Contacts of the helix formed by residues 452 - 461 (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 GLY 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A MET* 3.1 25.4 - - - +
430A VAL 2.9 10.5 + - - -
431A GLU* 3.2 13.1 - - - +
451A ILE* 1.3 70.5 - - - +
453A THR* 1.3 59.2 + - - -
454A ASN* 3.3 3.5 + - - -
455A ASP 3.5 1.9 + - - -
456A LEU* 2.9 29.4 + - - +
502A CYS* 4.8 0.4 - - - -
503A GLY* 4.2 7.2 - - - -
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Residues in contact with THR 453 (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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451A ILE* 3.4 16.6 + - + +
452A GLY* 1.3 69.9 - - - -
454A ASN* 1.3 63.2 + - - +
456A LEU* 4.0 7.2 - - - -
457A THR* 2.4 39.8 + - - -
474A TYR* 3.9 1.6 + - - -
476A PRO* 4.8 1.4 - - - +
481A VAL* 5.0 2.9 - - + -
485A ILE* 4.1 6.7 - - + -
501A MET* 3.8 26.5 - - + -
503A GLY* 3.3 16.5 - - - -
504A GLU 3.6 0.9 + - - -
505A LEU* 3.5 44.8 + - + +
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Residues in contact with ASN 454 (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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296A ARG* 4.7 10.1 - - - +
452A GLY* 3.3 1.3 - - - -
453A THR* 1.3 80.1 + - - +
455A ASP* 1.3 63.0 + - - +
457A THR* 3.8 2.1 - - - -
458A GLN* 3.1 15.2 + - - +
465A ARG* 3.3 50.7 - - - +
474A TYR* 3.3 18.3 + - - +
503A GLY* 4.3 4.7 - - - -
504A GLU* 3.5 46.2 + - - +
505A LEU 5.1 0.2 + - - -
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Residues in contact with ASP 455 (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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358A ARG* 2.4 49.6 + - - -
392A MET* 4.2 0.4 - - - -
431A GLU* 3.3 39.8 + - + +
452A GLY 3.5 1.8 + - - -
454A ASN* 1.3 78.1 - - - +
456A LEU* 1.3 58.0 + - - +
458A GLN* 2.7 33.9 + - - +
459A TYR* 2.8 33.7 + - + -
465A ARG* 3.5 9.4 + - - +
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Residues in contact with LEU 456 (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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430A VAL* 4.4 1.8 - - + +
431A GLU* 2.9 16.8 + - - +
432A THR 3.0 45.3 - - - +
433A PRO* 3.5 8.7 - - + -
436A ALA* 4.2 9.6 - - + -
451A ILE* 3.8 24.7 - - + -
452A GLY 2.9 20.0 + - - +
453A THR* 4.0 5.4 - - - -
455A ASP* 1.3 68.8 - - - +
457A THR* 1.3 64.4 + - - +
459A TYR* 4.6 1.8 - - - +
460A THR* 2.7 36.1 + - - +
481A VAL* 4.5 16.2 - - + -
484A LEU* 4.4 20.0 - - + -
485A ILE* 4.6 6.3 - - + +
488A VAL* 5.7 0.4 - - + -
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Residues in contact with THR 457 (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 2.4 27.4 + - - -
456A LEU* 1.3 73.0 - - - +
458A GLN* 1.3 56.9 + - - +
461A LEU* 2.8 48.7 + - + +
474A TYR* 3.2 33.0 - - + -
475A GLN 3.7 7.4 - - - +
476A PRO* 3.2 41.8 - - + +
481A VAL* 3.9 13.4 - - + +
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Residues in contact with GLN 458 (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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354A PHE* 3.1 41.3 - - - +
454A ASN 3.1 12.7 + - - +
455A ASP* 2.7 23.5 + - - +
457A THR* 1.3 74.9 - - - +
459A TYR* 1.3 76.2 + - + +
462A ALA* 2.7 29.8 + - - -
463A VAL* 2.9 32.5 + - - +
465A ARG* 3.1 35.1 + - + +
474A TYR* 4.3 1.8 - - - -
355B LEU* 3.9 14.7 - - + +
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Residues in contact with TYR 459 (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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354A PHE 2.6 21.8 + - - -
355A LEU* 3.8 17.0 - - + -
358A ARG* 2.6 27.4 + - - -
392A MET* 3.4 10.4 - - + +
431A GLU 3.5 14.1 - - - -
432A THR* 4.4 2.0 - - - -
433A PRO* 3.5 12.8 - - + -
455A ASP* 2.8 48.7 + - + +
456A LEU 4.4 0.2 - - - +
458A GLN* 1.3 89.2 + - + +
460A THR* 1.3 66.7 + - - +
462A ALA* 3.5 4.8 + - - +
355B LEU* 4.5 3.8 - - + -
433B PRO* 3.2 3.8 - - - +
459B TYR* 3.0 48.5 - - - +
462B ALA* 3.4 26.5 - - + -
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Residues in contact with THR 460 (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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433A PRO* 3.6 8.9 - - - +
456A LEU* 2.7 25.5 + - - +
457A THR 3.8 1.1 - - - -
459A TYR* 1.3 77.7 - - - +
461A LEU* 1.3 58.4 + - - +
480A SER* 4.1 13.0 - - - +
481A VAL* 4.1 10.7 - - + +
484A LEU* 3.3 34.1 - - + +
432B THR* 3.1 12.5 - - - +
433B PRO* 3.3 11.3 - - + +
434B ALA* 2.9 46.5 + - + +
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Residues in contact with LEU 461 (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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457A THR* 2.8 25.1 + - + +
460A THR* 1.3 78.0 - - - +
462A ALA* 1.3 67.4 + - - +
463A VAL* 3.1 11.6 - - + +
473A LEU 3.1 24.2 - - - +
474A TYR* 4.1 0.9 - - - -
475A GLN* 3.1 31.4 - - + +
478A SER* 4.0 9.2 - - - +
480A SER* 3.4 25.6 - - - +
481A VAL* 4.3 5.8 - - + -
361B ARG* 2.7 21.8 + - - -
394B ILE* 3.4 23.7 - - + +
434B ALA* 3.8 10.8 - - + -
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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
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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