Contacts of the helix formed by residues 499 - 507 (chain B) in PDB entry 5NTI
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 PRO 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A HIS* 5.9 1.3 - - - +
496A ALA 4.5 0.4 - - - +
497A ALA* 3.7 18.6 - - - +
498A PHE 4.7 0.7 - - - +
499A PRO* 5.3 0.7 - - + -
318B GLU 5.1 2.0 - - - +
321B ALA* 3.8 24.7 - - + +
322B HIS* 3.8 17.9 - - + +
325B THR* 3.3 42.0 - - + +
497B ALA 3.8 3.3 - - - +
498B PHE* 1.3 86.5 - - + +
500B PRO* 1.3 71.4 - - + +
502B TYR* 3.1 12.9 + - + +
503B LYS* 3.3 10.8 + - - +
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Residues in contact with PRO 500 (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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494A VAL 5.1 0.4 - - - +
495A GLN 3.4 24.9 - - - +
496A ALA 3.2 14.4 - - - +
497A ALA 3.8 0.4 - - - -
498A PHE 3.2 25.1 - - - +
500A PRO* 4.0 16.8 - - + -
498B PHE 3.4 4.0 - - - +
499B PRO* 1.3 83.5 - - + +
501B LEU* 1.3 59.6 + - - +
503B LYS* 3.2 10.8 + - + +
504B GLU* 3.0 19.8 + - - +
500Q LEU* 3.4 16.5 - - + +
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Residues in contact with LEU 501 (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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496A ALA* 2.8 23.7 + - + +
325B THR* 4.2 18.4 - - + -
328B ILE* 4.0 23.6 - - + -
329B GLN* 4.5 12.3 - - + +
332B VAL* 5.1 3.4 - - + -
499B PRO 3.2 0.4 - - - -
500B PRO* 1.3 72.0 - - - +
502B TYR* 1.3 63.1 + - - +
504B GLU* 3.3 10.3 + - - +
505B LEU* 3.0 41.7 + - + +
500Q LEU* 3.5 24.8 - - + +
501Q LEU* 4.4 11.2 - - + -
504Q LEU* 3.8 25.1 - - + -
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Residues in contact with TYR 502 (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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317B TRP* 3.5 21.0 - - - -
321B ALA* 4.0 23.1 - - + -
324B LEU* 3.8 15.0 - - + -
325B THR* 3.3 23.9 + - - +
328B ILE* 5.5 1.6 - - + -
479B HIS* 2.8 32.5 + + - -
483B LEU* 3.8 24.4 - - + +
494B VAL* 5.7 1.3 - - + -
498B PHE* 3.6 30.5 - + - -
499B PRO* 3.1 16.6 + - + +
501B LEU* 1.3 79.0 - - - +
503B LYS* 1.3 64.8 + - - +
505B LEU* 4.9 0.7 - - - -
506B PHE* 3.1 53.8 + + - +
601B C3S 4.7 2.3 - - + +
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Residues in contact with LYS 503 (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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487B GLN* 5.8 2.9 - - - +
494B VAL* 4.4 28.0 - - + +
495B GLN* 3.9 28.1 - - - +
498B PHE* 5.6 0.4 - - + -
499B PRO 3.3 6.9 + - - +
500B PRO* 3.2 13.7 + - + +
502B TYR* 1.3 82.2 - - - +
504B GLU* 1.3 60.9 + - - +
507B SER* 2.9 54.9 + - - +
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Residues in contact with GLU 504 (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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354B LYS* 4.1 16.9 + - + +
500B PRO 3.0 12.9 + - - +
501B LEU* 3.6 10.0 - - - +
503B LYS* 1.3 78.3 - - - +
505B LEU* 1.3 65.0 + - + +
507B SER 4.7 2.1 + - - +
499Q THR* 3.4 22.5 - - + +
500Q LEU* 2.7 36.7 + - + +
501Q LEU* 3.2 35.7 + - + +
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Residues in contact with LEU 505 (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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328B ILE* 3.9 41.5 - - + -
353B LEU 4.8 1.6 - - - +
354B LYS* 3.7 50.6 - - + +
357B ALA* 4.7 7.6 - - + -
480B VAL* 5.1 2.4 - - - +
501B LEU* 3.0 32.1 + - + +
504B GLU* 1.3 79.9 - - + +
506B PHE* 1.3 83.6 + - + +
501Q LEU* 3.8 26.5 - - + -
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Residues in contact with PHE 506 (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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324B LEU* 4.6 1.1 - - + -
328B ILE* 3.7 31.2 - - + -
354B LYS 5.5 5.4 - - - -
358B MET* 3.9 33.4 - - + -
476B CYS* 5.9 1.8 - - + -
479B HIS* 3.7 24.0 - + + -
480B VAL* 3.9 37.3 - - + +
483B LEU* 3.5 22.4 - - + +
484B GLN* 6.1 0.5 - - - +
502B TYR* 3.1 46.8 + + - +
504B GLU 3.4 0.2 - - - -
505B LEU* 1.3 102.6 - - + +
507B SER* 1.3 67.5 + - - +
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL* 5.9 1.0 - - - +
483B LEU* 3.8 12.1 - - - +
484B GLN* 6.0 6.3 - - - -
487B GLN* 2.7 34.1 + - - -
494B VAL* 4.3 4.7 - - - +
503B LYS* 2.9 47.5 + - - +
504B GLU 4.7 2.1 + - - +
506B PHE* 1.3 82.9 - - - +
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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