Contacts of the helix formed by residues 420 - 440 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LEU* 4.8 4.5 - - - +
355C LYS* 3.8 31.2 - - + +
356C TYR* 2.7 46.5 + - + -
359C MET* 4.2 10.8 - - - -
369C LEU* 4.0 3.1 - - - +
416C LYS 3.4 17.0 - - - +
417C MET 2.7 17.2 + - - +
419C MET* 1.3 78.6 - - - +
421C LEU* 1.3 65.7 + - - +
422C PRO* 3.3 0.7 - - - -
423C LEU* 3.2 17.0 + - - +
424C LEU* 3.4 7.6 + - - +
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU* 5.1 3.0 - - - +
356C TYR* 5.4 0.4 - - - +
369C LEU* 3.9 22.4 - - + +
372C ILE* 4.0 11.7 - - + -
373C ALA* 4.8 13.0 - - + -
376C ASN* 4.0 23.1 - - + +
417C MET 4.6 0.2 - - - +
418C LEU* 3.0 44.9 + - + +
420C THR* 1.3 80.3 + - - +
422C PRO* 1.3 64.4 - - - +
424C LEU* 2.9 33.6 + - + +
425C ARG* 3.0 12.0 + - - +
419F MET* 4.4 6.1 - - + -
422F PRO* 3.5 15.6 - - + +
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Residues in contact with PRO 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C LEU 3.8 2.7 - - - +
419C MET* 3.2 22.0 - - - +
420C THR 3.3 1.6 - - - +
421C LEU* 1.3 94.1 - - + +
423C LEU* 1.3 56.0 + - - +
425C ARG* 3.1 5.2 + - - +
426C GLN* 2.9 27.2 + - - +
376F ASN* 4.2 9.9 - - - +
418F LEU 5.6 0.2 - - - +
421F LEU* 4.0 16.8 - - + +
422F PRO* 3.8 33.0 - - + -
425F ARG* 3.7 33.2 + - + +
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ALA 5.7 0.4 - - - +
351C GLN* 3.9 35.7 - - + +
352C LEU* 4.4 21.5 - - + +
355C LYS* 4.0 16.4 - - - +
420C THR 3.2 9.4 + - - +
422C PRO* 1.3 76.1 - - - +
424C LEU* 1.3 59.8 + - - +
426C GLN* 3.5 33.9 - - - +
427C THR* 2.6 46.7 + - - +
378F ASP* 3.2 33.3 + - + +
425F ARG* 3.7 4.1 - - - +
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Residues in contact with LEU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU* 3.9 41.7 - - + +
310C ILE* 4.0 12.3 - - + -
311C LEU* 4.0 37.0 - - + -
352C LEU* 3.9 26.8 - - + +
356C TYR* 5.0 4.0 - - - +
369C LEU* 6.2 0.2 - - + -
373C ALA* 4.2 12.8 - - + -
420C THR 3.4 5.7 + - - +
421C LEU* 2.9 24.3 + - + +
423C LEU* 1.3 78.3 - - - +
425C ARG* 1.3 56.2 + - - +
427C THR* 4.0 0.2 - - - -
428C SER* 3.0 31.5 + - - -
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Residues in contact with ARG 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU* 2.7 35.4 + - - -
373C ALA 5.4 0.2 + - - -
376C ASN* 3.1 27.7 + - - +
377C SER* 4.0 9.7 + - - +
378C ASP* 3.2 14.3 + - - +
421C LEU 3.0 10.2 + - - +
422C PRO* 3.2 11.2 - - + +
424C LEU* 1.3 74.6 - - - +
426C GLN* 1.3 55.5 + - - +
428C SER* 3.3 3.6 + - - -
429C THR* 2.8 40.3 + - - +
422F PRO* 3.4 49.7 + - + +
423F LEU* 3.5 4.2 - - - +
425F ARG* 5.5 0.2 - - + -
426F GLN* 3.3 49.0 + - + +
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Residues in contact with GLN 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ALA* 6.3 0.6 - - - +
351C GLN* 4.9 3.4 + - - -
422C PRO 2.9 13.8 + - - +
423C LEU* 3.5 23.8 - - + +
425C ARG* 1.3 77.0 - - - +
427C THR* 1.3 66.4 + - - +
429C THR* 3.1 9.5 + - - -
430C LYS* 3.0 52.2 + - + +
377F SER 5.2 1.4 - - - +
378F ASP* 4.9 8.7 + - - +
380F MET* 6.2 3.2 - - - +
425F ARG* 2.9 38.1 + - + +
426F GLN* 6.4 0.7 - - - +
429F THR* 5.4 8.6 + - - +
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Residues in contact with THR 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ILE* 4.4 6.7 - - + -
345C LEU* 4.4 4.1 - - + +
348C ALA* 4.1 24.3 + - + +
349C ILE* 3.9 30.3 - - + +
352C LEU* 3.9 15.4 - - + +
423C LEU* 2.6 38.1 + - - +
424C LEU 4.0 2.0 - - - -
426C GLN* 1.3 77.4 + - - +
428C SER* 1.3 58.5 + - - +
430C LYS* 3.3 11.0 + - - +
431C ALA* 3.0 26.5 + - - +
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Residues in contact with SER 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C SER 5.2 3.5 + - - -
306C MET* 3.6 14.9 - - - +
307C GLU* 3.5 35.6 - - - +
310C ILE* 3.8 12.9 - - - +
424C LEU* 3.0 20.5 + - - -
425C ARG* 3.3 4.3 + - - -
427C THR* 1.3 73.9 - - - +
429C THR* 1.3 66.3 + - - +
431C ALA* 3.1 2.3 + - - +
432C VAL* 3.0 27.2 + - - +
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Residues in contact with THR 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ARG* 2.8 27.0 + - - +
426C GLN* 3.4 10.9 - - - -
428C SER* 1.3 72.1 + - - +
430C LYS* 1.3 61.2 + - + +
432C VAL* 3.1 7.7 + - - +
