Contacts of the helix formed by residues 420 - 439 (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 THR 420 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F LEU* 4.0 5.5 - - - +
355F LYS* 3.6 33.7 - - + +
356F TYR* 2.9 42.6 + - + -
359F MET* 4.1 10.8 - - - -
369F LEU* 4.2 2.9 - - - +
416F LYS 3.4 16.8 - - - +
417F MET* 2.5 18.0 + - - +
419F MET* 1.3 77.5 - - - +
421F LEU* 1.3 63.6 + - - +
422F PRO 3.5 0.9 - - - -
423F LEU* 3.6 7.1 + - - +
424F LEU* 3.4 17.5 + - - +
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Residues in contact with LEU 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C MET* 5.2 2.9 - - + -
422C PRO* 4.0 14.8 - - + +
307F GLU* 5.1 3.3 - - - +
356F TYR* 5.0 1.3 - - - +
369F LEU* 4.1 22.9 - - + +
372F ILE* 4.1 25.1 - - + +
373F ALA* 4.7 13.9 - - + +
376F ASN* 5.1 11.0 - - + +
417F MET 4.4 0.4 - - - +
418F LEU* 3.3 33.0 - - + +
419F MET 3.1 0.2 - - - -
420F THR* 1.3 79.3 - - - +
422F PRO* 1.3 72.3 - - + +
423F LEU 3.1 2.0 - - - -
424F LEU* 2.9 38.2 + - + +
425F ARG* 3.0 13.7 + - - +
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Residues in contact with PRO 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ASN* 4.2 7.6 - - - +
378C ASP* 4.7 0.4 - - - +
421C LEU* 3.5 31.9 - - + +
422C PRO* 3.8 22.4 - - + -
425C ARG* 3.4 37.7 + - + +
418F LEU 3.8 4.0 - - - +
419F MET* 3.3 19.7 - - - +
421F LEU* 1.3 93.9 - - + +
423F LEU* 1.3 55.4 + - - +
425F ARG* 3.3 1.9 + - - +
426F GLN* 2.9 26.7 + - - +
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Residues in contact with LEU 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ASP* 3.6 23.9 + - + +
425C ARG* 3.5 5.5 - - - +
348F ALA* 5.0 2.0 - - + +
351F GLN* 4.2 23.1 - - + +
352F LEU* 3.5 40.6 - - + +
355F LYS* 3.9 24.9 - - - +
420F THR 3.6 5.8 + - - +
421F LEU 3.1 0.6 - - - -
422F PRO* 1.3 76.4 - - - +
424F LEU* 1.3 59.1 + - - +
426F GLN* 3.0 33.4 - - - +
427F THR* 2.7 45.7 + - - +
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Residues in contact with LEU 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F GLU* 3.7 38.8 - - + +
310F ILE* 3.9 22.7 - - + -
311F LEU* 4.0 37.7 - - + +
314F VAL* 5.8 0.2 - - + -
352F LEU* 3.8 15.1 - - + +
356F TYR* 4.7 2.0 - - - +
373F ALA* 4.5 5.6 - - + -
420F THR 3.4 11.1 + - - +
421F LEU* 2.9 31.3 + - + +
423F LEU* 1.3 77.8 - - - +
425F ARG* 1.3 57.3 + - - +
427F THR* 3.9 0.7 - - - -
428F SER* 2.9 30.2 + - - -
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Residues in contact with ARG 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C PRO* 3.7 43.1 + - + +
423C LEU* 3.7 2.6 - - - +
426C GLN* 2.9 36.7 + - + +
303F SER 6.1 0.2 - - - -
307F GLU* 2.8 37.0 + - - +
376F ASN* 3.0 27.3 + - - +
377F SER* 3.8 16.0 + - - +
378F ASP* 3.3 20.0 + - - +
421F LEU 3.0 10.8 + - - +
422F PRO 3.6 7.6 - - - +
424F LEU* 1.3 75.2 - - - +
426F GLN* 1.3 67.1 + - - +
428F SER* 3.6 1.9 - - - -
429F THR* 2.8 36.5 + - - +
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Residues in contact with GLN 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C SER 4.7 5.5 - - - +
378C ASP 4.5 10.0 + - - +
425C ARG* 3.3 36.9 + - + +
426C GLN* 6.4 0.9 - - - +
429C THR* 4.8 5.9 + - - +
351F GLN* 5.2 2.0 + - - -
422F PRO 2.9 17.4 + - - +
423F LEU* 3.0 35.0 - - - +
425F ARG* 1.3 78.0 - - - +
427F THR* 1.3 61.9 + - - +
429F THR* 3.4 3.4 + - - -
430F LYS* 3.2 54.0 + - + +
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Residues in contact with THR 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ILE* 4.3 8.3 - - + -
345F LEU* 4.3 5.3 - - + +
348F ALA* 3.7 20.5 + - + +
349F ILE* 3.7 30.3 - - + -
352F LEU* 3.5 21.2 - - + +
423F LEU* 2.7 33.2 + - - +
424F LEU 4.0 1.6 - - - -
426F GLN* 1.3 73.1 + - - +
428F SER* 1.3 66.5 + - - +
430F LYS* 3.0 20.0 + - - +
431F ALA* 3.1 13.2 + - - +
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Residues in contact with SER 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F SER 5.2 3.8 + - - -
306F MET* 3.5 16.0 - - - +
307F GLU* 3.2 36.0 + - - +
310F ILE* 3.7 13.8 - - - +
424F LEU 2.9 20.8 + - - -
425F ARG* 3.6 4.2 - - - -
427F THR* 1.3 77.7 - - - +
429F THR* 1.3 63.0 + - - +
431F ALA 3.5 0.2 + - - -
432F VAL* 3.2 26.7 + - - +
