Contacts of the helix formed by residues 385 - 399 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383N ASP 4.3 6.0 + - - +
384N ALA* 1.3 73.6 - - - +
386N PRO* 1.3 68.4 - - - +
387N GLU* 3.1 25.4 - - + +
388N TYR* 3.1 6.1 + - + +
389N ILE* 3.0 22.8 + - - +
428N MET 5.1 1.4 + - - -
429N GLN* 2.6 34.3 + - - +
430N VAL 4.7 1.6 + - - +
81P ARG* 4.4 14.8 - - - +
83P LYS* 4.2 22.2 - - - +
302P ALA* 5.7 6.5 - - - +
303P THR* 5.4 3.3 + - - +
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Residues in contact with PRO 386 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371N LYS* 4.8 1.3 - - - -
384N ALA 3.7 3.3 - - - +
385N ASN* 1.3 79.1 - - + +
387N GLU* 1.3 81.7 + - - +
389N ILE* 3.0 13.1 + - + +
390N ALA* 2.7 35.7 + - - +
83P LYS* 4.9 2.9 - - - +
150P VAL* 4.8 7.2 - - + +
152P VAL* 3.9 11.4 - - + -
238P SER* 3.5 25.3 - - - +
239P ALA 3.9 11.0 - - - +
240P GLU* 3.6 33.2 - - + +
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Residues in contact with GLU 387 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385N ASN* 3.1 16.5 - - + +
386N PRO* 1.3 107.1 - - - +
388N TYR* 1.3 64.0 + - - +
390N ALA* 3.6 3.1 + - - +
391N GLU* 3.3 23.9 + - - +
429N GLN* 4.4 4.0 - - - +
81P ARG* 3.2 50.3 + - - +
83P LYS* 4.7 6.4 - - - -
150P VAL* 5.8 2.3 - - - +
152P VAL* 4.0 17.3 - - + +
158P ILE* 4.2 15.3 - - + +
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Residues in contact with TYR 388 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N GLU* 3.6 30.2 - - + +
338N MET 2.9 17.5 + - - -
339N LEU* 3.7 1.7 - - - +
384N ALA* 5.2 0.9 - - + -
385N ASN* 3.1 11.6 + - + +
386N PRO 3.1 0.6 - - - -
387N GLU* 1.3 79.3 - - - +
389N ILE* 1.3 65.7 + - - +
391N GLU* 3.1 13.3 + - + +
392N LEU* 3.1 37.0 + - + +
429N GLN* 3.0 62.5 + - + +
430N VAL 4.0 8.3 - - - -
431N ILE* 3.5 27.1 - - + -
462N PHE* 3.2 22.8 - + - -
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Residues in contact with ILE 389 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369N PHE* 5.7 3.4 - - + -
371N LYS* 3.8 35.7 - - + -
384N ALA* 4.0 12.8 - - + +
385N ASN 3.0 21.4 + - - +
386N PRO* 3.0 11.1 + - + +
388N TYR* 1.3 73.6 - - + +
390N ALA* 1.3 67.6 + - - +
392N LEU* 2.9 13.7 + - + +
393N ARG* 2.9 23.2 + - + +
431N ILE* 3.5 25.4 - - + -
115P GLN* 5.1 1.1 - - - +
237P VAL* 3.7 34.5 - - + +
238P SER* 3.7 8.5 - - - -
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Residues in contact with ALA 390 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386N PRO 2.7 13.6 + - - +
387N GLU 3.7 3.8 - - - +
389N ILE* 1.3 72.0 - - - +
391N GLU* 1.3 67.2 + - + +
393N ARG* 2.9 18.7 + - - +
394N ARG* 2.9 14.0 + - - +
152P VAL* 3.2 35.4 - - + -
153P LYS 3.6 12.8 - - - +
154P LYS* 4.0 5.5 - - - +
156P GLY* 5.2 2.2 - - - -
238P SER* 3.5 15.4 - - - +
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Residues in contact with GLU 391 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N GLU* 5.6 4.5 - - - +
387N GLU 3.3 12.9 + - - +
388N TYR* 3.1 20.3 + - + +
389N ILE 3.1 0.6 - - - -
390N ALA* 1.3 78.6 - - - +
392N LEU* 1.3 64.1 + - + +
394N ARG* 3.1 50.4 + - - +
395N ILE* 2.9 33.4 + - + +
154P LYS 4.5 4.7 - - - +
155P ASP 5.1 4.7 - - - +
156P GLY* 5.4 4.0 - - - -
