Contacts of the helix formed by residues 387 - 400 (chain D) in PDB entry 3NJ4
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 387 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378D LYS* 4.6 13.5 - - - +
379D TYR* 4.1 14.1 - - + +
385D PHE 3.8 4.5 - - - +
386D LEU* 1.3 88.7 - - + +
388D LYS* 1.3 59.0 + - - +
389D LYS* 2.9 12.8 - - + +
390D LEU* 2.8 51.0 + - + +
391D ASP* 3.1 8.3 + - - +
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Residues in contact with LYS 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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431C ARG* 4.5 7.3 - - - +
184D VAL* 4.2 10.5 - - - +
386D LEU 3.4 3.7 + - - -
387D PRO* 1.3 71.5 - - - +
389D LYS* 1.3 57.3 + - - +
390D LEU 3.2 0.2 - - - -
391D ASP* 3.7 11.7 - - + -
392D GLU* 2.9 54.5 + - + +
424D PRO* 4.3 7.6 - - + -
426D LYS* 3.0 34.5 - - + +
427D PRO 3.6 15.7 + - - -
428D ASP* 3.9 26.0 + - - +
430D TYR* 4.9 0.6 + - - +
432D TYR* 2.9 36.5 + - - +
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Residues in contact with LYS 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D PRO* 2.9 8.7 - - + +
388D LYS* 1.3 81.1 - - - +
390D LEU* 1.3 62.4 + - + +
392D GLU* 3.9 8.0 + - + +
393D ALA* 3.4 19.1 + - - +
422D ASP* 3.5 15.2 + - - +
423D GLY* 3.4 26.0 - - - +
424D PRO* 3.6 25.7 - - + +
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Residues in contact with LEU 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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367D MET* 3.9 22.1 - - + +
371D GLU* 4.2 19.5 - - + +
386D LEU* 3.5 38.4 - - + -
387D PRO* 2.8 29.2 + - + +
389D LYS* 1.3 77.2 - - + +
391D ASP* 1.3 62.0 + - - +
393D ALA* 3.0 8.5 + - + +
394D VAL* 2.9 32.7 + - - +
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Residues in contact with ASP 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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247C ILE* 4.1 4.7 - - + +
183D SER* 3.4 12.9 + - - -
184D VAL* 2.7 39.4 + - - +
185D THR* 2.7 57.5 + - - +
364D ASN* 5.0 2.5 - - - +
386D LEU* 5.0 7.6 - - + +
387D PRO 3.1 10.6 + - - +
388D LYS* 3.6 16.7 + - + +
390D LEU* 1.3 75.8 - - - +
392D GLU* 1.3 63.9 + - - +
394D VAL* 3.1 17.0 + - - +
395D ALA 3.4 0.3 + - - -
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Residues in contact with GLU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ASP* 4.7 6.3 - - - +
246C PRO* 3.4 18.2 - - + +
247C ILE* 3.7 26.7 - - + +
388D LYS* 2.9 37.8 + - + +
389D LYS* 4.0 7.0 + - - +
391D ASP* 1.3 76.4 - - - +
393D ALA* 1.3 60.9 - - - +
395D ALA* 3.5 1.2 + - - +
396D GLU* 3.1 21.4 + - - +
422D ASP 5.1 0.5 - - - +
423D GLY 3.9 1.1 - - - +
424D PRO* 3.1 23.7 - - - +
425D PHE* 2.9 41.0 + - + -
432D TYR* 5.0 0.9 - - - +
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Residues in contact with ALA 393 (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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367D MET* 4.4 11.4 - - + -
389D LYS 3.4 13.6 + - - +
390D LEU* 3.0 18.9 + - + +
392D GLU* 1.3 77.5 - - - +
394D VAL* 1.3 63.2 + - - +
396D GLU* 3.1 12.4 - - + +
397D ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 394 (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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185D THR* 3.6 13.9 - - - +
