Contacts of the helix formed by residues 480 - 497 (chain B) in PDB entry 1GKU
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 ASP 480 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B GLU* 4.7 3.4 + - - -
478B GLU 4.1 0.8 + - - +
479B VAL* 1.3 73.4 - - - +
481B PHE* 1.3 53.6 + - - +
482B GLU* 3.1 29.8 - - - +
483B LYS* 3.0 26.6 + - + +
484B LEU* 2.7 34.5 + - - +
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Residues in contact with PHE 481 (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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270B ILE* 5.9 0.7 - - + -
271B LEU* 3.6 34.5 - - + -
273B LYS* 3.4 54.7 - - + +
274B LEU* 3.5 20.4 - - + +
450B PHE* 3.9 23.1 - + - -
477B ASP* 4.9 7.2 - - + -
479B VAL* 3.5 31.8 + - + +
480B ASP* 1.3 73.1 + - - +
482B GLU* 1.3 66.3 + - - +
484B LEU* 4.2 2.5 - - - -
485B SER* 2.8 32.2 + - - -
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Residues in contact with GLU 482 (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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273B LYS* 5.0 6.8 + - - -
480B ASP* 3.1 19.5 - - - +
481B PHE* 1.3 82.3 + - - +
483B LYS* 1.3 64.9 + - - +
485B SER* 3.9 5.1 - - - -
486B ARG* 3.2 26.6 + - - +
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Residues in contact with LYS 483 (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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480B ASP* 3.0 34.8 + - + +
482B GLU* 1.3 79.0 - - - +
484B LEU* 1.3 61.7 + - - +
486B ARG* 3.4 21.5 + - + +
487B GLU* 3.2 45.5 + - + +
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Residues in contact with LEU 484 (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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255B GLU* 3.8 31.4 - - + +
257B VAL* 5.8 1.6 - - + -
274B LEU* 4.3 12.8 - - + -
446B LYS* 4.3 19.3 - - + -
447B GLY 4.7 0.4 - - - +
448B ALA* 4.3 19.7 - - + -
450B PHE* 4.7 7.9 - - + -
479B VAL* 4.1 16.2 - - + -
480B ASP 2.7 21.5 + - - +
481B PHE* 3.9 4.0 - - - +
483B LYS* 1.3 71.7 - - - +
485B SER* 1.3 63.9 + - - +
486B ARG 3.3 0.3 + - - -
487B GLU* 3.4 8.7 + - - +
488B LEU* 3.2 43.4 + - + +
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Residues in contact with SER 485 (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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273B LYS 4.9 3.3 + - - -
274B LEU* 2.9 34.8 + - - +
344B ARG* 3.1 29.2 + - - +
481B PHE 2.8 22.8 + - - -
482B GLU* 3.9 6.3 - - - -
483B LYS 3.4 0.2 - - - -
484B LEU* 1.3 72.9 - - - +
486B ARG* 1.3 61.9 + - - +
488B LEU* 4.7 1.6 - - - -
489B ASP* 3.6 12.1 + - - +
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Residues in contact with ARG 486 (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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482B GLU 3.2 14.5 + - - +
483B LYS* 3.4 25.7 - - + +
484B LEU 3.1 0.2 - - - -
485B SER* 1.3 76.0 - - - +
487B GLU* 1.3 66.6 + - + +
489B ASP* 2.9 8.3 + - - +
490B GLU* 2.8 46.3 + - + +
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Residues in contact with GLU 487 (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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255B GLU* 4.7 2.8 - - - +
446B LYS* 4.2 33.0 - - + +
483B LYS* 3.2 35.9 + - + +
484B LEU* 3.4 13.5 + - - +
486B ARG* 1.3 76.4 - - + +
488B LEU* 1.3 57.6 + - - +
490B GLU* 3.8 14.1 - - - +
491B SER* 2.8 36.4 + - - -
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Residues in contact with LEU 488 (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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274B LEU* 4.5 16.8 - - + -
344B ARG* 3.3 53.6 - - + +
345B PHE* 4.5 4.5 - - + -
446B LYS* 3.0 40.4 - - + +
447B GLY* 4.0 4.7 - - - +
448B ALA* 4.6 1.8 - - + -
484B LEU* 3.2 34.1 - - + +
485B SER 3.9 0.2 - - - +
486B ARG 3.2 0.4 - - - -
487B GLU* 1.3 76.6 - - - +
