Contacts of the helix formed by residues 385 - 399 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81R ARG* 4.6 13.4 - - - +
83R LYS* 4.3 21.1 - - - +
240R GLU* 5.6 0.2 - - - +
302R ALA* 5.9 5.5 - - - +
303R THR* 5.6 1.4 + - - -
383S ASP 4.3 6.5 + - - +
384S ALA* 1.3 73.6 - - - +
386S PRO* 1.3 62.5 - - - +
387S GLU* 3.1 25.8 - - + +
388S TYR* 3.2 6.4 + - + +
389S ILE* 2.9 27.9 + - - +
428S MET 5.2 1.4 + - - -
429S GLN* 2.7 34.3 + - - +
430S VAL 4.7 1.8 + - - +
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Residues in contact with PRO 386 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83R LYS* 5.2 2.0 - - - +
150R VAL* 4.9 5.8 - - + -
152R VAL* 3.9 11.7 - - + -
238R SER* 3.2 30.2 - - - +
239R ALA 3.7 11.2 - - - +
240R GLU* 3.7 32.3 - - + +
371S LYS* 4.9 0.7 - - - -
384S ALA 3.7 3.8 - - - +
385S ASN* 1.3 79.2 - - - +
387S GLU* 1.3 81.1 + - - +
389S ILE* 3.0 11.3 + - + +
390S ALA* 2.7 35.9 + - - +
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Residues in contact with GLU 387 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R ARG* 3.4 45.5 + - - +
83R LYS* 5.0 6.4 - - - -
150R VAL* 5.8 2.3 - - - +
152R VAL* 3.9 18.7 - - + +
158R ILE* 4.2 15.3 - - + +
385S ASN* 3.1 17.8 - - + +
386S PRO* 1.3 107.2 - - - +
388S TYR* 1.3 64.4 + - - +
390S ALA* 3.6 3.1 + - - +
391S GLU* 3.3 24.3 + - - +
429S GLN* 4.5 4.7 - - - +
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Residues in contact with TYR 388 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337S GLU* 3.6 30.0 - - + +
338S MET 3.0 17.0 + - - -
339S LEU* 3.6 1.7 - - - +
384S ALA* 5.2 0.7 - - + -
385S ASN* 3.2 11.3 + - + +
386S PRO 3.1 0.6 - - - -
387S GLU* 1.3 77.7 - - - +
389S ILE* 1.3 68.4 + - - +
391S GLU* 3.2 12.4 + - + +
392S LEU* 3.1 37.7 + - + +
429S GLN* 3.1 62.5 + - + +
430S VAL 4.0 9.0 - - - -
431S ILE* 3.6 26.9 - - + -
462S PHE* 3.2 23.8 - + - -
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Residues in contact with ILE 389 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R GLN* 4.9 1.3 - - - +
237R VAL* 3.6 42.2 - - + +
238R SER* 3.8 7.9 - - - -
369S PHE* 5.7 3.8 - - + -
371S LYS* 3.8 30.5 - - + -
384S ALA* 3.9 9.4 - - + +
385S ASN 2.9 22.3 + - - +
386S PRO* 3.4 10.1 - - + +
388S TYR* 1.3 73.8 - - + +
390S ALA* 1.3 66.6 + - - +
392S LEU* 2.9 13.7 + - + +
393S ARG* 2.9 23.3 + - + +
431S ILE* 3.5 27.4 - - + -
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Residues in contact with ALA 390 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152R VAL* 3.4 32.5 - - + -
153R LYS 3.6 13.9 - - - +
154R LYS* 4.2 6.0 - - - +
156R GLY* 5.3 1.6 - - - +
238R SER* 3.4 16.9 - - - +
386S PRO 2.7 14.3 + - - +
387S GLU 3.7 3.1 - - - +
389S ILE* 1.3 71.6 - - - +
391S GLU* 1.3 65.6 + - + +
393S ARG* 2.9 18.7 + - - +
394S ARG* 3.0 14.0 + - - +
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Residues in contact with GLU 391 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R LYS 4.2 6.2 - - - +
155R ASP 5.2 4.0 - - - +
156R GLY* 5.5 2.9 + - - -
337S GLU* 5.6 4.5 - - - +
387S GLU 3.3 12.0 + - - +
388S TYR* 3.2 18.5 + - + +
389S ILE 3.1 0.6 - - - -
390S ALA* 1.3 79.1 - - - +
392S LEU* 1.3 64.5 + - + +
394S ARG* 3.1 50.3 + - - +
395S ILE* 2.9 34.5 + - + +
465S ASN* 4.7 1.0 - - - +
