Contacts of the helix formed by residues 352 - 356 (chain B) in PDB entry 2N5T
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 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ASN* 3.0 14.4 - - - +
353A PRO* 3.0 14.4 - - - +
354A PHE* 2.8 46.8 + - - +
464A ASP* 2.6 36.5 + - - +
350B GLU* 4.1 3.1 - - - +
351B GLU* 1.3 87.8 + - - +
353B PRO* 1.3 71.8 - - - +
354B PHE 3.0 1.8 - - - -
355B LEU* 2.9 23.5 + - + +
356B GLY* 3.1 10.2 + - - -
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Residues in contact with PRO 353 (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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351A GLU* 3.3 27.8 - - + +
352A ASN* 3.3 7.4 - - - +
337B GLY 3.0 20.1 - - - +
338B GLY* 3.5 25.4 - - - +
341B GLU* 4.6 13.9 - - - +
350B GLU* 3.5 31.8 - - + +
352B ASN* 1.3 84.0 - - - +
354B PHE* 1.3 56.4 + - - +
356B GLY* 2.8 20.1 + - - -
358B ARG* 4.6 2.1 - - - +
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Residues in contact with PHE 354 (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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352A ASN* 2.7 27.8 + - - +
355A LEU* 3.5 7.6 - - + -
462A ALA* 4.4 1.7 - - - +
338B GLY* 3.9 4.3 - - - -
339B ASP* 3.4 52.7 - - + -
353B PRO* 1.3 72.9 - - - +
355B LEU* 1.3 56.3 + - - +
356B GLY 3.4 0.9 - - - -
358B ARG* 3.3 39.8 + - - +
361B ARG* 5.7 0.2 + - - -
392B MET* 4.7 0.5 - - - +
458B GLN* 3.1 33.7 - - - +
459B TYR* 2.6 30.7 + - - -
464B ASP* 3.2 27.4 - - - -
465B ARG* 3.8 18.8 - - + -
466B GLY* 4.8 2.9 - - - -
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Residues in contact with LEU 355 (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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354A PHE* 3.5 32.1 - - + -
355A LEU* 4.1 20.0 - - + -
458A GLN* 3.9 25.6 - - + +
459A TYR* 4.5 2.2 - - + -
462A ALA* 3.5 35.4 - - - -
463A VAL* 3.6 0.8 - - - +
464A ASP* 2.8 37.3 + - + +
470A ILE* 3.3 6.9 - - - +
352B ASN* 2.9 18.9 + - + +
354B PHE* 1.3 75.2 - - - +
356B GLY* 1.3 58.4 + - - +
459B TYR* 3.8 18.8 - - + -
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Residues in contact with GLY 356 (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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467A ASN* 3.4 15.0 - - - -
470A ILE* 3.5 7.2 - - - +
350B GLU* 3.6 6.5 - - - -
352B ASN 3.1 4.0 + - - -
353B PRO 2.8 15.5 + - - -
354B PHE 3.4 1.2 + - - -
355B LEU* 1.3 79.0 - - - +
357B TRP* 1.3 60.8 + - - -
358B ARG* 3.0 9.5 + - - +
361B ARG* 2.8 25.3 + - - -
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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
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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