Contacts of the helix formed by residues 499 - 507 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C GLU 5.1 1.8 - - - +
321C ALA* 4.4 2.5 - - + -
322C HIS* 3.8 33.4 - - + +
325C THR* 3.3 40.4 - - + +
497C ALA 3.7 4.4 - - - +
498C PHE* 1.4 88.4 - - + +
500C PRO* 1.3 73.5 - - + +
502C TYR* 3.1 17.1 + - + +
503C LYS* 3.2 9.9 + - - +
322D HIS* 5.9 1.1 - - - +
497D ALA* 3.5 20.4 - - - +
498D PHE 4.8 0.4 - - - +
499D PRO* 5.3 0.7 - - + -
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Residues in contact with PRO 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C PHE 3.3 4.5 - - - +
499C PRO* 1.3 84.0 - - + +
501C LEU* 1.3 55.3 + - - +
503C LYS* 3.2 11.9 + - + +
504C GLU* 2.9 28.1 + - - +
495D GLN 3.4 24.5 - - - +
496D ALA 3.3 13.5 - - - +
497D ALA 3.9 0.2 - - - -
498D PHE 3.3 23.3 - - - +
500D PRO* 4.4 14.6 - - + -
503D LYS* 6.1 0.9 - - - +
500R LEU* 3.6 14.6 - - + +
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Residues in contact with LEU 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C THR* 4.0 18.8 - - + -
328C ILE* 4.0 24.5 - - + -
329C GLN* 4.3 11.9 - - + -
332C VAL* 5.3 0.7 - - + -
499C PRO 3.2 0.2 - - - -
500C PRO* 1.3 70.3 - - - +
502C TYR* 1.3 66.1 + - - +
504C GLU* 3.2 7.7 + - - +
505C LEU* 2.9 38.8 + - + +
496D ALA* 2.8 24.8 + - + +
500R LEU* 3.7 21.2 - - + +
501R LEU* 4.2 20.0 - - + +
504R LEU* 3.8 31.9 - - + -
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Residues in contact with TYR 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C TRP* 3.2 22.5 - + - -
321C ALA* 3.8 30.3 - - + -
324C LEU* 3.7 15.7 - - + -
325C THR* 3.4 18.7 + - - +
328C ILE* 5.6 0.9 - - + -
479C HIS* 2.7 35.2 + + - -
483C LEU* 3.7 23.2 - - + +
494C VAL* 6.2 0.2 - - + -
498C PHE* 3.6 30.1 - + - -
499C PRO* 3.1 15.5 + - + +
501C LEU* 1.3 77.9 - - - +
503C LYS* 1.3 60.7 + - - +
505C LEU* 4.8 0.7 - - - -
506C PHE* 3.0 50.7 + + - +
507C SER* 5.6 0.2 - - - -
601C C3S 4.4 2.2 - - + +
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Residues in contact with LYS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C GLN* 5.1 6.1 - - - +
494C VAL* 4.2 30.5 - - + +
495C GLN* 5.0 17.9 - - - +
498C PHE* 5.5 2.0 - - + +
499C PRO 3.2 7.4 + - - +
500C PRO* 3.2 14.3 + - + +
501C LEU 3.2 0.4 - - - -
502C TYR* 1.3 84.6 - - + +
504C GLU* 1.3 61.8 + - - +
507C SER* 3.0 53.1 + - - +
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Residues in contact with GLU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C LYS* 3.8 21.4 + - + +
500C PRO 2.9 12.3 + - - +
501C LEU* 3.2 12.9 + - - +
503C LYS* 1.3 76.5 - - - +
505C LEU* 1.3 66.0 + - + +
507C SER 4.9 3.8 + - - +
499R THR* 3.5 18.7 - - + +
500R LEU* 2.7 39.2 + - + +
501R LEU* 3.1 35.9 + - - +
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Residues in contact with LEU 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE* 3.9 40.6 - - + -
353C LEU 5.0 0.9 - - - +
354C LYS* 4.0 40.6 - - + +
357C ALA* 4.7 7.6 - - + -
480C VAL* 5.5 1.6 - - - +
501C LEU* 2.9 32.5 + - + +
502C TYR* 5.3 0.2 - - - -
504C GLU* 1.3 83.8 - - + +
506C PHE* 1.3 82.7 + - + +
507C SER 5.3 0.4 - - - -
501R LEU* 3.9 32.5 - - + -
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Residues in contact with PHE 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 4.4 0.9 - - + -
328C ILE* 3.7 32.8 - - + -
354C LYS 5.4 6.3 - - - -
358C MET* 3.7 30.7 - - + -
476C CYS* 6.3 1.1 - - + -
479C HIS* 3.4 30.1 - + + +
480C VAL* 4.1 32.3 - - + +
483C LEU* 3.4 24.7 - - + +
502C TYR* 3.0 45.8 + + - +
505C LEU* 1.3 98.8 - - + +
507C SER* 1.3 67.0 + - - +
508C THR* 3.4 2.3 + - - -
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Residues in contact with SER 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C LEU* 3.8 9.9 - - - +
487C GLN* 3.3 26.3 + - - -
494C VAL* 4.2 4.5 - - - +
502C TYR* 4.1 0.4 + - - -
503C LYS* 3.0 49.1 + - - +
504C GLU 5.0 3.1 - - - +
505C LEU 5.3 0.5 - - - -
506C PHE* 1.3 76.5 + - - +
508C THR* 1.3 64.5 + - - +
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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