360D ASN* 3.6 36.1 - - - +
363D THR* 4.1 16.4 - - + -
364D ASN* 3.8 17.0 - - - +
367D MET* 3.4 27.8 - - + -
390D LEU 2.9 21.6 + - - +
391D ASP* 3.1 8.3 + - - +
393D ALA* 1.3 74.3 - - - +
395D ALA* 1.3 63.5 + - - +
397D ALA* 3.1 11.9 + - - +
398D HIS* 3.0 22.8 + - + -
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Residues in contact with ALA 395 (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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246C PRO 3.8 19.1 - - - +
247C ILE* 3.8 10.5 - - + +
250C LEU* 3.5 28.4 - - + +
185D THR* 3.7 18.1 - - + +
391D ASP 3.4 2.6 + - - -
392D GLU 3.9 4.0 - - - +
393D ALA 3.4 0.4 - - - -
394D VAL* 1.3 79.6 - - - +
396D GLU* 1.3 63.9 + - - +
398D HIS* 3.0 12.7 + - - +
399D LEU* 2.9 20.9 + - - +
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Residues in contact with GLU 396 (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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246C PRO* 3.9 13.1 - - + +
392D GLU 3.1 15.7 + - - +
393D ALA* 3.1 18.2 - - - +
395D ALA* 1.3 77.1 - - - +
397D ALA* 1.3 60.8 + - + +
398D HIS 3.3 0.7 + - - -
399D LEU* 3.4 21.6 + - - +
400D GLY 4.5 1.7 + - - -
406D LEU* 3.9 22.4 - - - +
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Residues in contact with ALA 397 (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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30D PRO* 4.0 17.0 - - - +
31D GLY* 4.1 21.8 - - - -
34D ARG* 4.7 22.1 - - + +
363D THR* 5.9 2.0 - - + -
393D ALA 3.1 9.8 + - - +
394D VAL* 3.1 12.8 + - - +
396D GLU* 1.3 78.0 - - + +
398D HIS* 1.3 60.3 + - + +
399D LEU 3.4 1.0 + - - -
400D GLY* 4.6 3.9 + - - -
401D LYS 5.3 1.0 + - - -
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Residues in contact with HIS 398 (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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250C LEU* 4.3 9.4 - - + -
30D PRO* 3.8 19.7 - - + -
31D GLY* 3.4 22.1 + - - -
356D PHE* 3.7 25.8 - + + -
359D SER* 2.5 45.9 + - - -
360D ASN* 3.1 27.5 + - - +
363D THR* 4.1 2.9 - - - -
394D VAL* 3.0 24.8 + - + -
395D ALA 3.0 8.9 + - - +
397D ALA* 1.3 76.3 - - + +
399D LEU* 1.3 66.1 + - - +
400D GLY 3.5 0.9 - - - -
401D LYS* 4.0 3.7 + - - +
402D LEU* 3.6 21.8 + - - +
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Residues in contact with LEU 399 (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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246C PRO* 3.8 18.8 - - + +
249C ALA* 4.6 1.1 - - + -
250C LEU* 4.1 19.5 - - + +
395D ALA 2.9 31.3 + - - +
396D GLU* 3.4 19.8 + - - +
398D HIS* 1.3 76.4 - - - +
400D GLY* 1.3 67.3 + - - +
402D LEU* 3.0 15.2 + - - +
403D ASN 3.2 7.4 + - - -
404D VAL* 3.3 38.5 + - + +
406D LEU* 3.8 46.4 - - + +
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Residues in contact with GLY 400 (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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396D GLU 4.5 2.6 + - - -
397D ALA 4.6 3.2 + - - -
398D HIS 3.5 0.6 - - - -
399D LEU* 1.3 77.4 - - - +
401D LYS* 1.3 54.5 + - - +
403D ASN* 2.6 31.8 + - - -
404D VAL 4.9 3.3 + - - -
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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