Contacts of the helix formed by residues 373 - 389 (chain K) in PDB entry 5GJQ
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 ALA 373 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K GLY* 3.0 26.7 + - - +
371K SER* 2.9 5.3 + - - +
372K GLY* 1.3 73.8 - - - +
374K ASP* 1.3 56.1 + - - +
375K ILE 3.2 1.3 - - - -
376K ASN* 2.5 39.0 + - - +
377K SER 3.6 1.0 + - - -
501K ADP 2.7 28.7 - - + +
291L ARG* 3.7 21.8 - - - +
292L PRO* 4.5 5.6 - - - +
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Residues in contact with ASP 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370K ILE* 3.1 24.0 - - + +
371K SER* 3.2 20.6 + - - +
373K ALA* 1.3 73.2 - - - +
375K ILE* 1.3 55.7 + - - +
376K ASN 2.6 6.4 + - - -
377K SER* 2.4 46.5 + - - +
378K ILE 3.3 1.7 + - - -
406K VAL* 4.0 11.0 - - + +
409K LYS* 4.6 13.9 + - - -
291L ARG* 4.1 7.3 - - - +
292L PRO* 2.7 36.6 - - - +
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Residues in contact with ILE 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336K PRO* 5.1 0.2 - - + -
341K LYS* 5.2 10.1 - - + +
344K ILE* 3.9 18.4 - - + -
345K PHE* 2.9 45.7 - - + +
348K ILE* 3.3 20.0 - - + +
370K ILE* 3.4 19.9 - - + +
371K SER 2.0 42.8 - - - +
372K GLY* 2.7 21.3 - - - +
374K ASP* 1.3 74.0 - - - +
376K ASN* 1.3 58.3 + - - +
378K ILE* 3.6 12.0 + - + +
379K CYS* 3.5 16.1 + - - -
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Residues in contact with ASN 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348K ILE* 3.8 23.6 - - + +
372K GLY 4.2 3.1 + - - +
373K ALA* 2.5 24.0 + - - +
374K ASP 2.6 0.4 + - - -
375K ILE* 1.3 70.8 - - - +
377K SER* 1.3 58.1 + - - -
378K ILE 3.0 5.6 - - - -
379K CYS* 3.4 3.3 + - - +
380K GLN* 3.0 42.3 + - - +
501K ADP 4.4 22.0 + - + +
165L ILE* 6.0 3.2 - - - +
292L PRO* 5.3 2.2 - - + -
293L GLY* 6.0 4.0 - - - +
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Residues in contact with SER 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373K ALA 3.6 1.0 + - - -
374K ASP 2.4 42.3 + - - -
376K ASN* 1.3 66.4 - - - +
378K ILE* 1.3 57.8 + - - -
380K GLN* 4.1 3.3 - - - +
381K GLU* 2.6 37.0 + - - +
406K VAL* 3.0 28.4 - - - +
292L PRO* 3.3 30.5 - - - +
296L ASP* 4.1 20.6 - - - -
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Residues in contact with ILE 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345K PHE* 4.5 13.9 - - + -
360K LEU* 6.1 0.2 - - + -
370K ILE* 4.5 6.7 - - + -
375K ILE* 3.6 21.8 - - + +
377K SER* 1.3 79.5 - - - +
379K CYS* 1.3 58.3 + - - +
381K GLU* 2.8 3.6 + - - +
382K SER* 2.7 33.4 + - - -
399K PHE* 4.4 19.3 - - + +
402K ALA* 3.2 24.9 - - + +
403K TYR* 3.9 31.0 - - + +
406K VAL* 2.9 39.3 - - + -
407K ILE* 4.4 3.4 - - + -
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Residues in contact with CYS 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345K PHE* 4.7 9.2 - - - -
348K ILE* 2.0 56.1 - - + -
349K THR* 4.0 17.5 - - - -
352K MET* 3.7 9.9 - - - +
375K ILE 3.5 9.1 + - - +
376K ASN* 3.4 7.2 + - - +
378K ILE* 1.3 81.2 - - - +
380K GLN* 1.3 56.9 + - - +
382K SER* 3.0 20.8 + - - -
399K PHE* 5.3 3.8 - - - -
164L ILE* 3.1 20.0 - - + +
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Residues in contact with GLN 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376K ASN* 3.0 39.4 + - - +
377K SER* 4.1 4.5 - - - +
379K CYS* 1.3 73.4 - - - +
381K GLU* 1.3 61.3 + - - +
382K SER 3.2 0.4 - - - -
383K GLY 3.1 5.5 + - - -
384K MET* 2.7 34.8 - - + +
164L ILE* 3.5 13.3 - - + +
165L ILE* 4.2 26.8 - - + +
166L PRO 4.4 14.9 + - - -
167L PRO* 5.4 0.2 - - - -
168L LYS* 4.4 16.3 - - - +
292L PRO* 5.5 1.8 - - - +
293L GLY* 5.3 6.5 + - - +
296L ASP* 2.4 38.0 - - - +
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Residues in contact with GLU 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377K SER* 2.6 27.5 + - - +