433C GLN* 2.9 56.1 + - - +
426F GLN* 4.8 5.5 + - - +
429F THR* 5.1 5.8 - - + -
430F LYS* 4.1 25.0 + - - +
433F GLN* 5.1 7.0 - - - +
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Residues in contact with LYS 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C LEU* 4.2 11.8 - - + +
348C ALA* 5.1 12.6 - - + -
426C GLN* 3.0 49.0 + - + +
427C THR* 3.4 13.7 - - + +
429C THR* 1.3 76.6 - - + +
431C ALA* 1.3 56.9 + - - +
433C GLN* 3.4 7.0 + - - +
434C HIS* 2.9 31.5 + - - +
380F MET* 6.0 4.8 - - - +
433F GLN* 6.2 1.8 - - - +
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C MET* 3.3 22.7 - - + -
310C ILE* 3.5 25.6 - - + -
345C LEU* 3.8 19.7 - - + +
427C THR 3.0 8.0 + - - +
428C SER 3.1 7.6 + - - +
430C LYS* 1.3 73.1 - - - +
432C VAL* 1.3 67.0 + - - +
434C HIS* 3.8 0.2 - - - +
435C PHE* 3.2 18.5 + - - +
502C OHT 3.4 18.0 - - + -
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Residues in contact with VAL 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C TRP* 4.4 16.8 - - + +
306C MET* 3.9 28.7 - - + -
428C SER* 3.0 18.4 + - - +
429C THR* 3.6 7.6 - - - +
431C ALA* 1.3 76.2 - - - +
433C GLN* 1.3 67.4 + - - +
435C PHE* 3.3 3.0 + - - +
436C TYR* 2.9 54.3 + - + -
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Residues in contact with GLN 433 (chain C).
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* 2.9 45.7 + - - +
430C LYS* 3.7 6.5 - - - +
432C VAL* 1.3 79.7 - - - +
434C HIS* 1.3 52.2 + - - +
436C TYR* 2.9 10.0 + - + +
437C ASN* 2.6 49.9 + - - +
430F LYS* 5.5 0.8 - - - +
433F GLN* 3.1 35.9 + - - +
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Residues in contact with HIS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C LEU* 5.4 2.6 - - + +
340C ALA 5.6 0.2 + - - -
341C GLY 3.7 17.0 + - - -
342C LEU* 3.6 31.8 - - + +
345C LEU* 3.8 20.8 - - + +
430C LYS 2.9 21.1 + - - +
431C ALA 3.8 4.3 - - - +
433C GLN* 1.3 71.8 - - - +
435C PHE* 1.3 62.6 + - - +
437C ASN* 3.4 15.0 + - - +
438C ILE* 3.2 48.3 + - + +
502C OHT 3.9 6.3 - + - -
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Residues in contact with PHE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C CYS* 3.8 17.0 - - - -
305C TRP* 6.0 2.9 - + + -
306C MET* 5.3 2.7 - - + -
431C ALA 3.2 10.8 + - - +
432C VAL* 3.5 9.0 - - - +
433C GLN 3.1 0.6 - - - -
434C HIS* 1.3 79.2 - - - +
436C TYR* 1.3 87.3 + + - +
438C ILE* 3.2 15.7 + - + +
439C LYS* 3.0 66.9 + - + +
502C OHT 3.4 68.5 - + + -
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Residues in contact with TYR 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C TRP* 4.9 8.3 - + - -
432C VAL* 2.9 47.3 + - + +
433C GLN* 2.9 9.7 + - + +
435C PHE* 1.3 101.4 - + - +
437C ASN* 1.3 61.6 + - - +
439C LYS* 4.2 5.1 - - + +
440C LEU* 3.4 35.1 + - + +
1320I LEU* 4.9 16.1 - - - +
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Residues in contact with ASN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433C GLN* 2.6 40.4 + - - +
434C HIS* 3.5 16.2 + - - +
436C TYR* 1.3 75.8 - - - +
438C ILE* 1.3 62.5 + - + +
440C LEU* 4.1 4.6 - - - +
441C GLU* 3.5 22.0 + - - +
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Residues in contact with ILE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C LEU* 5.2 22.4 - - + -
434C HIS* 3.2 42.4 + - + +
435C PHE* 3.4 20.0 - - + +
437C ASN* 1.3 77.5 - - + +
439C LYS* 1.3 73.7 + - + +
440C LEU 3.4 0.2 - - - -
441C GLU* 3.4 30.5 + - + +
442C GLY* 3.5 8.7 + - - -
443C LYS* 4.6 3.1 + - - +
444C VAL* 4.7 21.0 - - + +
502C OHT 5.5 2.0 - - + -
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Residues in contact with LYS 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C CYS* 5.4 4.0 - - - -
435C PHE* 3.0 56.1 + - + +
436C TYR* 4.2 7.4 - - - +
437C ASN 3.6 0.2 - - - -
438C ILE* 1.3 79.6 - - + +
440C LEU* 1.3 60.5 + - + +
441C GLU 3.0 5.5 + - - -
442C GLY* 3.1 14.9 + - - -
444C VAL* 6.3 1.1 - - - -
502C OHT 5.3 5.5 - - - -
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C TYR* 3.4 22.5 + - + +
437C ASN* 4.1 5.4 + - - +
438C ILE 3.4 0.4 - - - -
439C LYS* 1.3 79.7 - - + +
441C GLU* 1.3 56.4 + - - +
442C GLY 3.6 0.4 - - - -
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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