Contacts of the helix formed by residues 377 - 389 (chain D) in PDB entry 6RIN
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 PHE 377 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368D LEU* 5.6 5.6 - - + -
373D ALA* 3.0 33.3 + - + +
376D LEU* 1.3 85.3 - - + +
378D LYS* 1.3 64.7 + - - +
379D PRO* 3.2 5.8 - - - -
380D PHE* 3.0 41.0 + + + -
381D ILE* 3.0 21.5 + - + +
412D LEU* 5.6 2.7 - - + -
415D VAL* 5.2 4.5 - - + -
416D ILE* 3.3 36.1 - - + -
419D HIS* 4.1 13.2 - + - -
421D VAL* 4.5 13.9 - - + -
439D PRO* 5.6 2.5 - - + -
470D VAL* 3.7 40.4 - - + -
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Residues in contact with LYS 378 (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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1247C SER* 3.8 13.2 - - - +
374D LEU* 3.3 24.5 + - + +
375D GLU* 3.5 39.4 + - - +
376D LEU 3.0 4.4 + - - -
377D PHE* 1.3 74.9 - - - +
379D PRO* 1.3 67.8 - - + +
381D ILE* 3.3 8.7 + - + +
382D TYR* 3.0 60.0 + - + -
398D LYS* 4.8 7.6 - - - +
401D VAL* 3.9 18.1 + - + +
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Residues in contact with PRO 379 (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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1247C SER* 5.1 2.9 - - - -
1248C THR* 5.5 1.1 - - - +
1305C TYR* 4.4 20.2 - - + -
1308C ILE* 3.6 27.7 - - + +
1309C VAL* 5.0 6.5 - - + -
349D TYR* 3.8 31.2 - - + +
376D LEU 3.7 9.0 - - - +
377D PHE* 3.3 5.6 - - - -
378D LYS* 1.3 92.6 - - + +
380D PHE* 1.3 67.9 + - + +
382D TYR* 3.0 15.5 + - + +
383D GLY* 2.9 19.8 + - - -
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Residues in contact with PHE 380 (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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1308C ILE* 4.5 16.6 - - + -
1313C HIS* 3.4 36.1 - + - -
349D TYR* 6.3 0.9 - + - -
377D PHE* 3.0 35.1 + + + +
379D PRO* 1.3 81.0 - - + +
381D ILE* 1.3 62.9 + - - +
383D GLY* 3.2 2.1 + - - +
384D LYS* 3.0 31.2 + - + +
415D VAL* 4.7 20.4 - - + -
419D HIS* 3.8 29.8 - + - -
470D VAL* 5.3 1.1 - - + -
472D LEU* 4.2 29.2 - - + -
477D GLN* 5.4 1.6 - - - -
45E LYS* 6.1 2.5 - - - -
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Residues in contact with ILE 381 (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 LEU* 4.5 20.9 - - + +
377D PHE* 3.0 26.1 + - + +
378D LYS* 3.6 9.4 - - + +
380D PHE* 1.3 77.1 - - - +
382D TYR* 1.3 64.8 + - - +
384D LYS* 3.3 1.0 + - - +
385D LEU* 2.9 46.5 + - + +
401D VAL* 3.9 17.7 - - + -
408D VAL* 5.1 11.9 - - + +
411D ILE* 4.7 14.5 - - + +
412D LEU* 3.8 35.2 - - + +
415D VAL* 4.9 11.4 - - + -
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Residues in contact with TYR 382 (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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1305C TYR* 3.6 24.5 - + - -
1309C VAL* 5.3 7.4 - - + -
378D LYS* 3.0 54.6 + - + -
379D PRO* 3.3 12.6 - - + +
381D ILE* 1.3 75.9 - - - +
383D GLY* 1.3 63.8 + - - +
385D LEU* 3.2 6.9 + - + +
386D GLU* 3.0 24.6 + - - +
394D ILE* 3.7 31.0 - - + +
397D ALA* 4.1 14.4 - - + +
398D LYS* 3.4 40.5 - - + +
401D VAL* 3.6 29.4 - - + -
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Residues in contact with GLY 383 (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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1308C ILE 5.2 1.6 - - - -
1309C VAL* 3.7 27.9 - - - +
1311C GLY 6.2 0.2 - - - -
379D PRO 2.9 13.4 + - - -
380D PHE* 3.2 3.8 + - - -
381D ILE 3.1 0.2 - - - -
382D TYR* 1.3 77.7 - - - +
384D LYS* 1.3 63.8 + - - +
385D LEU 3.1 0.2 + - - -
386D GLU* 3.2 6.4 + - - +
387D LEU* 2.9 24.0 + - - +
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Residues in contact with LYS 384 (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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380D PHE* 3.0 18.3 + - + +
383D GLY* 1.3 75.5 - - - +
385D LEU* 1.3 63.1 + - - +
387D LEU* 3.3 26.4 + - + +
388D ARG* 2.9 40.8 + - - +
411D ILE* 3.9 22.4 - - + -
414D GLU* 5.0 13.0 + - - -
415D VAL* 3.5 24.9 - - + -
45E LYS* 5.8 6.4 - - - +
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Residues in contact with LEU 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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381D ILE* 2.9 41.4 + - + +
382D TYR* 3.3 10.8 - - - +
384D LYS* 1.3 78.9 - - - +
386D GLU* 1.3 64.3 + - - +
387D LEU 2.9 0.5 + - - -
388D ARG* 3.1 4.1 + - - +
389D GLY 2.9 18.5 + - - -
390D LEU* 3.6 32.5 + - + +
391D ALA* 5.3 4.7 - - + +
397D ALA* 4.6 18.6 - - + +
400D MET* 5.4 10.5 - - + -
401D VAL* 4.1 15.9 - - + -
407D VAL* 4.8 7.4 - - + -
408D VAL* 5.1 7.6 - - + -
411D ILE* 4.4 22.7 - - + -
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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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1309C VAL* 3.6 11.7 - - - +
1310C ASP* 3.2 23.4 - - - +
382D TYR 3.0 12.6 + - - +
383D GLY* 3.7 10.3 - - - +
385D LEU* 1.3 79.0 - - - +
387D LEU* 1.3 63.6 + - + +
389D GLY* 3.6 8.9 + - - +
391D ALA* 4.1 21.2 - - + +
392D THR 4.0 13.0 - - - +
393D THR* 5.0 7.9 - - - +
394D ILE* 5.3 7.4 + - - +
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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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383D GLY 2.9 18.2 + - - +
384D LYS* 3.5 31.0 - - + +
386D GLU* 1.3 78.1 - - + +
388D ARG* 1.3 63.2 + - + +
389D GLY* 3.0 9.5 + - - -
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Residues in contact with ARG 388 (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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384D LYS* 2.9 31.2 + - - +
385D LEU* 3.6 1.1 - - + +
387D LEU* 1.3 79.0 - - + +
389D GLY* 1.3 64.4 + - - +
390D LEU* 3.3 19.3 - - + +
411D ILE* 3.8 25.9 - - - +
414D GLU* 2.4 42.0 + - - -
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Residues in contact with GLY 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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385D LEU 2.9 8.2 + - - -
386D GLU* 3.6 9.2 + - - -
387D LEU 3.0 6.1 - - - -
388D ARG* 1.3 81.0 - - - +
390D LEU* 1.3 61.3 + - - +
391D ALA 3.8 2.9 - - - -
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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