Contacts of the helix formed by residues 499 - 507 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C HIS* 6.3 0.2 - - - +
497C ALA* 3.5 23.1 - - - +
498C PHE 4.6 1.1 - - - +
499C PRO* 6.1 0.7 - - + -
318D GLU* 5.4 1.8 - - + +
321D ALA* 4.3 10.1 - - + -
322D HIS* 4.0 22.4 - - + +
325D THR* 3.4 37.5 - - + +
497D ALA 3.6 4.4 - - - +
498D PHE* 1.4 88.3 - - + +
500D PRO* 1.3 71.2 - - + +
502D TYR* 3.1 19.0 + - + +
503D LYS* 3.1 11.8 + - - +
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Residues in contact with PRO 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494C VAL 5.2 0.2 - - - +
495C GLN 3.3 26.5 - - - +
496C ALA 3.3 11.7 - - - +
498C PHE 3.3 22.4 - - - +
500C PRO* 4.4 13.9 - - + -
498D PHE 3.4 4.2 - - - +
499D PRO* 1.3 83.5 - - + +
501D LEU* 1.3 55.7 + - - +
503D LYS* 3.6 11.3 + - + +
504D GLU* 3.1 22.7 + - - +
500S LEU* 3.4 20.0 - - + +
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Residues in contact with LEU 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C ALA* 2.7 27.9 + - + +
325D THR* 4.1 20.2 - - + -
328D ILE* 4.3 17.7 - - + -
329D GLN* 4.2 17.3 - - + +
332D VAL* 5.2 3.4 - - + -
499D PRO 3.2 0.4 - - - -
500D PRO* 1.3 69.4 - - - +
502D TYR* 1.3 65.7 + - - +
504D GLU* 3.4 5.5 + - - +
505D LEU* 3.2 48.5 + - + +
500S LEU* 3.9 17.0 - - + +
501S LEU* 4.5 11.4 - - + +
504S LEU* 3.8 32.3 - - + -
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Residues in contact with TYR 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D TRP* 3.4 22.2 - - - -
321D ALA* 3.8 23.3 - - + -
324D LEU* 3.8 15.7 - - + -
325D THR* 3.3 25.6 + - - +
328D ILE* 5.3 1.1 - - + -
479D HIS* 2.9 34.3 + + - -
483D LEU* 3.5 30.7 - - + +
494D VAL* 6.1 0.4 - - + -
498D PHE* 3.7 24.0 - + - -
499D PRO* 3.1 15.0 + - + +
501D LEU* 1.3 79.4 - - - +
503D LYS* 1.3 65.8 + - - +
505D LEU* 5.1 0.9 - - - -
506D PHE* 3.1 50.1 + + - +
601D C3S 4.4 2.4 - - + +
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Residues in contact with LYS 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C PRO* 6.1 1.0 - - - +
487D GLN* 5.2 4.9 - - - +
494D VAL* 4.0 30.7 + - + +
495D GLN* 4.0 29.1 + - - +
498D PHE* 5.5 3.1 - - + +
499D PRO 3.1 9.5 + - - +
500D PRO* 3.8 12.3 - - + +
501D LEU 3.3 0.2 - - - -
502D TYR* 1.3 83.5 - - + +
504D GLU* 1.3 59.0 + - - +
507D SER* 2.9 56.5 + - - +
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Residues in contact with GLU 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D LYS* 4.3 14.4 + - - -
500D PRO 3.1 17.3 + - - +
501D LEU* 3.8 7.8 - - - +
502D TYR 3.4 0.2 - - - -
503D LYS* 1.3 76.0 - - - +
505D LEU* 1.3 63.6 + - + +
507D SER 4.9 3.6 + - - +
499S THR* 3.4 19.6 - - + -
500S LEU* 2.9 36.2 + - + +
501S LEU* 3.1 33.1 + - - +
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Residues in contact with LEU 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D ILE* 4.0 22.2 - - + -
353D LEU 4.9 1.6 - - - +
354D LYS* 3.9 42.9 - - + +
357D ALA* 4.9 5.4 - - + -
480D VAL* 5.2 1.9 - - - +
501D LEU* 3.2 40.9 + - + +
502D TYR 4.0 2.2 - - - +
504D GLU* 1.3 80.5 - - + +
506D PHE* 1.3 90.4 + - + +
507D SER 5.4 0.4 - - - -
501S LEU* 3.7 32.8 - - + -
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Residues in contact with PHE 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D LEU* 4.6 0.4 - - + -
328D ILE* 3.7 31.4 - - + -
354D LYS 5.2 6.7 - - - -
357D ALA* 5.6 1.1 - - + -
358D MET* 3.8 31.4 - - + -
476D CYS* 6.4 0.7 - - + -
479D HIS* 3.4 33.4 - + + +
480D VAL* 3.8 37.2 - - + +
483D LEU* 3.5 24.6 - - + +
502D TYR* 3.1 40.3 + + - +
505D LEU* 1.3 102.2 - - + +
507D SER* 1.3 64.4 + - - +
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Residues in contact with SER 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D VAL* 5.8 2.2 - - - -
483D LEU* 3.9 10.7 - - - +
487D GLN* 2.7 30.1 + - - -
494D VAL* 5.0 1.0 - - - +
503D LYS* 2.9 41.7 + - - +
504D GLU 5.1 3.6 - - - +
505D LEU 5.4 0.2 - - - -
506D PHE* 1.3 82.1 - - - +
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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