Contacts of the helix formed by residues 420 - 441 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LEU* 4.2 3.6 - - - +
355B LYS* 3.6 35.0 - - + +
356B TYR* 2.4 45.4 + - + -
359B MET* 4.4 8.7 - - - -
369B LEU* 4.7 1.0 - - - +
416B LYS 3.5 15.3 - - - +
417B MET* 2.8 16.1 + - - +
419B MET* 1.3 76.7 - - - +
421B LEU* 1.3 66.7 + - - +
422B PRO* 3.4 1.3 - - - -
423B LEU* 3.4 8.4 + - - +
424B LEU* 3.4 16.1 + - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 4.9 3.7 - - - +
311B LEU* 5.8 0.2 - - + -
356B TYR* 5.6 1.1 - - - +
369B LEU* 4.5 19.7 - - + +
372B ILE* 4.1 23.3 - - + -
373B ALA* 4.1 28.9 - - + +
376B ASN* 4.4 15.7 - - - +
417B MET 4.8 0.4 - - - +
418B LEU* 3.3 27.6 + - + +
420B THR* 1.3 77.6 + - - +
422B PRO* 1.3 64.1 - - + +
424B LEU* 2.6 40.7 + - + +
425B ARG* 2.9 13.4 + - - +
419E MET* 4.7 4.0 - - + -
422E PRO* 3.8 14.4 - - + -
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Residues in contact with PRO 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU 3.9 4.0 - - - +
419B MET* 3.7 12.3 - - - +
420B THR 3.5 4.0 - - - -
421B LEU* 1.3 92.5 - - + +
423B LEU* 1.3 60.2 + - - +
425B ARG* 3.6 1.4 + - - +
426B GLN* 3.1 23.6 + - - +
376E ASN* 4.0 13.7 - - - +
418E LEU 5.4 0.2 - - - +
421E LEU* 3.9 27.6 - - + +
422E PRO* 3.9 19.3 - - + -
425E ARG* 3.5 41.7 + - + +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA* 5.3 1.1 - - + +
351B GLN* 3.8 36.3 - - + +
352B LEU* 3.6 36.3 - - + +
355B LYS* 4.5 10.1 - - - +
420B THR 3.4 9.7 + - - +
421B LEU 3.1 0.8 - - - -
422B PRO* 1.3 77.0 - - - +
424B LEU* 1.3 61.3 + - - +
426B GLN* 3.4 24.4 + - - +
427B THR* 2.8 45.7 + - - +
378E ASP* 3.7 29.7 + - + +
425E ARG* 3.6 3.2 - - - +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 3.6 39.0 - - + +
310B ILE* 3.7 20.2 - - + -
311B LEU* 4.0 36.6 - - + +
314B VAL* 5.7 0.2 - - + -
352B LEU* 3.7 25.9 - - + +
356B TYR* 5.3 2.5 - - - +
373B ALA* 4.3 2.7 - - + -
420B THR 3.4 9.5 + - - +
421B LEU* 2.6 34.9 + - + +
423B LEU* 1.3 74.2 - - - +
425B ARG* 1.3 56.3 + - - +
428B SER* 2.8 31.0 + - - -
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER 6.0 0.4 - - - -
307B GLU* 2.8 36.4 + - - -
373B ALA* 5.4 0.4 + - - +
376B ASN* 3.0 29.7 + - - +
377B SER* 3.9 11.9 + - - +
378B ASP* 3.2 27.3 + - - +
421B LEU* 2.9 10.1 + - - +
422B PRO 3.7 8.3 - - - +
424B LEU* 1.3 73.9 - - - +
426B GLN* 1.3 66.8 + - - +
428B SER* 3.3 2.6 + - - -
429B THR* 2.9 30.2 + - - +
422E PRO* 3.4 27.2 - - + +
423E LEU 3.7 10.5 - - - +
425E ARG* 5.6 0.2 - - + -
426E GLN* 3.1 50.8 + - + +
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO 3.1 11.4 + - - +
423B LEU* 3.6 19.1 - - + +
425B ARG* 1.3 78.1 - - - +
427B THR* 1.3 65.0 + - - +
429B THR* 3.2 9.7 + - - +
430B LYS* 3.1 50.5 + - - +
377E SER 4.9 2.8 + - - -
378E ASP* 4.8 7.9 - - - +
425E ARG* 2.8 49.9 - - + +
426E GLN* 6.2 1.3 - - - +
429E THR* 4.9 10.5 - - + +
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 3.9 17.0 - - + -
345B LEU* 4.4 3.5 - - + +
348B ALA* 4.0 21.7 + - + +
349B ILE* 4.0 25.6 - - + +
352B LEU* 4.0 17.9 - - + +
423B LEU* 2.8 34.4 + - - +
424B LEU 4.0 0.9 - - - -
426B GLN* 1.3 70.6 - - - +
428B SER* 1.3 68.1 + - - +
430B LYS* 3.0 21.2 + - - +
431B ALA* 3.0 11.6 + - - +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B SER 5.0 4.2 + - - -
306B MET* 3.5 16.4 - - - +
307B GLU* 3.4 30.9 + - - +
310B ILE* 3.7 13.2 - - - +
424B LEU 2.8 21.4 + - - -
425B ARG* 3.4 5.1 - - - -
427B THR* 1.3 76.2 - - - +
429B THR* 1.3 58.6 + - - +
431B ALA* 3.1 5.4 + - - +
432B VAL* 2.9 32.1 + - - +
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Residues in contact with THR 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG* 2.9 21.3 + - - +
426B GLN* 3.4 11.4 - - - +
427B THR 3.2 0.2 - - - -
428B SER* 1.3 78.0 + - - +
430B LYS* 1.3 58.2 + - + +
432B VAL* 3.4 7.8 + - - +
433B GLN* 2.9 49.1 + - + +
426E GLN* 5.1 7.1 + - - +
429E THR* 5.1 14.6 - - + -
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Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 4.0 15.3 - - + -