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Residues in contact with LEU 392 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339S LEU* 4.0 5.8 - - + -
369S PHE* 3.6 26.2 - - + -
388S TYR* 3.1 31.4 + - + +
389S ILE* 2.9 8.1 + - + +
391S GLU* 1.3 76.6 - - + +
393S ARG* 1.3 58.2 + - + +
395S ILE* 3.3 9.5 + - + +
396S LEU* 2.8 39.5 + - + +
431S ILE* 3.5 38.4 - - + -
462S PHE* 3.6 35.9 - - + -
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Residues in contact with ARG 393 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R VAL 3.8 2.4 + - - -
154R LYS* 4.1 25.5 - - + +
232R SER* 4.9 0.2 + - - -
234R GLU* 2.6 47.1 + - - +
235R ASP* 2.7 42.8 + - - +
237R VAL* 4.5 8.3 - - + -
238R SER* 2.7 37.0 + - - +
389S ILE* 2.9 21.6 + - + +
390S ALA* 2.9 18.6 + - - +
392S LEU* 1.3 79.8 - - + +
394S ARG* 1.3 66.0 + - - +
396S LEU* 3.1 11.6 + - - +
397S SER* 2.7 20.1 + - - -
403S TRP* 4.3 19.9 + - + +
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Residues in contact with ARG 394 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R LYS* 3.6 42.7 - - + +
155R ASP* 5.3 8.5 + - - +
390S ALA 3.0 3.1 + - - +
391S GLU* 3.1 42.6 + - - +
393S ARG* 1.3 78.7 - - - +
395S ILE* 1.3 72.0 - - - +
397S SER* 3.0 18.1 + - - -
398S LYS* 3.2 8.5 + - + +
465S ASN* 2.9 30.7 + - - +
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Residues in contact with ILE 395 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S LYS* 5.0 4.9 - - - +
391S GLU* 2.9 24.5 + - + +
392S LEU* 3.6 19.3 - - + +
394S ARG* 1.3 86.8 - - - +
396S LEU* 1.3 62.3 + - + +
397S SER 2.8 11.3 + - - -
398S LYS* 3.2 14.9 + - + +
399S GLU* 3.3 16.7 + - + +
461S ALA* 2.9 31.6 - - + +
462S PHE* 4.8 10.5 - - + -
464S ASN 4.9 3.1 - - - +
465S ASN* 4.0 27.8 - - - +
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Residues in contact with LEU 396 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339S LEU* 6.5 0.7 - - + -
367S ILE* 4.6 3.4 - - + -
369S PHE* 3.4 40.2 - - + -
392S LEU* 2.8 27.9 + - + +
393S ARG* 3.4 5.2 - - - +
395S ILE* 1.3 73.2 - - + +
397S SER* 1.3 54.2 + - - +
400S SER 2.3 24.9 - - - +
401S VAL* 3.3 25.6 - - + +
403S TRP* 4.1 25.1 + - + +
458S GLY* 3.4 41.5 - - - +
461S ALA* 4.3 8.3 - - + +
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Residues in contact with SER 397 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R LYS* 3.2 25.4 + - - -
393S ARG 2.7 15.9 + - - -
394S ARG* 3.0 13.5 - - - -
395S ILE 2.8 0.4 - - - -
396S LEU* 1.3 81.1 + - - +
398S LYS* 1.3 68.5 + - - +
400S SER* 2.9 14.2 + - - +
403S TRP* 4.9 5.0 + - - -
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Residues in contact with LYS 398 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394S ARG* 3.2 8.4 + - + +
395S ILE* 3.8 8.3 - - + +
397S SER* 1.3 81.5 - - - +
399S GLU* 1.3 99.5 + - + +
400S SER* 2.8 7.1 + - - -
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Residues in contact with GLU 399 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395S ILE* 3.3 9.7 + - + +
398S LYS* 1.3 108.2 + - + +
400S SER* 1.3 70.3 + - - +
401S VAL* 3.5 8.0 + - - +
461S ALA* 3.6 37.3 - - + +
463S LEU* 4.9 10.2 - - + +
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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