Contacts of the helix formed by residues 342 - 359 (chain F) in PDB entry 2GPV
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 LEU 342 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F LEU* 4.3 6.5 - - + -
268F LEU* 3.9 27.6 - - + -
332F MET* 4.4 8.3 - - + -
337F SER* 2.9 12.7 + - - +
340F ALA* 3.8 23.3 - - + +
341F GLY* 1.3 75.3 - - - +
343F LEU* 1.3 64.9 + - - +
344F ASP 3.3 2.7 - - - -
345F LEU* 3.4 20.1 + - + +
346F ASN* 3.0 39.8 + - - +
434F HIS* 3.5 32.1 - - + +
505F OHT 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F GLU* 4.1 28.3 - - + +
337F SER* 3.6 11.8 + - - -
338F LYS* 3.7 42.0 - - + -
341F GLY* 3.6 2.8 + - - -
342F LEU* 1.3 78.2 - - - +
344F ASP* 1.3 71.4 + - - +
346F ASN* 4.5 0.5 - - - +
347F ASN* 2.9 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F LEU 3.3 0.4 - - - -
343F LEU* 1.3 88.3 - - - +
345F LEU* 1.3 64.2 + - - +
347F ASN* 3.4 9.9 + - - +
348F ALA* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F LEU* 3.4 20.6 + - + +
344F ASP* 1.3 79.4 - - - +
346F ASN* 1.3 60.7 + - - +
348F ALA* 3.2 6.8 + - + +
349F ILE* 3.1 26.1 + - + +
427F THR* 4.3 12.1 - - + +
430F LYS* 4.3 9.9 - - + +
431F ALA* 3.6 42.8 - - + +
434F HIS* 3.5 35.7 - - + +
505F OHT 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 346 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F LEU* 3.4 21.5 - - + +
326F TYR* 2.6 23.6 + - - -
332F MET* 3.6 27.5 - - - +
337F SER* 2.7 31.3 + - - +
342F LEU* 3.0 23.4 + - - +
343F LEU 4.5 0.7 - - - +
345F LEU* 1.3 74.5 - - - +
347F ASN* 1.3 60.0 + - - +
349F ILE* 3.0 8.4 + - - +
350F LEU* 2.8 34.9 + - + +
505F OHT 4.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 347 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C MET* 6.4 1.8 - - - -
334F GLU* 4.9 6.2 + - - +
343F LEU* 2.9 51.0 + - - +
344F ASP* 3.4 11.1 + - - +
346F ASN* 1.3 77.2 - - - +
348F ALA* 1.3 56.5 + - - +
350F LEU* 3.3 20.2 + - - +
351F GLN* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C MET* 6.2 4.9 - - - -
344F ASP 3.1 12.8 + - - +
345F LEU* 3.3 15.0 - - + +
346F ASN 3.1 0.4 - - - -
347F ASN* 1.3 74.9 - - - +
349F ILE* 1.3 64.6 + - - +
350F LEU 3.3 0.2 - - - -
351F GLN* 3.5 25.8 - - - +
352F LEU* 3.7 5.5 + - - +
423F LEU* 5.0 2.3 - - + +
427F THR* 3.7 28.6 + - + +
430F LYS* 5.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ILE* 4.4 17.3 - - + -
313F VAL* 4.3 11.2 - - + -
314F VAL* 3.7 19.1 - - + -
324F LEU* 3.5 25.6 - - + -
326F TYR* 3.8 21.8 - - + +
345F LEU* 3.1 19.0 + - + +
346F ASN* 3.0 12.6 + - - +
348F ALA* 1.3 75.5 - - - +
350F LEU* 1.3 59.6 + - - +
351F GLN 3.1 1.8 - - - -
352F LEU* 3.1 12.3 + - - +
353F VAL* 3.0 22.3 + - - +
427F THR* 3.7 17.3 - - + -
505F OHT 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F ASP* 3.9 34.3 - - + +
323F GLU 4.0 18.4 - - - +
324F LEU* 3.5 29.6 - - + -
346F ASN* 2.8 16.1 + - + +
347F ASN* 3.3 26.2 + - - +
349F ILE* 1.3 72.5 - - - +
351F GLN* 1.3 59.1 + - - +
353F VAL* 3.6 14.8 - - + +
354F LYS* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ASP* 2.8 39.1 + - - +
379C SER 3.3 14.8 + - - -
380C MET* 3.5 27.6 - - + +
347F ASN 3.2 10.7 + - - +
348F ALA* 3.5 19.7 - - - +
