Contacts of the strand formed by residues 286 - 291 (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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TRP* 4.0 15.3 - - + -
275A LEU 4.2 0.7 - - - -
276A TYR* 3.3 4.2 - - - -
277A GLN* 3.0 44.7 + - + +
285A ASN* 1.3 87.9 + - - +
287A LEU* 1.3 61.5 + - - +
288A TRP* 4.4 6.7 - - + +
307A VAL* 3.6 7.2 - - - +
308A ASN* 3.7 18.6 - - - +
309A GLU* 3.4 44.6 - - - +
310A TYR* 3.6 37.2 - - + +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 4.4 7.2 - - + -
275A LEU 3.4 4.5 - - - +
276A TYR* 3.6 28.7 - - + -
285A ASN* 4.6 0.4 - - - +
286A LEU* 1.3 76.7 - - - +
288A TRP* 1.3 71.7 + - - +
289A VAL* 4.7 7.2 - - + -
306A VAL* 3.4 9.8 + - + +
307A VAL* 2.9 51.1 + - + +
314A TYR* 4.1 21.8 - - + -
316A ILE* 3.7 30.1 - - + -
326A ILE* 3.9 19.1 - - + -
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Residues in contact with TRP 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.5 37.5 - + - -
273A LEU 4.0 0.2 - - - +
274A TYR* 3.5 4.3 - - - -
275A LEU* 2.9 42.8 + - + +
277A GLN* 3.4 27.7 - - - +
286A LEU* 4.4 5.9 - - + +
287A LEU* 1.3 85.5 - - - +
289A VAL* 1.3 67.9 + - - +
303A TRP* 3.6 38.6 - + + -
304A ARG 3.2 6.5 - - - +
305A LYS* 3.5 48.2 - - + +
307A VAL 3.5 9.3 + - - -
308A ASN* 3.0 29.3 + - - -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.5 33.9 - - + -
273A LEU 3.6 1.8 - - - +
274A TYR* 3.8 28.0 - - + -
287A LEU* 4.7 8.3 - - + -
288A TRP* 1.3 80.8 - - - +
290A ALA* 1.3 63.7 + - - +
291A GLU* 5.8 0.2 - - + -
302A HIS 4.0 0.3 - - - +
303A TRP* 3.9 1.6 - - - -
304A ARG* 2.8 45.2 + - + +
306A VAL* 3.8 25.6 - - + -
324A VAL* 6.0 0.9 - - + -
342A LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.4 7.4 - - - -
273A LEU* 2.8 38.6 + - + +
289A VAL* 1.3 77.4 - - - +
291A GLU* 1.3 62.1 + - - +
301A ILE* 3.5 30.1 - - + -
302A HIS 3.3 19.3 - - - +
303A TRP* 3.6 16.3 - - + -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 3.4 24.7 - - + +
272A TYR* 3.8 23.6 + - + -
289A VAL* 4.4 0.4 + - + -
290A ALA* 1.3 73.7 - - - +
292A LEU* 1.3 64.7 + - - +
293A ASP* 4.2 4.5 + - - +
298A LYS* 6.0 0.7 - - - -
301A ILE* 4.2 13.2 - - - +
302A HIS 4.5 2.8 + - - -
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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
------------------------------------------------------------
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