Contacts of the helix formed by residues 401 - 415 (chain G) in PDB entry 1Q57
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 GLU 401 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B LYS* 4.9 12.9 + - - -
402G THR* 1.3 79.5 + - + +
403G ASP* 3.7 32.0 - - - +
404G ARG* 3.2 53.3 + - + +
405G LEU* 3.3 19.9 + - - +
429G VAL 4.7 2.6 - - - +
430G VAL* 2.5 34.1 + - - +
431G SER* 2.5 36.4 - - - +
432G ALA* 4.0 12.9 - - + +
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Residues in contact with THR 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401G GLU* 1.3 83.8 - - + +
403G ASP* 1.3 82.2 + - - +
405G LEU* 3.2 5.4 + - - +
406G LEU* 2.9 29.6 + - - +
429G VAL* 5.2 9.2 - - - -
430G VAL 3.8 2.8 + - - -
431G SER 4.9 0.4 - - - -
432G ALA* 5.8 3.1 - - + -
441G MET* 3.6 33.7 - - + +
445G LEU* 4.1 21.9 - - - +
448G LYS* 3.7 20.6 + - - +
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Residues in contact with ASP 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LYS* 5.7 8.1 - - - -
221B GLN* 4.8 4.4 - - + +
401G GLU* 3.7 22.5 - - - +
402G THR* 1.3 85.1 - - - +
404G ARG* 1.3 64.1 + - - +
406G LEU* 3.2 6.5 + - - +
407G ALA* 2.9 24.5 + - - +
448G LYS* 3.0 33.3 + - - +
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Residues in contact with ARG 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLN* 3.5 31.3 + - + +
394G TYR* 4.9 11.0 - - - +
401G GLU* 3.2 47.5 + - + +
402G THR 3.4 0.4 - - - -
403G ASP* 1.3 78.6 - - - +
405G LEU* 1.3 62.1 + - - +
407G ALA* 3.6 0.2 - - - +
408G LYS* 3.1 30.1 + - + +
431G SER* 4.7 5.4 + - - -
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Residues in contact with LEU 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340G ALA* 4.9 1.8 - - + -
342G LEU* 4.4 23.3 - - + -
394G TYR* 3.3 40.8 - - + +
401G GLU 3.3 17.7 + - - +
402G THR* 3.2 6.9 + - - +
404G ARG* 1.3 75.9 - - - +
406G LEU* 1.3 66.5 + - + +
408G LYS* 2.8 27.6 + - - +
409G LEU* 2.9 37.5 + - + +
423G LEU* 4.2 22.7 - - + -
429G VAL 5.6 5.2 - - - +
445G LEU* 5.7 7.2 - - + -
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Residues in contact with LEU 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G THR* 2.9 19.7 + - - +
403G ASP* 3.5 7.2 - - - +
405G LEU* 1.3 82.5 - - + +
407G ALA* 1.3 57.1 + - - +
409G LEU* 3.4 10.1 + - + +
410G ALA* 3.0 28.4 + - - +
445G LEU* 3.2 35.2 - - + -
448G LYS* 3.9 24.0 - - + +
449G LEU* 3.2 22.9 - - + -
452G PHE* 4.1 28.0 - - + -
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Residues in contact with ALA 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLN* 3.5 54.1 - - + +
403G ASP 2.9 11.0 + - - +
404G ARG 3.6 3.6 - - - +
405G LEU 3.0 0.2 - - - -
406G LEU* 1.3 74.0 - - - +
408G LYS* 1.3 65.2 + - + +
410G ALA* 3.3 7.8 + - - +
411G TYR* 3.2 21.3 + - - +
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Residues in contact with LYS 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLN* 4.3 13.7 - - - +
261B ILE 4.1 7.3 + - - +
262B PRO* 3.9 1.6 - - + +
263B ASP* 2.7 56.8 + - - +
264B GLY* 3.1 8.9 - - - +
265B VAL* 4.3 10.9 - - + +
394G TYR* 3.7 34.5 - - + -
404G ARG* 3.1 24.5 - - + +
405G LEU 2.8 10.8 + - - +
