Contacts of the helix formed by residues 385 - 399 (chain D) in PDB entry 2GLJ
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 ASN 385 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C ARG* 4.6 13.1 - - - +
83C LYS* 4.3 21.7 - - - +
240C GLU* 5.5 0.2 - - - +
302C ALA* 5.8 5.7 - - - +
303C THR* 5.6 1.6 + - - -
383D ASP 4.3 6.3 + - - +
384D ALA* 1.3 72.7 - - - +
386D PRO* 1.3 69.7 - - - +
387D GLU* 3.1 25.6 - - + +
388D TYR* 3.1 8.2 + - + +
389D ILE* 3.0 22.2 + - - +
428D MET 5.2 1.0 + - - -
429D GLN* 2.7 34.7 + - - +
430D VAL 4.7 1.2 + - - -
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Residues in contact with PRO 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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83C LYS* 5.1 2.5 - - - +
150C VAL* 4.9 6.5 - - + +
152C VAL* 3.9 11.2 - - + -
238C SER* 3.3 28.0 - - - +
239C ALA 3.8 11.0 - - - +
240C GLU* 3.7 32.5 - - + +
371D LYS* 4.8 0.7 - - - -
384D ALA 3.7 4.0 - - - +
385D ASN* 1.3 79.4 - - + +
387D GLU* 1.3 80.7 + - - +
389D ILE* 2.9 13.7 + - + +
390D ALA* 2.7 35.3 + - - +
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Residues in contact with GLU 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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81C ARG* 3.4 45.0 + - - +
83C LYS* 4.9 6.4 + - - -
150C VAL* 5.8 2.3 - - - +
152C VAL* 4.0 19.6 - - + +
158C ILE* 4.2 15.4 - - + +
385D ASN* 3.1 17.8 - - + +
386D PRO* 1.3 107.4 - - - +
388D TYR* 1.3 62.5 + - - +
390D ALA* 3.6 2.8 + - - +
391D GLU* 3.3 23.9 + - - +
429D GLN* 4.4 5.2 - - - +
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Residues in contact with TYR 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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337D GLU* 3.6 30.6 - - + +
338D MET 3.0 16.8 + - - -
339D LEU* 3.7 1.7 - - - +
384D ALA* 5.2 0.9 - - + -
385D ASN* 3.1 13.0 + - + +
387D GLU* 1.3 77.9 - - - +
389D ILE* 1.3 67.1 + - - +
391D GLU* 3.1 13.5 + - + +
392D LEU* 3.1 48.4 + - + +
429D GLN* 3.2 60.7 + - + +
430D VAL 4.0 8.5 - - - -
431D ILE* 3.6 16.6 - - + -
462D PHE* 3.1 24.3 - + - -
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Residues in contact with ILE 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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115C GLN* 4.9 1.6 - - - +
237C VAL* 3.6 39.5 - - + +
238C SER* 3.8 7.9 - - - -
369D PHE* 5.7 4.0 - - + -
371D LYS* 3.8 30.1 - - + -
384D ALA* 4.0 9.6 - - + +
385D ASN 3.0 18.9 + - - +
386D PRO* 2.9 11.6 + - + +
388D TYR* 1.3 73.5 - - - +
390D ALA* 1.3 66.5 + - - +
392D LEU* 2.9 14.2 + - + +
393D ARG* 2.9 23.7 + - + +
431D ILE* 3.5 28.3 - - + -
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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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152C VAL* 3.4 33.2 - - + +
153C LYS 3.6 13.7 - - - +
154C LYS* 4.2 5.8 - - - +
156C GLY* 5.3 2.0 - - - -
238C SER* 3.4 15.1 - - - +
386D PRO 2.7 14.7 + - - +
387D GLU 3.7 2.7 - - - +
389D ILE* 1.3 71.6 - - - +
391D GLU* 1.3 65.3 + - + +
393D ARG* 2.9 19.8 + - - +
394D ARG* 2.9 14.0 + - - +
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Residues in contact with GLU 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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154C LYS 4.4 5.5 - - - +
155C ASP 5.2 4.0 - - - +
156C GLY* 5.5 3.0 + - - -
337D GLU* 5.6 4.9 - - - +
387D GLU 3.3 12.4 + - - +
388D TYR* 3.1 18.8 + - + +
389D ILE 3.1 0.6 - - - -
390D ALA* 1.3 78.7 - - + +
392D LEU* 1.3 65.5 + - + +
394D ARG* 3.1 51.4 + - - +
395D ILE* 2.9 33.1 + - + +
465D ASN* 4.8 3.9 - - - +
