Contacts of the helix formed by residues 384 - 392 (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 GLY 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299C ILE* 6.0 0.2 - - - +
305C VAL* 6.3 0.4 - - - +
373C ASN 5.4 0.7 - - - -
374C ARG 3.5 17.0 - - - -
375C THR* 3.5 8.5 - - - +
383C GLY* 1.3 76.6 - - - +
385C MET* 1.3 65.0 + - - -
386C GLU* 3.2 23.6 + - - -
387C LEU* 3.4 17.7 + - - +
388C PHE* 3.9 4.2 - - - -
401C PHE* 3.9 2.0 - - - -
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Residues in contact with MET 385 (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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481A GLU* 3.3 42.8 - - + +
484A GLN* 3.5 19.1 - - + +
485A ILE* 3.8 23.1 - - + -
374C ARG 4.4 0.8 + - - -
384C GLY* 1.3 70.9 - - - -
386C GLU* 1.3 70.3 + - - +
387C LEU 3.2 0.2 - - - -
388C PHE* 3.1 23.2 + - - +
389C ARG* 4.3 0.5 + - - +
397C ILE* 3.8 10.1 - - + +
398C SER* 3.8 26.2 - - - +
401C PHE* 3.7 43.6 - - + -
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Residues in contact with GLU 386 (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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481A GLU* 3.1 33.1 - - - +
302C ARG* 5.5 5.2 + - - +
305C VAL* 3.9 20.1 - - + +
309C GLN* 3.0 37.4 + - - +
384C GLY* 3.7 18.7 + - - -
385C MET* 1.3 84.8 + - - +
387C LEU* 1.3 62.5 + - - +
388C PHE 3.0 6.2 + - - -
389C ARG* 3.3 16.7 + - - +
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Residues in contact with LEU 387 (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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300C PHE* 3.6 34.3 - - + -
305C VAL* 3.8 33.7 - - + -
308C TYR* 3.4 54.7 - - + +
309C GLN* 4.6 0.6 + - - -
316C MET* 3.6 10.0 - - + +
378C PHE* 4.0 21.1 - - + -
383C GLY* 4.0 14.8 - - - -
384C GLY 3.4 15.2 + - - +
385C MET 3.2 0.4 - - - -
386C GLU* 1.3 80.4 - - + +
388C PHE* 1.3 71.8 + - + +
389C ARG 3.4 1.9 + - - -
390C ALA 4.8 0.7 + - - -
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Residues in contact with PHE 388 (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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316C MET* 3.8 20.0 - - + -
320C CYS* 3.9 22.2 - - - -
376C VAL* 4.3 6.7 - - + -
378C PHE* 4.1 34.8 - + - -
383C GLY 5.0 0.2 - - - -
384C GLY 3.9 14.1 - - - -
385C MET* 3.1 20.1 + - - +
386C GLU 3.0 1.8 - - - -
387C LEU* 1.3 88.3 - - + +
389C ARG* 1.3 63.5 + - - +
390C ALA* 3.3 2.9 - - - -
391C LEU* 3.2 27.9 + - + +
393C CYS 5.3 1.7 + - - -
394C SER* 6.0 0.9 - - - -
397C ILE* 3.9 28.5 - - + +
401C PHE* 4.1 16.2 - + - -
601C C3S 4.1 26.0 - - + -
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Residues in contact with ARG 389 (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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474A SER* 4.8 11.3 + - - +
477A SER* 3.5 38.6 + - - -
478A GLN* 4.6 2.8 - - - +
481A GLU* 3.3 33.7 + - - +
309C GLN* 3.2 45.9 + - + +
385C MET 4.3 1.0 + - - +
386C GLU* 3.3 15.7 + - - +
387C LEU 3.4 1.4 - - - -
388C PHE* 1.3 77.8 - - - +
390C ALA* 1.3 58.0 + - - +
391C LEU 3.0 0.2 - - - -
392C GLY* 2.9 23.4 + - - -
394C SER* 5.9 11.5 - - - +
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Residues in contact with ALA 390 (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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308C TYR 3.8 18.6 - - - +
309C GLN* 4.3 8.9 + - - +
311C LYS 3.4 26.0 - - - +
312C SER 4.4 0.9 - - - +
313C MET* 3.4 25.9 + - - +
316C MET* 3.9 20.0 - - + -
387C LEU 4.8 1.0 + - - -
388C PHE 3.3 0.8 - - - -
389C ARG* 1.3 77.9 - - - +
391C LEU* 1.3 62.1 + - - +
392C GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 391 (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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313C MET* 3.8 8.2 - - - +
316C MET* 3.7 17.5 - - + +
317C TRP* 2.9 68.9 + - + +
320C CYS* 4.0 14.4 - - - -
388C PHE* 3.2 21.1 - - + +
389C ARG 3.0 0.2 + - - -
390C ALA* 1.3 79.4 - - - +
392C GLY* 1.3 61.3 + - - +
393C CYS* 3.5 14.2 + - - +
397C ILE* 3.7 29.6 - - + -
601C C3S 3.7 18.4 - - + -
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Residues in contact with GLY 392 (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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313C MET* 4.4 12.5 - - - +
389C ARG 2.9 14.6 + - - -
390C ALA 3.1 2.8 - - - -
391C LEU* 1.3 78.5 - - - +
393C CYS* 1.3 57.8 + - - +
394C SER* 3.9 2.2 - - - -
482C ARG* 3.1 22.2 + - - -
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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