Contacts of the helix formed by residues 420 - 439 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D LEU* 3.8 12.1 - - - +
355D LYS* 3.8 33.2 - - + +
356D TYR* 2.7 41.8 + - + -
359D MET* 4.1 12.3 - - + -
369D LEU* 4.1 1.0 - - - +
416D LYS 3.4 17.0 - - - +
417D MET 2.7 17.2 + - - +
419D MET* 1.3 78.4 - - + +
421D LEU* 1.3 61.7 + - - +
422D PRO* 3.5 1.6 - - - -
423D LEU* 3.6 4.6 + - - +
424D LEU* 3.4 15.4 + - - +
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Residues in contact with LEU 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A MET* 5.1 4.0 - - + -
422A PRO* 3.9 13.5 - - + -
307D GLU* 4.5 3.7 - - - +
356D TYR* 5.0 0.4 - - - +
369D LEU* 4.2 25.8 - - + +
372D ILE* 3.8 24.5 - - + -
373D ALA* 4.5 17.0 - - + +
376D ASN* 4.8 12.6 - - - +
417D MET 4.4 0.7 - - - +
418D LEU* 3.5 31.2 - - + +
420D THR* 1.3 78.4 - - - +
422D PRO* 1.3 66.6 - - + +
423D LEU 3.2 0.4 - - - -
424D LEU* 2.9 23.6 + - + +
425D ARG* 2.7 30.3 + - - +
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Residues in contact with PRO 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 4.3 5.8 - - - +
378A ASP* 4.8 0.7 - - - +
421A LEU* 3.5 31.2 - - + -
422A PRO* 3.7 23.3 - - + -
425A ARG* 3.5 37.1 + - + +
418D LEU 3.8 3.8 - - - +
419D MET 3.5 20.0 - - - +
420D THR 3.5 0.2 - - - -
421D LEU* 1.3 95.2 - - + +
423D LEU* 1.3 54.9 + - - +
425D ARG* 3.7 0.7 - - + +
426D GLN* 2.9 28.2 + - - +
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASP* 3.2 28.0 + - + +
425A ARG* 3.9 0.9 - - - +
348D ALA* 5.6 1.1 - - + +
351D GLN* 4.2 32.5 - - + +
352D LEU* 3.8 22.7 - - + +
355D LYS* 3.5 31.0 - - - +
420D THR 3.6 6.1 + - - +
421D LEU 3.2 0.8 - - - -
422D PRO* 1.3 76.0 - - - +
424D LEU* 1.3 60.9 + - - +
426D GLN* 3.0 30.2 + - - +
427D THR* 2.8 44.3 + - - +
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Residues in contact with LEU 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLU* 3.5 46.7 - - + +
310D ILE* 3.9 22.0 - - + -
311D LEU* 3.6 39.9 - - + +
352D LEU* 3.5 17.9 - - + +
356D TYR* 4.9 0.9 - - - +
373D ALA* 4.6 4.3 - - + -
420D THR 3.4 10.8 + - - +
421D LEU* 2.9 24.5 + - + +
423D LEU* 1.3 77.9 - - - +
425D ARG* 1.3 57.2 + - - +
427D THR* 3.8 0.5 - - - -
428D SER* 2.8 24.8 + - - -
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Residues in contact with ARG 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PRO* 3.2 51.5 + - + +
423A LEU* 3.7 2.4 - - - +
426A GLN* 2.8 42.1 + - + +
307D GLU* 2.9 33.4 + - - +
376D ASN 3.0 17.0 + - - -
377D SER* 3.8 13.4 + - - +
378D ASP* 2.7 27.7 + - - +
421D LEU 2.7 14.4 + - - +
422D PRO* 3.7 5.6 - - + +
424D LEU* 1.3 74.7 - - - +
426D GLN* 1.3 67.7 + - - +
428D SER* 3.1 4.6 + - - -
429D THR* 2.9 34.6 + - - +
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Residues in contact with GLN 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A SER 5.0 3.6 - - - +
378A ASP* 4.5 9.3 + - - +
425A ARG* 3.5 34.6 + - + +
426A GLN* 6.4 1.1 - - - +
429A THR* 4.9 12.0 + - + +
351D GLN* 5.4 1.2 + - - -
422D PRO 2.9 18.4 + - - +
423D LEU* 3.0 34.1 - - - +
425D ARG* 1.3 77.4 - - - +
427D THR* 1.3 63.9 + - - +
429D THR* 3.3 6.5 + - - -
430D LYS* 3.2 38.8 + - - +
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Residues in contact with THR 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D ILE* 4.2 9.0 - - + -
345D LEU* 4.3 6.7 - - + +
348D ALA* 3.8 31.2 + - + +
349D ILE* 4.0 26.2 - - + +
352D LEU* 4.1 9.2 - - - +
423D LEU* 2.8 37.8 + - - +
424D LEU 4.0 2.9 - - - -
426D GLN* 1.3 71.6 + - - +
428D SER* 1.3 66.7 + - - +
430D LYS* 3.3 9.3 + - - +
431D ALA* 3.1 21.0 + - - +
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Residues in contact with SER 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D SER 5.3 3.8 + - - -
306D MET* 3.6 12.9 - - - +
307D GLU* 3.3 35.1 + - - +
310D ILE* 3.7 13.1 - - - +
424D LEU 2.8 19.9 + - - -
425D ARG* 3.1 6.2 + - - -
427D THR* 1.3 77.9 - - - +
429D THR* 1.3 63.9 + - - +
431D ALA* 3.2 3.1 + - - +
432D VAL* 3.1 26.2 + - - +
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Residues in contact with THR 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A GLN* 5.4 5.9 - - - +