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Residues in contact with LEU 392 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339N LEU* 4.1 7.9 - - + -
369N PHE* 3.5 27.4 - - + -
388N TYR* 3.5 27.8 - - + +
389N ILE* 2.9 9.3 + - + +
391N GLU* 1.3 77.0 - - + +
393N ARG* 1.3 57.9 + - - +
395N ILE* 3.3 10.4 + - + +
396N LEU* 2.8 40.2 + - + +
431N ILE* 3.4 38.4 - - + -
462N PHE* 3.6 36.1 - - + -
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Residues in contact with ARG 393 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389N ILE* 2.9 19.7 + - + +
390N ALA* 3.0 8.1 - - - +
392N LEU* 1.3 81.7 - - - +
394N ARG* 1.3 60.7 + - - +
396N LEU* 3.1 11.2 + - - +
397N SER* 2.7 25.4 + - - -
403N TRP* 4.2 22.2 + - + +
152P VAL 3.4 4.4 + - - -
153P LYS 4.6 0.2 - - - -
154P LYS* 3.9 28.7 - - + +
232P SER* 5.1 0.2 + - - -
234P GLU* 2.9 33.4 + - - +
235P ASP* 2.6 45.2 + - - +
237P VAL* 4.6 6.7 - - + -
238P SER* 2.4 51.6 + - - +
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Residues in contact with ARG 394 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390N ALA 2.9 3.7 + - - +
391N GLU* 3.1 43.1 + - - +
393N ARG* 1.3 79.7 - - - +
395N ILE* 1.3 78.2 + - - +
397N SER* 3.0 16.8 + - - -
398N LYS* 3.2 9.7 + - + +
465N ASN* 3.5 29.8 + - - +
154P LYS* 3.6 41.4 - - + +
155P ASP* 5.2 9.4 + - - +
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Residues in contact with ILE 395 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100N LYS* 5.0 1.8 - - - +
391N GLU* 2.9 24.7 + - + +
392N LEU* 3.6 20.2 - - + +
394N ARG* 1.3 89.2 - - - +
396N LEU* 1.3 57.3 + - + +
397N SER 2.7 15.7 + - - -
398N LYS* 3.2 15.3 + - + +
399N GLU* 3.3 17.1 + - + +
461N ALA* 2.8 31.2 - - + +
462N PHE* 4.8 10.5 - - + -
464N ASN 5.3 0.9 - - - +
465N ASN* 3.9 28.7 - - - +
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Residues in contact with LEU 396 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339N LEU* 6.5 0.4 - - + -
367N ILE* 4.6 7.0 - - + -
369N PHE* 3.5 39.3 - - + -
392N LEU* 2.8 26.9 + - + +
393N ARG* 3.4 5.4 - - - +
395N ILE* 1.3 73.0 - - + +
397N SER* 1.3 56.2 + - - +
400N SER 2.3 26.4 - - - +
401N VAL* 3.3 24.7 - - + +
403N TRP* 4.2 20.3 + - + -
458N GLY* 3.4 40.2 - - - +
461N ALA* 4.3 8.7 - - + +
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Residues in contact with SER 397 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393N ARG 2.7 16.1 + - - -
394N ARG* 3.0 13.0 - - - -
395N ILE 2.7 0.4 + - - -
396N LEU* 1.3 81.4 + - - +
398N LYS* 1.3 69.6 + - - +
400N SER* 2.9 13.5 + - - +
403N TRP* 5.0 5.4 + - - -
154P LYS* 3.1 29.5 + - - -
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Residues in contact with LYS 398 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394N ARG* 3.2 8.9 + - + +
395N ILE* 3.8 8.3 - - + +
397N SER* 1.3 77.4 - - - +
399N GLU* 1.3 97.9 + - + +
400N SER* 2.8 11.1 + - - -
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Residues in contact with GLU 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395N ILE* 3.3 11.0 + - + +
398N LYS* 1.3 108.1 + - + +
400N SER* 1.3 68.9 + - - +
401N VAL* 3.5 7.7 + - + +
461N ALA* 3.6 37.5 - - + +
463N LEU* 4.9 9.9 - - + +
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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