE 3.4 4.9 - - - +
339A THR* 3.6 22.4 - - + +
352A PHE* 3.9 33.1 - + - -
372A PHE* 3.7 26.6 - + + -
389A LYS 4.7 5.9 + - - -
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.9 19.7 - - + -
306A VAL* 5.9 0.2 - - + -
314A TYR* 3.9 20.9 - - + -
315A ASN 3.5 20.0 - - - +
316A ILE* 3.8 5.6 - - + +
317A ILE* 3.9 4.5 - - - -
324A VAL* 3.7 24.2 - - + +
325A TYR* 1.3 79.7 - - - +
327A LYS* 1.3 76.8 + - - +
328A THR* 4.5 1.3 - - - -
337A VAL* 3.3 2.7 - - - +
338A ILE* 2.8 41.9 + - + +
340A ILE* 3.5 36.3 - - + -
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Residues in contact with LYS 327 (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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313A ASP* 3.8 7.1 + - - +
314A TYR* 3.5 1.2 - - - -
315A ASN* 2.9 56.1 + - + +
317A ILE* 3.6 19.4 - - + +
326A ILE* 1.3 72.6 - - - +
328A THR* 1.3 64.0 + - - +
335A TYR* 4.0 27.7 - - + -
336A LYS 3.4 10.5 - - - +
337A VAL* 5.1 0.7 - - + -
361A LEU* 4.0 33.7 + - + +
362A ALA 4.0 18.9 + - - +
363A GLN* 4.4 5.2 - - - +
364A VAL* 4.5 12.1 - - + +
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Residues in contact with THR 328 (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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313A ASP 2.8 18.6 + - - -
314A TYR* 3.6 18.8 - - - -
326A ILE* 4.5 0.7 - - - -
327A LYS* 1.3 76.0 - - - +
329A ASN* 1.3 64.3 + - - +
330A LEU* 3.0 26.7 + - + +
335A TYR* 3.2 8.2 - - - -
336A LYS* 3.0 40.8 + - + +
338A ILE* 3.9 40.2 - - + -
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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