Contacts of the helix formed by residues 420 - 440 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A LEU* 4.4 4.4 - - - +
355A LYS* 4.0 29.6 - - + +
356A TYR* 2.4 47.7 + - + -
359A MET* 4.3 9.2 - - - -
369A LEU* 4.8 0.9 - - - +
416A LYS 3.4 12.8 - - - +
417A MET* 2.7 21.4 + - - +
418A LEU 3.1 0.2 - - - -
419A MET* 1.3 77.9 - - - +
421A LEU* 1.3 69.7 + - - +
422A PRO* 3.4 2.0 - - - -
423A LEU* 3.2 14.2 + - - +
424A LEU* 3.4 9.7 + - - +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLU* 5.3 3.0 - - - +
311A LEU* 6.2 0.2 - - + -
356A TYR* 5.3 0.9 - - - +
369A LEU* 4.0 22.2 - - + +
372A ILE* 4.3 11.4 - - + -
373A ALA* 4.8 15.7 - - + +
376A ASN* 3.7 25.8 - - + +
418A LEU* 3.1 42.0 + - + +
420A THR* 1.3 81.0 + - - +
422A PRO* 1.3 66.3 - - + +
424A LEU* 2.9 27.5 + - + +
425A ARG* 2.9 20.3 + - - +
419D MET* 4.5 4.5 - - + -
422D PRO* 3.5 14.8 - - + +
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Residues in contact with PRO 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU 3.9 2.7 - - - +
419A MET* 3.6 12.3 - - - +
420A THR 3.4 4.3 - - - -
421A LEU* 1.3 95.2 - - + +
423A LEU* 1.3 55.1 + - - +
425A ARG* 3.3 3.4 + - + +
426A GLN* 2.8 24.6 + - - +
376D ASN* 4.2 12.1 - - - +
378D ASP* 4.4 1.1 - - - +
418D LEU 5.6 0.4 - - - +
421D LEU* 3.9 15.9 - - + -
422D PRO* 3.7 34.1 - - + -
425D ARG* 3.2 39.6 + - + +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ALA* 5.3 0.9 - - + +
351A GLN* 4.0 44.2 - - + +
352A LEU* 4.0 23.1 - - + +
355A LYS* 4.4 11.7 - - - +
420A THR 3.2 9.0 + - - +
421A LEU 3.2 0.8 - - - -
422A PRO* 1.3 77.9 - - - +
424A LEU* 1.3 53.9 + - - +
426A GLN* 3.3 22.8 + - - +
427A THR* 2.7 52.5 + - - +
378D ASP* 3.5 34.9 + - + +
425D ARG* 3.7 4.6 - - - +
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 3.6 47.1 - - + +
310A ILE* 3.8 23.6 - - + -
311A LEU* 4.0 33.9 - - + -
352A LEU* 3.9 17.8 - - + +
356A TYR* 5.1 3.1 - - - +
373A ALA* 4.3 10.1 - - + -
420A THR 3.4 8.4 + - - +
421A LEU* 2.9 22.3 + - + +
423A LEU* 1.3 79.7 - - - +
425A ARG* 1.3 55.8 + - - +
427A THR* 3.8 0.3 - - - -
428A SER* 2.8 31.0 + - - -
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Residues in contact with ARG 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLU* 2.8 36.8 + - - -
373A ALA* 5.3 0.4 + - - +
376A ASN* 3.1 28.7 + - - +
377A SER* 4.1 11.9 + - - +
378A ASP* 3.2 24.9 + - - +
421A LEU 2.9 10.8 + - - +
422A PRO* 3.4 12.8 - - + +
423A LEU 3.2 0.2 - - - -
424A LEU* 1.3 74.4 - - - +
426A GLN* 1.3 66.1 + - - +
428A SER* 3.3 2.8 + - - -
429A THR* 3.0 30.6 + - - +
422D PRO* 3.5 45.8 + - + +
423D LEU* 3.7 0.6 - - - +
425D ARG* 5.4 0.4 - - + -
426D GLN* 3.5 43.7 + - + +
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Residues in contact with GLN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLN* 5.8 1.4 + - - -
422A PRO 2.8 15.6 + - - +
423A LEU* 3.6 19.1 - - + +
425A ARG* 1.3 77.8 - - - +
427A THR* 1.3 65.0 + - - +
429A THR* 3.4 6.2 + - - -
430A LYS* 3.0 52.9 + - + +
377D SER 5.0 1.6 - - - +
378D ASP* 4.7 8.7 + - - +
425D ARG* 2.8 38.8 + - + +
426D GLN* 6.4 0.9 - - - +
429D THR* 5.4 6.1 - - - +
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 4.1 11.0 - - + -
345A LEU* 4.7 3.3 - - + +
348A ALA* 4.1 21.5 + - + +
349A ILE* 4.1 22.4 - - + +
352A LEU* 3.7 24.1 - - + +
423A LEU* 2.7 37.2 + - - +
424A LEU 3.8 2.9 - - - -
426A GLN* 1.3 76.3 - - - +
428A SER* 1.3 66.8 + - - +
430A LYS* 3.1 12.9 + - + +
431A ALA* 3.0 19.8 + - - +
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A SER 5.0 4.7 + - - -
306A MET* 3.7 13.9 - - - +
307A GLU* 3.5 34.8 + - - +
310A ILE* 3.9 12.5 - - - +
424A LEU 2.8 19.3 + - - -
425A ARG* 3.6 4.5 + - - -
427A THR* 1.3 73.9 - - - +
429A THR* 1.3 58.4 + - - +
431A ALA* 2.8 22.5 + - - +
432A VAL* 2.8 19.8 + - - +
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Residues in contact with THR 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ARG* 3.0 22.3 + - - +
426A GLN* 3.7 9.5 - - - -
428A SER* 1.3 79.4 + - - +
430A LYS* 1.3 62.9 + - - +
432A VAL* 3.8 7.5 - - + +
433A GLN* 2.9 40.1 + - - +
426D GLN* 4.9 11.9 + - + +
429D THR* 5.8 10.5 - - + -
