Contacts of the helix formed by residues 384 - 392 (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 GLY 384 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373D ASN 5.5 0.4 - - - -
374D ARG 3.5 18.6 - - - -
375D THR* 3.7 6.5 - - - +
383D GLY* 1.3 77.4 - - - +
385D MET* 1.3 62.6 + - - -
386D GLU* 3.0 27.8 + - - -
387D LEU* 3.1 18.0 + - - +
388D PHE* 4.1 2.4 - - - -
401D PHE* 3.7 2.5 - - - -
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Residues in contact with MET 385 (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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374D ARG* 4.4 16.1 + - + -
384D GLY* 1.3 70.5 - - - -
386D GLU* 1.3 65.8 + - + +
387D LEU 3.2 0.2 - - - -
388D PHE* 3.1 25.0 + - - +
389D ARG* 4.2 0.5 + - - -
394D SER 5.5 0.9 - - - +
397D ILE* 3.8 19.9 - - + +
398D SER* 3.7 28.0 - - - +
401D PHE* 3.5 50.8 - - + -
402D ASP* 5.0 4.7 - - - +
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Residues in contact with GLU 386 (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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302D ARG* 3.2 25.5 + - - -
305D VAL* 3.7 23.2 - - - +
309D GLN* 3.1 32.0 + - - +
383D GLY* 4.8 0.7 - - - -
384D GLY* 3.5 28.0 + - - +
385D MET* 1.3 75.5 - - + +
387D LEU* 1.3 64.1 + - - +
388D PHE 3.1 1.0 + - - -
389D ARG* 3.2 21.3 + - - +
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Residues in contact with LEU 387 (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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300D PHE* 3.7 28.7 - - + -
305D VAL* 4.3 18.4 - - + +
308D TYR* 3.5 61.8 - - + +
309D GLN* 4.7 0.4 + - - -
316D MET* 3.6 9.2 - - + +
376D VAL 5.0 0.2 - - - +
378D PHE* 4.7 10.5 - - + -
383D GLY* 3.4 36.3 - - - +
384D GLY 3.1 10.9 + - - +
386D GLU* 1.3 80.8 + - - +
388D PHE* 1.3 75.1 + - + +
389D ARG 3.3 3.2 + - - -
390D ALA 4.8 0.3 + - - -
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Residues in contact with PHE 388 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316D MET* 3.8 17.9 - - + -
320D CYS* 4.0 21.5 - - - -
376D VAL* 4.1 26.2 - - + -
378D PHE* 3.9 38.1 - + + -
384D GLY 4.1 7.2 - - - -
385D MET* 3.1 21.0 + - - +
386D GLU 3.1 1.8 - - - -
387D LEU* 1.3 89.0 - - + +
389D ARG* 1.3 63.4 + - - +
390D ALA 3.3 2.9 - - - -
391D LEU* 3.3 33.4 + - + +
392D GLY 4.5 0.3 + - - -
393D CYS 5.3 1.6 + - - -
394D SER* 5.8 1.6 + - - -
397D ILE* 4.1 22.4 - - + +
401D PHE* 4.2 6.5 - + - -
601D C3S 4.1 19.7 - - + -
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Residues in contact with ARG 389 (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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309D GLN* 3.1 47.4 + - + +
385D MET 4.2 0.4 + - - -
386D GLU* 3.2 22.2 + - - +
387D LEU 3.3 1.8 - - - -
388D PHE* 1.3 77.1 - - - +
390D ALA* 1.3 63.7 + - - +
391D LEU 3.0 1.6 + - - -
392D GLY* 3.1 14.0 + - - -
393D CYS 4.8 0.7 + - - -
394D SER* 5.9 6.6 + - - -
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Residues in contact with ALA 390 (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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308D TYR 3.7 18.8 + - - +
309D GLN* 4.3 7.8 - - - +
311D LYS 3.2 27.6 - - - +
312D SER 4.3 1.6 - - - +
313D MET* 3.3 25.7 - - - +
316D MET* 3.9 19.1 - - + -
388D PHE 3.3 1.0 - - - -
389D ARG* 1.3 78.4 - - - +
391D LEU* 1.3 61.0 + - - +
392D GLY* 3.1 1.5 + - - -
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Residues in contact with LEU 391 (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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313D MET* 3.9 7.3 - - - +
316D MET* 3.7 18.2 - - + +
317D TRP* 2.8 69.2 + - + +
320D CYS* 4.2 5.6 - - - -
388D PHE* 3.4 40.6 - - + +
389D ARG 3.0 1.0 + - - -
390D ALA* 1.3 76.7 - - - +
392D GLY* 1.3 61.7 + - - +
393D CYS* 3.8 14.8 - - - +
397D ILE* 3.9 18.8 - - + -
601D C3S 4.1 20.2 - - + -
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Residues in contact with GLY 392 (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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313D MET* 4.7 12.4 - - - +
389D ARG 3.1 13.1 + - - -
390D ALA 3.1 3.1 - - - -
391D LEU* 1.3 79.6 - - - +
393D CYS* 1.3 51.4 + - - +
394D SER 4.0 0.7 - - - -
482D ARG* 2.8 30.7 + - - -
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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