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Residues in contact with LEU 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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339D LEU* 4.1 6.3 - - + -
369D PHE* 3.6 26.2 - - + -
388D TYR* 3.4 30.5 - - + +
389D ILE* 2.9 8.4 + - + +
391D GLU* 1.3 76.1 - - + +
393D ARG* 1.3 58.3 + - + +
395D ILE* 3.3 10.3 + - + +
396D LEU* 2.8 40.1 + - + +
431D ILE* 3.5 38.1 - - + -
462D PHE* 3.6 36.6 - - + -
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Residues in contact with ARG 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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152C VAL 3.7 3.6 + - - -
154C LYS* 4.1 26.9 - - + +
232C SER* 5.0 0.4 + - - -
234C GLU* 2.6 47.1 + - - +
235C ASP* 2.7 41.0 + - - +
237C VAL* 4.5 8.5 - - + -
238C SER* 2.6 38.7 + - - -
389D ILE* 2.9 21.2 + - + +
390D ALA* 2.9 17.7 + - - +
392D LEU* 1.3 80.4 - - - +
394D ARG* 1.3 61.2 + - - +
396D LEU* 3.1 11.7 + - - +
397D SER* 2.7 24.6 + - - -
403D TRP* 4.3 20.4 + - + +
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Residues in contact with ARG 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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154C LYS* 3.7 42.1 - - + +
155C ASP* 5.3 7.3 + - - +
390D ALA 2.9 3.0 + - - +
391D GLU* 3.1 43.4 + - - +
393D ARG* 1.3 77.8 - - - +
395D ILE* 1.3 74.1 + - - +
397D SER* 3.0 17.2 + - - -
398D LYS* 3.2 9.5 + - + +
465D ASN* 4.0 33.1 + - - +
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Residues in contact with ILE 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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100D LYS* 5.0 0.7 - - - +
391D GLU* 2.9 23.2 + - + +
392D LEU* 3.6 20.2 - - + +
394D ARG* 1.3 82.4 - - - +
396D LEU* 1.3 55.3 + - + +
397D SER 2.7 14.9 + - - -
398D LYS* 3.2 15.5 + - + +
399D GLU* 3.3 16.5 + - + +
461D ALA* 2.8 31.0 - - + +
462D PHE* 4.8 6.7 - - + -
464D ASN 4.8 2.9 - - - +
465D ASN* 3.4 46.4 - - - +
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Residues in contact with LEU 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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339D LEU* 6.6 0.2 - - + -
367D ILE* 4.6 3.8 - - + -
369D PHE* 3.4 40.2 - - + -
392D LEU* 2.8 26.7 + - + +
393D ARG* 3.4 5.6 - - - +
395D ILE* 1.3 74.2 - - + +
397D SER* 1.3 54.6 + - - +
400D SER 2.3 27.4 - - - +
401D VAL* 3.3 25.3 - - + +
403D TRP* 4.2 24.4 + - + -
458D GLY* 3.4 39.5 - - - +
461D ALA* 4.4 7.2 - - + +
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Residues in contact with SER 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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154C LYS* 3.3 26.0 + - - -
393D ARG 2.7 16.5 + - - -
394D ARG* 3.0 13.0 - - - -
395D ILE 2.7 0.4 + - - -
396D LEU* 1.3 81.4 + - - +
398D LYS* 1.3 70.2 + - - +
400D SER* 2.9 14.4 + - - +
403D TRP* 5.0 4.7 + - - -
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Residues in contact with LYS 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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394D ARG* 3.2 8.2 + - + +
395D ILE* 3.8 8.5 - - + +
397D SER* 1.3 78.2 - - - +
399D GLU* 1.3 99.3 + - + +
400D SER* 2.8 10.9 + - - -
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Residues in contact with GLU 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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395D ILE* 3.3 9.7 + - + +
398D LYS* 1.3 107.7 + - + +
400D SER* 1.3 70.8 + - - +
401D VAL* 3.5 8.4 + - + +
461D ALA* 3.6 36.2 - - + +
463D LEU* 4.9 10.0 - - + +
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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