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Residues in contact with THR 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C GLN* 5.4 8.3 + - - +
429C THR* 5.1 7.2 - - + -
425F ARG* 2.8 31.0 + - - +
426F GLN* 3.6 5.8 - - - +
428F SER* 1.3 74.5 + - - +
430F LYS* 1.3 73.1 + - - +
432F VAL* 3.2 7.7 + - + +
433F GLN* 2.9 51.5 + - + +
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Residues in contact with LYS 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C THR* 4.1 25.7 + - - +
433C GLN* 5.5 0.6 - - - +
345F LEU* 4.3 12.6 - - + -
348F ALA* 5.5 9.0 - - + -
426F GLN* 3.2 46.6 + - + +
427F THR* 3.0 12.8 + - - +
429F THR* 1.3 85.4 - - - +
431F ALA* 1.3 56.8 + - - +
433F GLN* 3.8 10.5 + - - +
434F HIS* 2.9 30.8 + - - +
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Residues in contact with ALA 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F MET* 3.8 25.8 - - + -
310F ILE* 4.0 9.9 - - + -
345F LEU* 3.6 25.3 - - + +
427F THR 3.1 10.6 + - - +
428F SER 3.8 6.5 - - - +
429F THR 3.3 0.2 - - - -
430F LYS* 1.3 74.3 - - - +
432F VAL* 1.3 57.1 + - - +
434F HIS* 3.0 3.1 + - - +
435F PHE* 2.7 35.0 + - - +
505F OHT 3.6 12.2 - - + -
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Residues in contact with VAL 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F TRP* 4.4 11.7 - - + +
306F MET* 3.6 32.8 - - + -
428F SER* 3.2 17.4 + - - +
429F THR* 3.5 10.1 - - + +
431F ALA* 1.3 78.1 - - - +
433F GLN* 1.3 65.8 + - + +
435F PHE* 3.1 11.8 + - - +
436F TYR* 3.2 44.3 + - + +
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Residues in contact with GLN 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C THR* 5.1 2.8 - - - +
430C LYS* 6.2 1.6 - - - +
433C GLN* 3.1 28.2 + - - +
429F THR* 2.9 40.2 + - + +
430F LYS* 3.8 10.1 + - - +
432F VAL* 1.3 79.1 - - + +
434F HIS* 1.3 51.7 + - - +
436F TYR* 3.1 9.7 + - - +
437F ASN* 2.7 50.1 + - - +
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Residues in contact with HIS 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LEU* 5.4 0.4 - - - +
340F ALA 5.4 0.8 + - - -
341F GLY 3.8 16.7 + - - -
342F LEU* 3.5 16.1 - - + +
345F LEU* 3.5 27.6 - - + -
430F LYS 2.9 22.7 + - - +
431F ALA 3.0 4.0 + - - +
433F GLN* 1.3 73.8 - - - +
435F PHE* 1.3 60.6 + - - +
437F ASN* 3.8 9.8 - - - +
438F ILE* 3.2 51.3 + - + +
505F OHT 3.6 17.0 - + - -
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Residues in contact with PHE 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F CYS* 3.6 26.7 - - - -
305F TRP* 5.5 4.9 - + - -
306F MET* 5.1 3.1 - - + -
431F ALA 2.7 15.1 + - - +
432F VAL* 3.4 11.2 - - - +
433F GLN 3.1 0.2 - - - -
434F HIS* 1.3 71.2 - - - +
436F TYR* 1.3 84.8 + + - +
438F ILE* 3.3 13.5 + - + +
439F LYS* 3.2 52.6 + - + +
505F OHT 3.7 72.9 - + + -
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Residues in contact with TYR 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305F TRP* 4.2 18.9 + + - -
432F VAL* 3.2 40.1 + - + +
433F GLN* 3.1 7.2 + - - +
435F PHE* 1.3 99.5 - + - +
437F ASN* 1.3 62.3 + - - +
439F LYS* 3.1 29.4 + - - +
440F LEU* 4.0 10.4 - - - +
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Residues in contact with ASN 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433F GLN* 2.7 45.4 + - - +
434F HIS* 3.8 12.2 - - - +
435F PHE 3.2 0.2 - - - -
436F TYR* 1.3 74.2 - - - +
438F ILE* 1.3 60.2 + - + +
440F LEU* 3.3 26.3 - - - +
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Residues in contact with ILE 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LEU* 3.8 39.5 - - + -
434F HIS* 3.2 49.9 + - + +
435F PHE* 3.4 14.8 - - + +
436F TYR 3.2 0.2 - - - -
437F ASN* 1.3 78.4 - - + +
439F LYS* 1.3 57.2 + - + +
440F LEU* 3.0 15.5 + - - +
505F OHT 4.3 8.1 - - + -
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Residues in contact with LYS 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435F PHE* 3.2 48.7 + - + +
436F TYR* 3.1 23.2 + - - +
438F ILE* 1.3 75.2 - - + +
440F LEU* 1.3 69.2 + - - +
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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
------------------------------------------------------------
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