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Residues in contact with LYS 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 4.0 14.1 - - + -
348A ALA* 5.5 9.9 - - + -
426A GLN* 3.0 56.2 + - + +
427A THR* 3.1 13.0 + - + +
429A THR* 1.3 75.1 - - - +
431A ALA* 1.3 65.1 + - - +
433A GLN* 3.1 16.6 + - - +
434A HIS* 2.8 23.4 + - - +
429D THR* 4.4 19.8 - - - +
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A MET* 3.8 15.5 - - + -
310A ILE* 3.7 27.4 - - + -
345A LEU* 3.5 21.3 - - + -
427A THR 3.0 5.7 + - - +
428A SER 2.8 10.1 + - - +
430A LYS* 1.3 75.5 - - - +
432A VAL* 1.3 63.9 + - - +
434A HIS* 2.9 14.9 + - - +
435A PHE 3.0 10.2 + - - -
500A OHT 3.7 14.5 - - + -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A TRP* 4.3 17.0 - - + +
306A MET* 3.8 33.9 - - + -
428A SER* 2.8 26.9 + - - +
429A THR* 3.8 7.4 - - + +
431A ALA* 1.3 71.9 - - - +
433A GLN* 1.3 64.4 + - - +
435A PHE* 3.6 4.7 + - + +
436A TYR* 3.3 40.8 + - + -
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Residues in contact with GLN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A THR* 2.9 30.7 + - - +
430A LYS* 3.1 21.7 - - - +
432A VAL* 1.3 73.8 - - - +
434A HIS* 1.3 68.6 + - - +
435A PHE 2.8 1.2 + - - -
436A TYR* 3.0 6.4 + - - +
437A ASN* 2.8 40.8 + - - +
429D THR* 5.9 4.8 - - - +
433D GLN* 4.8 17.6 + - - +
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Residues in contact with HIS 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 5.3 0.4 - - - +
340A ALA 5.3 0.4 + - - -
341A GLY 3.5 19.9 + - - -
342A LEU* 3.4 30.1 - - + +
344A ASP* 6.5 0.7 - - + -
345A LEU* 4.1 19.0 - - + +
430A LYS 2.8 15.6 + - - +
431A ALA 3.4 7.6 - - - +
433A GLN* 1.3 72.1 - - - +
435A PHE* 1.3 62.3 + - - +
437A ASN* 3.1 18.6 + - - +
438A ILE* 3.2 40.0 + - + +
500A OHT 3.7 11.9 - + + -
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Residues in contact with PHE 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A CYS* 4.4 13.0 - - - -
305A TRP* 6.0 4.5 - + + -
306A MET* 5.3 2.5 - - + -
431A ALA 3.0 9.4 + - - +
432A VAL* 3.9 7.6 - - + +
433A GLN 2.8 1.2 + - - -
434A HIS* 1.3 77.2 - - - +
436A TYR* 1.3 86.5 + + - +
438A ILE* 3.3 25.1 + - + +
439A LYS* 3.1 46.7 + - + +
500A OHT 3.1 81.4 - + + -
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Residues in contact with TYR 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A TRP* 6.1 2.9 - + - -
432A VAL* 3.3 32.4 + - + +
433A GLN* 3.0 7.6 + - - +
435A PHE* 1.3 100.4 - + - +
437A ASN* 1.3 61.7 + - - +
438A ILE 3.2 1.2 + - - -
439A LYS* 3.3 20.3 + - + +
440A LEU* 3.6 26.6 + - + +
1319G GLY 5.4 2.8 + - - -
1320G LEU* 4.8 14.2 - - + +
1321G GLU* 5.2 3.8 + - - -
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Residues in contact with ASN 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A GLN* 2.8 46.7 + - - +
434A HIS* 3.1 16.8 + - + +
436A TYR* 1.3 78.8 - - - +
438A ILE* 1.3 59.1 + - + +
439A LYS 3.6 0.2 - - - -
440A LEU* 4.5 4.2 - - - +
441A GLU* 3.4 22.8 + - - +
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Residues in contact with ILE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 3.8 40.2 - - + -
434A HIS* 3.2 37.4 + - + +
435A PHE* 3.3 22.4 - - + +
437A ASN* 1.3 79.3 - - + +
439A LYS* 1.3 65.8 + - + +
440A LEU 3.4 0.4 - - - -
441A GLU* 2.7 42.6 - - - +
442A GLY* 3.6 2.8 + - - -
443A LYS 4.4 0.7 + - - -
444A VAL* 4.7 17.7 - - + +
500A OHT 5.2 2.2 - - + -
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A PHE* 3.1 54.7 + - + +
436A TYR* 3.3 15.7 + - + +
438A ILE* 1.3 79.6 - - + +
440A LEU* 1.3 69.4 + - + +
442A GLY* 3.1 21.7 + - - -
444A VAL* 5.9 7.0 - - + -
500A OHT 5.8 2.8 - - - -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A TYR* 3.6 21.2 + - + +
437A ASN* 4.9 3.6 - - - +
439A LYS* 1.3 88.7 - - + +
441A GLU* 1.3 57.5 + - - +
442A GLY 3.1 4.7 + - - -
436E TYR* 4.3 5.1 - - - +
439E LYS* 3.9 30.1 - - + +
440E LEU* 4.1 34.5 - - + +
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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
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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