407G ALA* 1.3 71.9 - - + +
409G LEU* 1.3 62.9 + - - +
411G TYR* 3.1 18.4 + - - +
412G MET* 3.1 17.1 + - - +
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Residues in contact with LEU 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340G ALA* 5.0 7.6 - - + -
394G TYR* 5.8 1.1 - - + -
405G LEU* 2.9 58.7 + - + +
406G LEU* 3.5 15.7 - - + +
408G LYS* 1.3 78.0 - - - +
410G ALA* 1.3 62.2 + - - +
412G MET* 3.2 16.7 - - - +
413G ARG 3.2 15.6 + - - -
421G ILE* 3.0 40.0 - - + +
423G LEU* 4.8 16.8 - - + -
449G LEU* 5.4 2.7 - - + -
452G PHE* 3.3 22.8 - - + -
460G LEU* 4.4 6.3 - - + -
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Residues in contact with ALA 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ALA* 5.4 9.9 - - + +
406G LEU 3.0 14.6 + - - +
407G ALA* 3.5 12.3 - - - +
408G LYS 3.1 0.2 - - - -
409G LEU* 1.3 78.0 - - - +
411G TYR* 1.3 51.3 + - - +
413G ARG* 3.0 5.7 + - - +
414G SER* 2.6 40.0 + - - +
452G PHE* 3.4 23.1 - - + -
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Residues in contact with TYR 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ALA* 5.5 6.9 - - - +
226B GLY* 5.2 9.2 - - - -
259B PRO 5.9 2.2 - - - -
261B ILE* 5.1 14.4 - - + +
262B PRO* 3.2 50.7 - - + +
265B VAL* 3.5 22.9 - - + -
407G ALA 3.2 8.7 + - - +
408G LYS* 3.1 9.7 + - - +
410G ALA* 1.3 75.3 - - - +
412G MET* 1.3 64.5 + - - +
414G SER* 4.5 3.1 - - - -
415G GLY* 2.7 44.1 + - - +
416G LEU* 3.2 29.4 + - + +
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Residues in contact with MET 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B VAL* 3.5 24.7 - - + -
338G GLY* 3.0 31.6 - - - -
339G LEU 3.9 3.4 - - - +
340G ALA* 5.6 0.7 - - - -
392G HIS* 4.1 5.8 - - + +
394G TYR* 4.4 22.7 - - - -
408G LYS 3.1 17.6 + - - +
409G LEU* 3.2 17.5 - - - +
410G ALA 3.1 0.2 - - - -
411G TYR* 1.3 76.7 - - - +
413G ARG* 1.3 51.8 + - - +
416G LEU* 3.0 12.6 - - + +
417G GLY 2.8 31.2 + - - -
418G CYS* 3.3 16.1 + - - -
421G ILE* 2.9 28.3 - - + -
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Residues in contact with ARG 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409G LEU 3.2 1.8 + - - -
410G ALA 3.0 8.9 + - - +
412G MET* 1.3 79.9 - - - +
414G SER* 1.3 63.7 + - - +
417G GLY* 2.9 29.0 + - - -
418G CYS* 3.4 24.5 + - - -
419G ASP* 4.6 9.5 - - - +
421G ILE* 4.4 1.9 - - - +
452G PHE* 3.5 20.6 - - + -
456G THR* 3.0 40.2 + - - +
457G GLY* 3.0 9.5 + - - -
458G VAL* 2.9 42.5 - - + +
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Residues in contact with SER 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ALA* 3.0 38.9 - - - +
226B GLY* 3.5 12.1 - - - -
410G ALA* 2.6 20.7 + - - +
411G TYR* 4.5 0.7 - - - -
413G ARG* 1.3 81.4 - - - +
415G GLY* 1.3 64.2 + - - +
417G GLY* 4.4 1.6 + - - -
452G PHE* 5.8 0.7 - - - -
456G THR* 5.6 4.7 - - - +
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Residues in contact with GLY 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLY* 4.7 6.9 - - - -
411G TYR* 2.7 39.5 + - - +
414G SER* 1.3 76.2 - - - +
416G LEU* 1.3 60.7 + - - -
417G GLY 3.2 3.4 + - - -
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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