378K ILE* 2.8 12.6 + - - +
380K GLN* 1.3 73.9 - - - +
382K SER* 1.3 61.3 + - - +
384K MET* 3.2 21.9 + - - +
385K LEU* 3.2 13.2 + - - +
398K ASP 4.9 0.2 - - - -
402K ALA* 4.0 7.6 - - + -
405K THR* 3.4 29.6 - - + +
406K VAL* 4.5 1.1 - - + -
148L VAL* 4.9 0.2 - - - +
296L ASP* 2.7 31.4 - - - +
297L ARG* 2.2 45.0 + - + +
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Residues in contact with SER 382 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352K MET* 3.3 8.0 - - - +
378K ILE 2.7 16.3 + - - -
379K CYS* 3.0 14.7 + - - -
381K GLU* 1.3 72.9 - - - +
383K GLY* 1.3 53.9 + - - +
385K LEU* 3.2 3.2 + - - +
386K ALA* 2.7 36.4 + - - +
394K VAL* 3.1 32.4 - - - +
398K ASP* 3.8 23.0 + - - +
399K PHE* 4.2 12.1 - - - -
402K ALA* 4.9 0.2 - - - -
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Residues in contact with GLY 383 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380K GLN 3.1 7.9 + - - -
382K SER* 1.3 81.9 + - - +
384K MET* 1.3 58.3 + - - +
386K ALA* 4.3 4.3 - - - -
387K VAL* 2.6 49.9 + - - +
159L PHE* 4.8 0.2 - - - -
162L VAL* 4.3 1.6 - - - -
164L ILE* 3.6 25.0 - - - +
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Residues in contact with MET 384 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380K GLN* 2.7 23.8 - - + +
381K GLU* 3.2 28.4 + - - +
383K GLY* 1.3 78.1 - - - +
385K LEU* 1.3 50.1 + - - +
387K VAL* 4.2 2.4 - - - +
388K ARG* 2.6 47.5 + - - +
147L GLU* 5.5 6.2 - - + +
148L VAL* 4.6 16.8 - - + -
159L PHE* 3.1 36.8 - - + -
164L ILE* 4.0 2.5 - - - -
165L ILE 3.7 11.9 - - - +
167L PRO* 3.5 31.2 - - + -
296L ASP* 5.5 0.9 - - - +
297L ARG* 4.6 5.6 - - - +
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Residues in contact with LEU 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381K GLU 3.2 8.0 + - - +
382K SER* 3.2 8.6 + - - +
384K MET* 1.3 79.9 - - - +
386K ALA* 1.3 63.7 + - - +
387K VAL 3.5 0.3 + - - -
388K ARG* 3.6 29.5 + - - +
389K GLU* 3.6 34.1 + - - +
391K ARG* 5.1 0.2 + - - -
397K LYS* 4.0 3.6 - - + +
398K ASP* 3.2 29.3 - - - +
401K LYS* 3.2 55.6 - - + +
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Residues in contact with ALA 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382K SER 2.7 20.8 + - - +
383K GLY* 3.9 4.0 - - - +
385K LEU* 1.3 73.5 - - - +
387K VAL* 1.3 62.3 + - + +
390K ASN 3.4 2.6 + - - -
391K ARG* 2.7 43.6 + - - +
393K ILE 3.6 23.6 - - - +
394K VAL* 3.8 10.3 - - + -
398K ASP* 3.6 14.8 + - - +
162L VAL* 4.8 2.0 - - + -
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Residues in contact with VAL 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383K GLY* 2.6 34.8 + - - +
384K MET* 4.2 1.3 - - - +
386K ALA* 1.3 71.4 - - - +
388K ARG* 1.3 65.5 + - - +
389K GLU 3.1 2.9 - - - -
390K ASN* 2.9 20.4 + - - +
391K ARG 4.6 1.8 - - - +
151L LEU* 6.1 1.7 - - + +
155L ASN* 5.1 15.9 + - - +
158L LEU* 5.5 4.5 - - + -
159L PHE* 4.4 36.8 - - + +
162L VAL* 3.4 33.9 - - + -
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Residues in contact with ARG 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384K MET* 2.6 31.0 + - - +
385K LEU* 3.9 19.3 - - - +
386K ALA 3.5 0.4 - - - -
387K VAL* 1.3 74.8 - - - +
389K GLU* 1.3 66.9 + - + +
390K ASN 3.9 0.2 + - - -
401K LYS* 4.1 18.0 - - - +
143L ARG* 3.4 37.5 - - - +
144L GLU* 4.2 10.5 + - - +
147L GLU* 2.6 66.5 + - + +
151L LEU* 5.5 4.7 - - + -
297L ARG* 5.9 2.0 - - - +
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Residues in contact with GLU 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385K LEU* 3.6 32.4 + - - +
386K ALA 4.0 2.0 - - - +
387K VAL 3.1 0.4 - - - -
388K ARG* 1.3 89.3 + - + +
390K ASN* 1.3 75.5 + - - +
391K ARG* 4.0 22.7 + - - +
398K ASP* 5.6 0.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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