Contacts of the helix formed by residues 425 - 435 (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 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328B HIS* 4.1 9.9 + - - -
352B PRO* 3.0 34.8 + - - +
353B SER* 3.6 6.8 + - - +
354B PHE* 3.5 38.9 - - + -
423B PHE 3.3 1.4 + - - -
424B PRO* 1.3 69.8 - - - +
426B LEU* 1.3 59.3 + - - +
427B ARG* 3.2 11.6 + - - +
428B THR* 2.6 41.6 + - - -
429B TYR* 3.5 8.8 + - - +
462B PHE* 3.9 2.4 - - - -
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Residues in contact with LEU 426 (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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424B PRO* 3.3 16.2 + - + +
425B ASP* 1.3 72.3 - - - +
427B ARG* 1.3 63.9 + - - +
428B THR 3.2 0.2 - - - -
429B TYR* 3.8 8.5 - - + -
430B ILE* 2.8 36.1 + - + +
462B PHE* 3.9 23.8 - - + +
465B ARG* 3.4 35.4 - - + -
466B ALA* 3.3 35.7 - - + +
469B TYR* 3.9 30.3 - - + +
472B GLU* 4.1 13.5 - - + -
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 5.9 1.1 - - + -
425B ASP* 3.2 9.1 + - - +
426B LEU* 1.3 78.6 - - - +
428B THR* 1.3 61.1 + - - +
430B ILE* 3.7 7.1 - - - +
431B GLN* 2.9 48.0 + - + +
469B TYR* 5.3 12.0 + - - -
865B GLY 4.6 15.4 + - - -
866B VAL* 5.5 4.2 - - - +
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Residues in contact with THR 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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327B ALA* 3.3 33.4 - - + -
328B HIS* 3.4 22.2 - - + +
348B PHE* 4.1 1.1 - - + -
352B PRO* 3.9 15.0 - - + -
425B ASP* 2.6 34.2 + - - -
427B ARG* 1.3 77.0 - - - +
429B TYR* 1.3 60.6 + - - +
431B GLN* 3.9 9.7 + - + +
432B GLY* 2.7 28.8 + - - -
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Residues in contact with TYR 429 (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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256B ASP* 2.5 32.0 + - - -
348B PHE* 3.4 33.4 - + - -
352B PRO* 4.2 4.6 - - + +
425B ASP 3.5 4.1 + - - +
426B LEU* 3.9 10.1 - - + +
427B ARG 3.4 0.4 - - - -
428B THR* 1.3 77.9 - - - +
430B ILE* 1.3 59.3 + - + +
432B GLY 3.3 0.2 + - - -
433B SER* 2.7 49.3 + - - -
449B SER* 2.6 32.9 + - - -
451B LEU* 4.3 10.1 - - + -
462B PHE* 3.7 36.8 - + + -
472B GLU* 3.9 17.5 - - - -
474B LYS* 3.7 25.1 - - - -
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Residues in contact with ILE 430 (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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250B THR* 5.2 20.0 - - + +
252B ARG* 4.6 13.8 + - - +
426B LEU* 2.8 31.9 + - + +
427B ARG* 3.7 7.0 - - - +
429B TYR* 1.3 77.2 - - + +
431B GLN* 1.3 55.9 + - + +
433B SER* 3.4 5.9 + - - -
434B GLY* 2.7 34.9 + - - -
469B TYR* 3.8 35.7 - - + -
472B GLU* 3.8 24.0 - - - +
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Residues in contact with GLN 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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427B ARG* 2.9 34.0 + - + +
428B THR* 3.9 9.8 + - - +
430B ILE* 1.3 79.1 - - + +
432B GLY* 1.3 64.6 + - - +
434B GLY* 3.3 8.7 + - - -
435B ARG* 3.5 28.1 + - - +
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Residues in contact with GLY 432 (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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281B TYR* 3.0 34.9 + - - -
327B ALA* 6.1 1.1 - - - -
346B ALA* 4.6 2.4 - - - +
348B PHE* 3.7 13.9 - - - -
428B THR* 2.7 22.3 + - - -
429B TYR 3.6 0.7 - - - -
431B GLN* 1.3 76.1 - - - +
433B SER* 1.3 59.9 + - - +
435B ARG* 3.4 14.1 + - - +
436B THR 4.6 0.3 + - - -
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Residues in contact with SER 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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252B ARG* 2.7 29.6 + - - -
254B VAL* 4.0 5.1 - - - +
346B ALA* 4.7 4.9 - - - -
348B PHE* 3.7 4.9 - - - -
429B TYR* 2.7 30.3 + - - -
430B ILE 3.4 1.7 + - - -
432B GLY* 1.3 70.5 - - - -
434B GLY* 1.3 63.2 + - - +
435B ARG 3.1 1.1 - - - -
436B THR* 2.9 32.1 + - - +
449B SER* 3.6 32.3 - - - -
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Residues in contact with GLY 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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252B ARG* 5.2 10.3 - - - -
430B ILE 2.7 20.2 + - - -
431B GLN* 3.7 4.5 - - - -
432B GLY 3.1 0.8 - - - -
433B SER* 1.3 78.0 - - - +
435B ARG* 1.3 55.4 + - - +
436B THR 3.0 2.6 + - - -
437B SER* 2.9 29.1 + - - +
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Residues in contact with ARG 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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279B ILE* 6.0 0.2 - - + -
281B TYR* 3.1 41.7 + - - +
327B ALA* 4.2 15.2 + - - +
335B ARG 5.9 1.4 + - - -
336B GLY* 5.9 1.2 - - - -
337B LEU* 4.0 52.7 - - - +
338B ASP* 5.9 0.2 - - - -
339B LEU 4.8 4.0 - - - +
340B PRO* 5.7 1.9 - - - +
343B ILE* 3.5 27.2 - - + +
431B GLN* 3.5 21.0 + - - +
432B GLY* 3.4 10.2 + - - +
433B SER 3.1 1.2 - - - -
434B GLY* 1.3 75.3 - - - +
436B THR* 1.3 57.6 + - - +
437B SER 3.5 1.1 - - - -
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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