429A THR* 5.8 9.4 - - + -
430A LYS* 4.4 19.6 + - - +
433A GLN* 5.9 4.9 - - - +
425D ARG* 2.9 25.7 + - - +
426D GLN* 3.7 8.6 - - - -
428D SER* 1.3 76.7 + - - +
430D LYS* 1.3 62.6 + - - +
432D VAL* 3.4 9.8 + - + +
433D GLN* 3.0 26.0 + - + +
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Residues in contact with LYS 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A MET* 5.1 16.2 - - - +
344D ASP* 5.1 7.7 + - + +
345D LEU* 4.3 11.2 - - + -
348D ALA* 4.4 24.2 - - + +
426D GLN* 3.2 31.6 + - + +
427D THR* 3.3 10.3 + - - +
429D THR* 1.3 78.0 - - - +
431D ALA* 1.3 54.4 + - - +
433D GLN* 3.3 7.5 + - - +
434D HIS* 2.6 39.1 + - - +
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D MET* 3.8 22.7 - - + -
310D ILE* 3.9 10.8 - - + -
345D LEU* 3.8 25.5 - - + +
427D THR 3.1 10.0 + - - +
428D SER 3.2 8.7 + - - +
430D LYS* 1.3 78.4 - - - +
432D VAL* 1.3 51.9 + - - +
434D HIS* 3.2 2.1 + - - +
435D PHE* 2.6 37.1 + - - +
503D OHT 3.5 11.0 - - + -
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D TRP* 4.6 11.0 - - + +
306D MET* 3.9 30.7 - - + -
428D SER* 3.1 15.9 + - - +
429D THR* 3.5 11.0 - - + +
430D LYS 3.3 0.2 - - - -
431D ALA* 1.3 76.3 - - - +
433D GLN* 1.3 64.4 + - - +
435D PHE* 2.9 7.6 + - - +
436D TYR* 2.8 50.2 + - + -
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Residues in contact with GLN 433 (chain D).
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* 4.8 15.7 + - - +
429D THR* 3.0 21.2 + - + +
430D LYS* 3.6 6.3 - - - +
432D VAL* 1.3 77.3 - - - +
434D HIS* 1.3 53.6 + - - +
436D TYR* 3.1 8.1 + - - +
437D ASN* 2.7 76.5 + - - +
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Residues in contact with HIS 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LEU* 5.8 0.4 - - - +
341D GLY 4.0 14.5 + - - -
342D LEU* 3.6 22.3 - - + +
345D LEU* 3.6 30.7 - - + -
430D LYS 2.6 21.5 + - - +
431D ALA 3.4 4.3 - - - +
433D GLN* 1.3 73.4 - - - +
435D PHE* 1.3 62.0 + - - +
437D ASN* 3.4 10.7 + - - +
438D ILE* 3.0 48.1 + - + +
503D OHT 3.8 10.9 - + - -
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Residues in contact with PHE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B MET* 5.5 0.4 - - + -
269D CYS* 3.9 21.1 - - - -
305D TRP* 5.4 4.9 - + - -
306D MET* 5.2 2.7 - - + -
431D ALA 2.6 17.5 + - - +
432D VAL* 2.9 11.0 + - - +
434D HIS* 1.3 72.5 - - - +
436D TYR* 1.3 80.8 + + - +
438D ILE* 3.2 28.5 + - + +
439D LYS* 3.2 46.2 + - + +
503D OHT 3.7 76.2 - + + -
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Residues in contact with TYR 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B LEU* 3.9 5.6 - - + +
441B GLU* 3.1 56.6 + - + +
442B GLY 4.4 0.9 + - - -
443B LYS* 3.9 15.6 - - + +
446B MET* 4.0 20.5 - - + +
305D TRP* 4.5 6.4 - + - -
432D VAL* 2.8 49.7 + - + +
433D GLN* 4.0 9.0 - - - +
435D PHE* 1.3 82.7 - + - +
437D ASN* 1.3 66.2 + - - +
439D LYS* 3.2 44.6 + - + +
440D LEU* 4.5 6.6 - - - +
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Residues in contact with ASN 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D GLN* 2.7 67.3 + - - +
434D HIS* 3.6 11.6 + - - +
436D TYR* 1.3 73.8 - - - +
438D ILE* 1.3 63.8 + - + +
440D LEU* 3.3 29.6 + - - +
441D GLU* 4.4 3.5 + - - +
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Residues in contact with ILE 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LEU* 4.1 36.6 - - + -
434D HIS* 3.0 41.5 + - + +
435D PHE* 3.2 22.0 - - + +
437D ASN* 1.3 73.6 - - + +
439D LYS* 1.3 55.9 + - + +
440D LEU 2.9 10.9 + - - -
441D GLU* 3.1 49.6 + - + +
503D OHT 4.3 16.2 - - + -
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Residues in contact with LYS 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B LEU* 3.0 50.1 + - + +
441B GLU 4.4 1.8 - - - -
442B GLY* 4.7 4.4 + - - +
435D PHE* 3.2 40.7 + - + +
436D TYR* 3.2 41.0 + - + +
437D ASN 3.2 1.8 - - - -
438D ILE* 1.3 75.5 - - - +
440D LEU* 1.3 64.3 + - + +
441D GLU 4.5 2.6 - - - +
503D OHT 5.5 3.9 - - - -
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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
------------------------------------------------------------
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