349F ILE 3.1 0.2 - - - -
350F LEU* 1.3 76.7 - - - +
352F LEU* 1.3 61.6 + - - +
354F LYS* 3.5 10.9 + - + +
355F LYS* 3.1 22.9 + - - +
423F LEU* 4.2 20.5 - - + +
426F GLN* 5.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ILE* 4.3 15.5 - - + -
314F VAL* 3.9 15.3 - - + -
348F ALA 3.7 7.6 + - - +
349F ILE* 3.1 11.3 + - - +
351F GLN* 1.3 76.2 - - - +
353F VAL* 1.3 65.8 + - - +
355F LYS* 3.3 5.6 + - + +
356F TYR* 3.1 41.8 + - + -
420F THR* 4.0 10.1 - - - +
423F LEU* 3.5 31.9 - - + +
424F LEU* 3.8 23.8 - - + +
427F THR* 3.5 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F VAL* 3.9 21.8 - - + -
317F SER* 3.7 29.4 - - - +
318F LEU* 3.9 7.5 - - + +
320F PHE 5.1 0.4 - - - +
323F GLU 5.6 0.2 - - - +
324F LEU* 3.8 25.6 - - + -
349F ILE 3.0 14.3 + - - +
350F LEU* 3.3 15.5 + - + +
352F LEU* 1.3 75.7 - - - +
354F LYS* 1.3 63.3 + - - +
356F TYR 3.4 0.3 + - - -
357F LYS* 3.0 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C VAL* 3.5 35.6 - - - +
350F LEU 2.9 17.5 + - - +
351F GLN* 3.7 10.8 - - + +
353F VAL* 1.3 78.5 - - - +
355F LYS* 1.3 66.5 + - - +
357F LYS* 3.4 15.9 + - + +
358F SER* 3.1 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 355 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ASN* 4.5 3.6 + - - -
378C ASP* 2.8 37.4 + - - -
389C GLN* 5.6 6.1 - - - +
351F GLN* 3.1 12.6 + - - +
352F LEU* 3.7 6.3 - - + +
353F VAL 3.3 0.2 - - - -
354F LYS* 1.3 79.0 - - - +
356F TYR* 1.3 65.9 + - + +
357F LYS 2.9 2.1 + - - -
358F SER* 2.9 20.4 + - - -
359F MET* 3.5 16.0 + - + +
419F MET 4.2 4.4 + - - -
420F THR* 3.6 43.1 - - + +
423F LEU* 3.9 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 356 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F LEU* 3.7 30.7 - - + +
314F VAL* 3.6 17.7 - - + -
318F LEU* 3.7 18.3 - - + +
352F LEU* 3.1 34.0 + - + +
355F LYS* 1.3 78.1 - - + +
357F LYS* 1.3 60.9 + - - +
359F MET* 3.2 19.6 + - - +
361F LEU* 3.3 47.3 + - + +
369F LEU* 4.0 19.8 - - + +
417F MET* 4.8 1.6 - - - -
420F THR* 2.9 51.1 + - + -
421F LEU* 5.0 1.0 - - - +
424F LEU* 4.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LEU* 3.2 32.5 - - + +
320F PHE 2.7 29.7 + - - -
321F GLU* 3.3 24.3 + - - +
322F ASP 5.0 1.6 - - - +
353F VAL* 3.0 37.0 + - - +
354F LYS* 3.4 11.4 - - - +
355F LYS 2.9 0.4 + - - -
356F TYR* 1.3 72.3 - - - +
358F SER* 1.3 64.6 + - - +
359F MET 3.1 1.8 - - - -
360F LYS* 3.1 19.6 + - - +
361F LEU 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 358 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C VAL* 6.2 0.2 - - - +
354F LYS* 3.1 15.2 + - - +
355F LYS* 2.9 8.9 + - - -
357F LYS* 1.3 77.7 - - - +
359F MET* 1.3 61.0 + - - +
360F LYS* 3.3 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 359 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C GLN* 6.1 0.4 - - - +
355F LYS* 3.7 18.6 - - + +
356F TYR* 3.2 13.8 + - - +
357F LYS 3.1 0.8 - - - -
358F SER* 1.3 80.4 - - - +
360F LYS* 1.3 70.2 + - - +
361F LEU* 4.5 0.9 - - + +
413F ARG* 2.7 37.8 + - + +
416F LYS* 3.4 43.1 - - + +
417F MET* 3.5 31.2 - - + +
420F THR* 4.1 23.1 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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