489B ASP* 1.3 59.0 + - - +
491B SER* 3.3 3.3 + - - -
492B ARG* 2.8 41.6 + - - +
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Residues in contact with ASP 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 3.0 40.7 + - - -
485B SER* 3.6 8.2 + - - +
486B ARG* 2.9 9.7 + - - +
488B LEU* 1.3 76.2 - - - +
490B GLU* 1.3 62.5 + - + +
492B ARG* 3.5 5.4 + - - +
493B ASP* 2.9 38.9 + - - +
496B ARG* 5.4 2.2 + - - +
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Residues in contact with GLU 490 (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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486B ARG* 2.8 54.1 + - + +
487B GLU* 3.8 12.2 + - - +
489B ASP* 1.3 79.6 - - + +
491B SER* 1.3 61.3 + - - +
493B ASP* 3.3 11.2 + - - +
494B ARG* 3.1 28.9 + - - +
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Residues in contact with SER 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B PHE* 4.4 1.6 - - - -
445B THR* 3.8 15.5 - - - +
446B LYS* 3.3 31.6 + - - -
487B GLU 2.8 18.6 + - - -
488B LEU* 3.3 7.6 + - - -
490B GLU* 1.3 76.9 - - - +
492B ARG* 1.3 66.8 + - - +
494B ARG* 3.6 23.7 + - - +
495B TYR* 3.2 22.0 + - - +
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Residues in contact with ARG 492 (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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340B PRO 3.3 22.4 + - - +
341B GLU* 3.7 16.8 - - + +
343B ILE 2.9 28.2 + - - -
344B ARG* 3.5 27.9 + - - +
436B THR* 3.1 28.1 + - - +
445B THR* 4.5 8.8 + - - -
446B LYS 3.0 21.8 + - - +
488B LEU* 2.8 38.4 + - - +
489B ASP* 4.0 4.0 - - - +
490B GLU 3.2 0.4 - - - -
491B SER* 1.3 83.9 + - - +
493B ASP* 1.3 61.3 + - - +
494B ARG 3.2 0.9 - - - -
495B TYR* 3.2 8.2 + - + +
496B ARG* 2.9 50.7 + - - +
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Residues in contact with ASP 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ASP* 2.9 21.3 + - - +
490B GLU* 3.3 11.4 + - - +
492B ARG* 1.3 76.7 - - - +
494B ARG* 1.3 64.1 + - + +
496B ARG* 2.5 42.6 + - - +
497B ARG* 3.1 31.2 + - - +
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Residues in contact with ARG 494 (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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440B PHE* 3.2 39.2 - - + -
442B GLY* 3.3 20.4 + - - -
443B GLY* 5.4 0.2 - - - -
444B LEU 4.1 19.0 + - - +
490B GLU 3.1 13.3 + - - +
491B SER* 3.6 24.1 - - - +
492B ARG 3.2 0.2 - - - -
493B ASP* 1.3 77.6 - - + +
495B TYR* 1.3 56.6 + - - +
497B ARG* 3.0 21.0 + - - +
498B ARG 3.0 10.6 + - - -
501B PHE* 3.5 30.5 - - + -
503B LEU* 5.8 0.2 - - - +
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Residues in contact with TYR 495 (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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80B THR* 3.6 10.8 - - - +
340B PRO* 3.4 41.2 - - + +
341B GLU* 3.9 29.6 - - + -
438B ARG* 3.5 26.7 + - + -
440B PHE* 3.6 34.0 - + + -
445B THR* 4.2 11.9 - - + -
491B SER 3.2 12.1 + - - +
492B ARG* 3.2 13.0 + - + +
494B ARG* 1.3 75.2 - - - +
496B ARG* 1.3 58.9 + - - +
497B ARG 2.9 4.9 - - - -
498B ARG* 2.8 64.3 + - - +
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU* 2.8 67.6 + - - +
489B ASP* 4.2 4.0 + - - +
492B ARG* 2.9 23.7 + - - +
493B ASP* 2.5 44.1 + - - +
495B TYR* 1.3 78.3 - - - +
497B ARG* 1.3 58.0 + - + +
498B ARG* 3.3 5.8 + - - +
499B GLN* 3.4 12.8 + - - -
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Residues in contact with ARG 497 (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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493B ASP* 3.1 17.2 + - - +
494B ARG* 3.0 12.7 + - - +
495B TYR 2.9 0.8 - - - -
496B ARG* 1.3 79.8 - - + +
498B ARG* 1.3 48.4 + - - +
499B GLN* 2.6 28.9 + - - +
500B GLU* 2.7 45.4 + - + +
501B PHE* 3.5 12.8 - - + -
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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