348B ALA* 5.2 11.2 - - + -
426B GLN* 3.1 52.1 + - - +
427B THR* 3.0 13.3 + - - +
429B THR* 1.3 73.5 - - + +
431B ALA* 1.3 66.9 + - - +
433B GLN* 3.1 11.7 + - - +
434B HIS* 2.9 27.0 + - - +
429E THR* 6.3 1.9 - - - +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B MET* 3.5 29.2 - - + -
310B ILE* 3.9 15.5 - - + -
345B LEU* 3.8 20.7 - - + +
427B THR 3.0 6.2 + - - +
428B SER 3.3 9.2 - - - +
430B LYS* 1.3 77.1 - - - +
432B VAL* 1.3 63.5 + - - +
434B HIS* 3.6 0.5 + - - +
435B PHE 3.3 5.5 + - - -
501B OHT 3.1 30.1 - - + -
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TRP* 4.4 13.9 - - + +
306B MET* 3.8 31.9 - - + -
428B SER* 2.9 22.0 + - - +
429B THR* 3.7 9.2 - - - +
430B LYS 3.2 0.2 - - - -
431B ALA* 1.3 73.2 - - - +
433B GLN* 1.3 69.9 + - + +
435B PHE* 3.1 10.3 + - - +
436B TYR* 3.2 44.4 + - + +
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B THR* 2.9 40.5 + - + +
430B LYS* 3.6 10.2 - - - +
432B VAL* 1.3 77.5 - - + +
434B HIS* 1.3 55.2 + - - +
435B PHE 2.6 13.7 + - - -
436B TYR* 3.0 5.4 + - - +
437B ASN* 2.8 25.5 + - + +
429E THR* 5.6 5.3 - - - +
433E GLN* 4.8 18.4 - - - +
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Residues in contact with HIS 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 5.4 0.8 - - - +
340B ALA 5.7 0.4 + - - -
341B GLY 3.7 23.3 + - - -
342B LEU* 4.2 10.7 - - + +
345B LEU* 4.1 19.7 - - + +
430B LYS 2.9 19.1 + - - +
431B ALA 3.8 4.3 - - - +
433B GLN* 1.3 71.8 - - - +
435B PHE* 1.3 56.4 + - - +
437B ASN* 3.3 10.3 + - - +
438B ILE* 3.1 47.0 + - + +
501B OHT 3.8 20.6 - + + -
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B CYS* 4.8 11.0 - - + -
305B TRP* 5.8 4.0 - + - -
306B MET* 5.2 2.5 - - + -
431B ALA 3.3 8.8 + - - +
432B VAL* 3.1 11.5 + - - +
433B GLN 2.6 6.1 + - - -
434B HIS* 1.3 71.6 - - - +
436B TYR* 1.3 82.5 + + - +
437B ASN 3.0 1.6 - - - -
438B ILE* 3.0 25.2 + - + +
439B LYS* 3.0 46.0 + - + +
501B OHT 3.4 79.2 - + + -
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Residues in contact with TYR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B TRP* 5.0 8.4 - + - -
432B VAL* 3.2 44.6 + - + -
433B GLN* 3.0 7.1 + - - +
435B PHE* 1.3 93.0 - + - +
437B ASN* 1.3 61.7 + - - +
439B LYS* 3.4 19.6 + - + +
440B LEU* 3.5 18.8 + - - +
1320H LEU* 4.6 19.2 - - - +
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Residues in contact with ASN 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B GLN* 2.8 19.6 + - - +
434B HIS* 3.3 16.8 + - - +
436B TYR* 1.3 79.4 - - - +
438B ILE* 1.3 64.0 + - - +
439B LYS 3.5 0.2 - - - -
440B LEU* 3.8 11.2 + - - +
441B GLU* 3.6 27.2 + - - +
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Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 4.0 35.7 - - + -
434B HIS* 3.1 42.1 + - + +
435B PHE* 3.0 28.3 + - + +
437B ASN* 1.3 80.5 - - - +
439B LYS* 1.3 65.7 + - + +
440B LEU 3.3 1.1 - - - -
441B GLU* 3.9 15.3 - - + +
442B GLY* 3.2 18.7 + - - -
443B LYS 4.6 1.6 + - - -
444B VAL* 5.5 10.1 - - + +
501B OHT 4.5 4.9 - - + -
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Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B CYS* 5.8 4.4 - - - -
435B PHE* 3.0 49.2 + - + +
436B TYR* 3.4 15.7 + - + +
438B ILE* 1.3 78.2 - - + +
440B LEU* 1.3 65.1 + - + +
442B GLY* 3.4 11.5 + - - -
501B OHT 6.0 2.5 - - - -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B TYR 3.5 14.5 + - - +
437B ASN* 3.9 11.7 - - - +
438B ILE 3.3 0.2 - - - -
439B LYS* 1.3 76.8 - - + +
441B GLU* 1.3 62.7 + - + +
442B GLY* 3.0 6.4 + - - -
436D TYR* 3.9 5.1 - - + +
439D LYS* 3.0 52.0 + - + +
440D LEU* 3.9 29.2 - - + -
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ASN* 3.6 21.2 + - - +
438B ILE* 4.0 15.7 - - + +
439B LYS 3.5 0.4 - - - -
440B LEU* 1.3 78.3 - - + +
442B GLY* 1.3 66.2 - - - +
443B LYS* 2.7 37.7 + - + +
436D TYR* 3.1 47.5 + - + -
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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
------------------------------------------------------------
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