Contacts of the strand formed by residues 246 - 252 (chain A) in PDB entry 2W8D
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 ASN 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY 5.5 0.2 - - - -
245A LYS* 1.3 78.1 - - - +
247A VAL* 1.3 55.5 + - - +
337A TYR* 4.4 0.2 - - - -
400A GLN* 3.2 24.8 + - - +
401A PRO* 3.2 11.2 - - - +
402A PHE* 2.8 60.7 + - + +
460A LEU* 4.3 2.0 - - - +
463A LYS* 3.0 27.1 + - - +
464A SER* 3.2 19.7 + - - +
465A ILE* 2.7 32.7 + - - +
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Residues in contact with VAL 247 (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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245A LYS 4.3 3.8 - - - +
246A ASN* 1.3 78.4 - - - +
248A ILE* 1.3 67.0 + - - +
249A TYR* 3.5 36.8 - - + -
337A TYR* 4.6 3.8 - - + -
402A PHE* 2.9 10.6 + - - +
403A TYR* 3.8 24.5 - - + -
404A THR* 3.0 27.2 + - - -
465A ILE* 3.3 11.2 - - + +
467A VAL* 4.5 4.7 - - + -
530A ILE* 4.3 14.6 - - + -
534A LEU* 3.9 29.8 - - + -
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 1.3 76.8 - - - +
249A TYR* 1.3 63.5 + - - +
250A VAL* 3.9 3.8 + - + -
395A LEU* 4.5 3.6 - - + -
402A PHE* 3.8 17.7 - - + -
404A THR* 3.5 13.2 - - - +
406A PHE* 3.9 15.5 - - + -
451A PHE* 3.9 29.2 - - + -
455A LEU* 3.9 33.4 - - + -
460A LEU* 5.0 2.0 - - + +
464A SER* 4.0 24.0 - - - +
465A ILE 2.8 11.0 + - - +
466A ILE* 3.4 11.5 - - + +
467A VAL 2.9 25.7 + - - -
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Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 3.5 30.3 - - + -
248A ILE* 1.3 74.9 - - - +
250A VAL* 1.3 59.0 + - - +
251A SER 4.3 0.4 - - - +
304A MSE 3.8 39.0 + - + -
305A GLU* 5.0 0.9 - - - -
328A VAL* 5.8 1.6 - - - +
403A TYR* 3.4 31.1 + + - -
404A THR 2.7 17.5 + - - +
405A LYS* 3.5 14.8 - - + -
406A PHE* 2.8 33.4 + - - +
467A VAL* 3.2 29.6 - - + -
469A TYR* 3.8 22.2 - + + +
526A VAL* 3.7 7.7 - - + +
527A ALA* 4.3 4.5 - - - -
530A ILE* 3.5 26.1 - - + +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 4.3 5.8 - - + +
249A TYR* 1.3 77.7 - - - +
251A SER* 1.3 62.6 + - - +
252A LEU* 3.6 22.3 + - + -
388A PHE* 4.3 4.5 - - + -
406A PHE* 3.5 11.9 - - + +
408A THR* 4.1 11.9 - - + -
448A ILE* 4.1 13.7 - - + -
451A PHE* 3.8 29.6 - - + -
466A ILE* 4.8 2.0 - - + -
467A VAL 2.9 9.1 + - - -
468A MSE 3.3 25.5 - - + +
469A TYR* 3.0 31.3 + - - -
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR 4.3 0.4 - - - -
250A VAL* 1.3 70.3 - - - +
252A LEU* 1.3 53.4 + - - +
253A GLU* 3.4 2.3 + - - -
297A TPO 4.4 3.4 - - - +
406A PHE 2.9 13.6 + - - -
407A ILE* 4.0 25.2 - - - +
408A THR* 2.7 36.2 + - - +
469A TYR* 3.5 30.2 + - - -
471A ASP* 3.7 25.3 + - - +
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Residues in contact with LEU 252 (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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250A VAL* 3.8 16.6 - - + +
251A SER* 1.3 68.3 + - - +
253A GLU* 1.3 67.7 + - - +
254A SER 3.3 1.4 + - - -
255A LEU* 3.4 27.7 + - + -
273A LEU* 4.4 12.1 - - + -
408A THR* 3.7 2.0 - - - -
444A LEU* 4.1 15.9 - - + -
448A ILE* 3.8 35.4 - - + -
468A MSE 4.0 21.3 - - + +
469A TYR 2.7 25.5 + - - +
470A GLY* 3.2 21.7 - - - +
471A ASP 3.3 2.7 + - - -
504A PRO* 4.9 1.6 - - + -
506A PHE* 4.8 10.3 - - + -
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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