Contacts of the helix formed by residues 467 - 474 (chain A) 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 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ASP* 3.0 28.9 + - + +
465A ARG 3.5 0.6 - - - -
466A GLY* 1.3 74.0 - - - +
468A ASP* 1.3 63.7 + - - +
469A MET* 3.0 24.4 + - - +
470A ILE* 3.3 24.8 + - + +
471A SER* 3.2 19.3 + - - -
350B GLU* 3.4 19.8 + - - +
356B GLY* 3.4 25.3 - - - -
357B TRP* 3.9 1.0 - - - +
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Residues in contact with ASP 468 (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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466A GLY 3.4 6.5 + - - +
467A ASN* 1.3 71.3 - - - +
469A MET* 1.3 88.4 + - - +
471A SER* 3.0 28.1 + - - +
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Residues in contact with MET 469 (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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467A ASN* 3.0 13.4 + - - +
468A ASP* 1.3 87.9 + - - +
470A ILE* 1.3 59.4 + - - +
472A HIS* 3.9 12.6 + - - -
348B PRO* 4.4 20.9 - - + -
350B GLU* 4.9 3.6 - - - +
357B TRP* 2.9 64.8 - - + +
365B ASP* 4.7 4.5 - - - +
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Residues in contact with ILE 470 (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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463A VAL* 3.6 17.6 - - + +
464A ASP 4.2 1.6 - - - +
467A ASN* 3.3 24.7 + - + +
468A ASP 3.2 0.6 - - - -
469A MET* 1.3 76.6 - - - +
471A SER* 1.3 67.4 + - - +
472A HIS* 2.8 13.4 + - + -
473A LEU* 2.8 25.6 + - + +
474A TYR 3.8 1.2 + - - -
355B LEU 3.3 25.8 - - - +
356B GLY 3.5 11.7 - - - +
357B TRP* 3.4 39.9 - - + -
361B ARG* 3.6 22.0 - - + +
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Residues in contact with SER 471 (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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464A ASP 5.9 1.1 - - - -
467A ASN 3.2 11.2 + - - -
468A ASP* 3.0 24.1 + - - +
469A MET 3.5 0.2 - - - -
470A ILE* 1.3 78.0 - - - +
472A HIS* 1.3 55.0 + - - +
473A LEU 3.0 0.2 - - - -
474A TYR* 2.8 38.5 + - - +
475A GLN* 4.0 1.0 + - - -
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Residues in contact with HIS 472 (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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469A MET 3.9 16.0 + - - -
470A ILE* 2.8 13.2 + - + -
471A SER* 1.3 79.7 + - - +
473A LEU* 1.3 87.3 + - + +
474A TYR 3.4 0.4 - - - -
475A GLN* 2.9 21.7 + - - +
361B ARG* 6.4 0.7 - - + -
365B ASP* 4.6 19.1 + - - -
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Residues in contact with LEU 473 (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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461A LEU* 3.1 16.1 - - - +
463A VAL* 3.8 15.4 - - + +
470A ILE* 2.8 19.8 + - + +
472A HIS* 1.3 106.0 - - + +
474A TYR* 1.3 58.3 + - - +
475A GLN* 3.1 12.7 + - - +
361B ARG* 3.2 48.7 - - + +
394B ILE* 5.2 7.7 - - + +
395B SER* 5.9 0.4 - - - +
398B GLU* 3.6 24.5 - - + +
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Residues in contact with TYR 474 (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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453A THR 3.9 0.7 + - - -
454A ASN* 3.3 42.0 + - - +
457A THR* 3.2 24.2 - - + -
458A GLN 4.3 0.9 - - - -
461A LEU* 4.2 0.4 - - - -
463A VAL* 3.3 28.7 - - + +
464A ASP 5.5 2.2 - - - +
465A ARG* 4.0 20.1 - - + +
471A SER* 2.8 22.7 + - - +
472A HIS 3.4 0.2 - - - -
473A LEU* 1.3 76.2 - - - +
475A GLN* 1.3 69.6 + - - +
476A PRO* 3.6 29.1 - - + +
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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