Contacts of the helix formed by residues 452 - 461 (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 GLY 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B MET* 3.1 25.8 - - - +
430B VAL 2.9 10.1 + - - -
431B GLU* 3.2 13.5 - - - +
451B ILE* 1.3 70.6 - - - +
453B THR* 1.3 59.3 + - - -
454B ASN* 3.3 3.8 + - - -
455B ASP 3.5 2.1 + - - -
456B LEU* 2.9 29.7 + - - +
502B CYS* 4.8 0.2 - - - -
503B GLY* 4.2 7.4 - - - -
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Residues in contact with THR 453 (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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451B ILE* 3.4 15.7 + - + +
452B GLY* 1.3 70.3 - - - -
454B ASN* 1.3 63.5 + - - +
456B LEU* 4.0 7.4 - - + -
457B THR* 2.4 39.4 + - - -
474B TYR* 3.9 1.6 + - - -
476B PRO* 4.8 1.3 - - - +
481B VAL* 5.1 2.9 - - + -
485B ILE* 4.2 5.8 - - + -
501B MET* 3.8 27.8 - - + -
503B GLY* 3.4 15.5 - - - -
504B GLU 3.6 0.7 + - - -
505B LEU* 3.5 44.1 + - + +
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Residues in contact with ASN 454 (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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296B ARG* 4.7 10.3 - - - +
452B GLY* 3.3 1.2 - - - -
453B THR* 1.3 79.4 + - - +
455B ASP* 1.3 63.2 + - - +
457B THR* 3.8 2.3 - - - -
458B GLN* 3.1 15.9 + - - +
465B ARG* 3.3 50.3 - - - +
474B TYR* 3.3 17.7 + - - +
503B GLY* 4.3 4.5 - - - -
504B GLU* 3.5 45.5 + - - +
505B LEU 5.1 0.2 + - - -
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Residues in contact with ASP 455 (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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358B ARG* 2.4 50.2 + - - -
392B MET* 4.2 0.2 - - - -
431B GLU* 3.3 40.2 + - + +
452B GLY 3.5 1.8 + - - -
454B ASN* 1.3 77.4 - - - +
456B LEU* 1.3 57.9 + - - +
458B GLN* 2.7 33.2 + - - +
459B TYR* 2.8 33.6 + - + -
465B ARG* 3.4 9.3 + - - +
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Residues in contact with LEU 456 (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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430B VAL* 4.5 2.0 - - + +
431B GLU* 2.9 15.9 + - - +
432B THR 3.0 46.4 - - - +
433B PRO* 3.5 8.1 - - + -
436B ALA* 4.2 10.1 - - + -
451B ILE* 3.8 24.2 - - + -
452B GLY 2.9 19.2 + - - +
453B THR* 4.0 5.2 - - - -
455B ASP* 1.3 69.9 - - - +
457B THR* 1.3 63.3 + - - +
459B TYR* 4.6 1.8 - - - +
460B THR* 2.7 35.6 + - - +
481B VAL* 4.5 15.5 - - + -
484B LEU* 4.4 20.4 - - + -
485B ILE* 4.6 5.8 - - + +
488B VAL* 5.7 0.7 - - + -
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Residues in contact with THR 457 (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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453B THR 2.4 27.7 + - - -
456B LEU* 1.3 73.3 - - - +
458B GLN* 1.3 56.0 + - - +
461B LEU* 2.8 48.0 + - + +
474B TYR* 3.2 32.8 - - + -
475B GLN 3.7 7.4 - - - +
476B PRO* 3.2 41.4 - - + +
481B VAL* 3.9 14.2 - - - +
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Residues in contact with GLN 458 (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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355A LEU* 3.9 14.7 - - + +
354B PHE* 3.1 41.6 - - - +
454B ASN 3.1 11.7 + - - +
455B ASP* 2.7 23.5 + - - +
457B THR* 1.3 73.1 - - - +
459B TYR* 1.3 77.5 + - + +
462B ALA* 2.7 29.8 + - - -
463B VAL* 2.9 32.1 + - - +
465B ARG* 3.1 35.0 + - + +
474B TYR* 4.3 1.5 - - - -
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Residues in contact with TYR 459 (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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355A LEU* 4.4 3.8 - - + -
433A PRO* 3.3 2.6 - - - +
459A TYR* 3.0 49.4 - - - +
462A ALA* 3.4 26.9 - - + -
354B PHE 2.6 27.7 + - - -
355B LEU* 3.8 16.2 - - + -
358B ARG* 2.6 22.0 + - - -
392B MET* 3.4 9.9 - - + +
431B GLU 3.5 13.9 - - - -
432B THR* 4.4 1.6 - - - -
433B PRO* 3.5 12.8 - - + -
455B ASP* 2.8 49.4 + - + +
456B LEU 4.4 0.2 - - - +
458B GLN* 1.3 87.4 + - + +
460B THR* 1.3 67.5 + - - +
461B LEU 3.3 0.2 - - - -
462B ALA* 3.5 4.0 + - - +
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Residues in contact with THR 460 (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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432A THR* 3.3 3.1 - - - +
433A PRO* 3.3 17.2 - - - +
434A ALA* 3.0 48.9 + - + +
433B PRO* 3.6 9.0 - - - +
456B LEU* 2.7 26.0 + - - +
457B THR 3.8 1.3 - - - -
459B TYR* 1.3 77.9 - - - +
461B LEU* 1.3 59.8 + - - +
480B SER* 4.1 11.9 - - - +
481B VAL* 4.1 11.4 - - + +
484B LEU* 3.3 34.2 - - + +
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Residues in contact with LEU 461 (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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361A ARG* 2.7 27.9 + - - -
394A ILE* 3.5 23.6 - - + +
434A ALA* 3.9 10.5 - - + -
457B THR* 2.8 23.8 + - + +
460B THR* 1.3 78.7 - - + +
462B ALA* 1.3 62.7 + - - +
463B VAL* 3.1 11.8 - - + +
473B LEU 3.1 22.9 - - - +
474B TYR* 4.1 0.9 - - - -
475B GLN* 3.1 33.0 - - + +
478B SER* 4.0 9.4 - - - +
480B SER* 3.5 24.2 - - - +
481B VAL* 4.5 3.4 - - + -
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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