Contacts of the helix formed by residues 376 - 385 (chain B) in PDB entry 1ZQ1
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 TYR 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 6.3 1.3 - - + -
147A GLU* 5.0 1.1 - - - +
205A GLN 3.5 16.3 + - - -
206A ARG* 5.7 0.2 + - - -
207A SER* 5.1 13.0 + - - -
210A ARG* 5.5 3.1 + - - -
1000A ASP* 3.3 48.4 + - + +
339B LEU* 4.3 21.2 - - + +
341B HIS* 3.1 38.3 - + + +
372B ASN 5.3 0.2 + - - -
373B LEU 4.3 1.3 - - - +
374B ASN 4.8 0.4 - - - +
375B VAL* 1.3 97.4 - - + +
377B SER* 1.3 66.0 - - - +
378B THR 3.4 2.9 - - - +
379B GLY* 3.1 3.5 + - - -
380B ARG* 3.0 30.1 + - - +
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 5.7 2.9 + - - +
145A PHE* 4.7 18.5 - - - -
376B TYR* 1.3 70.6 - - - +
378B THR* 1.3 66.0 + - - +
380B ARG* 3.1 23.3 + - - +
381B LYS* 2.9 30.2 + - - +
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Residues in contact with THR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 4.0 7.4 - - - -
147A GLU* 2.3 43.9 + - - +
341B HIS* 4.0 13.5 - - + -
342B THR 3.3 25.4 - - - +
344B ASN* 3.4 22.1 + - - +
347B ILE* 4.6 5.8 - - + -
376B TYR* 3.4 0.9 - - - +
377B SER* 1.3 76.2 - - - +
379B GLY* 1.3 62.1 + - - +
381B LYS* 3.2 12.6 + - - +
382B LEU* 3.1 23.2 + - + +
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B HIS* 3.7 16.9 + - - -
373B LEU* 3.1 34.3 - - - +
376B TYR 3.1 8.5 + - - -
378B THR* 1.3 77.3 - - - +
380B ARG* 1.3 65.0 + - - +
382B LEU* 3.0 8.0 + - - +
383B LEU 2.9 19.4 + - - -
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.5 36.7 + - - +
40A GLU* 3.0 38.1 + - - +
41A LEU* 4.1 18.7 - - + +
373B LEU 3.1 8.2 + - - +
374B ASN* 3.2 19.9 + - - +
375B VAL 3.1 17.9 + - - -
376B TYR 3.0 4.8 + - - +
377B SER* 3.1 46.5 + - - +
379B GLY* 1.3 76.2 - - - +
381B LYS* 1.3 61.0 + - - +
383B LEU* 3.3 7.8 + - - +
384B LYS* 3.1 23.7 + - - +
436C THR* 3.6 23.4 + - - -
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 6.1 0.2 - - - -
344B ASN* 2.5 43.5 + - - +
347B ILE* 4.6 22.7 - - + +
377B SER* 2.9 20.3 + - - +
378B THR* 3.3 9.6 - - - +
379B GLY 3.0 0.2 - - - -
380B ARG* 1.3 76.5 - - - +
382B LEU* 1.3 64.4 + - - +
384B LYS* 3.1 18.4 + - - +
385B ALA* 3.1 12.0 + - - +
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Residues in contact with LEU 382 (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 GLY 4.0 15.9 - - - +
341B HIS* 4.2 1.6 - - - -
342B THR* 3.8 27.6 - - - +
347B ILE* 3.4 27.8 - - + -
350B ILE* 3.5 34.1 - - + -
362B MSE 4.4 7.6 - - + -
373B LEU* 4.4 10.8 - - + -
378B THR 3.1 14.4 + - - +
379B GLY* 3.0 7.7 + - - +
381B LYS* 1.3 79.9 - - - +
383B LEU* 1.3 61.8 + - - +
385B ALA* 3.2 9.2 + - + +
387B VAL* 3.2 43.2 + - + +
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Residues in contact with LEU 383 (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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39A TYR* 5.5 3.4 - - - +
373B LEU* 3.5 45.5 - - + +
374B ASN* 3.4 31.0 - - - +
379B GLY 2.9 6.1 + - - -
380B ARG* 3.6 11.0 - - - +
382B LEU* 1.3 73.3 - - - +
384B LYS* 1.3 53.8 - - - +
385B ALA 2.9 4.0 - - - -
386B GLY* 2.6 29.3 + - - -
387B VAL 3.8 13.0 + - - +
389B PRO* 4.2 15.7 - - + -
416B ARG* 4.8 11.3 + - - +
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Residues in contact with LYS 384 (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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41A LEU* 3.8 22.8 + - + +
42A SER* 3.4 30.9 + - - +
43A ALA* 3.8 10.1 - - - +
351B GLU* 4.4 7.2 - - - +
380B ARG 3.1 10.4 + - - +
381B LYS* 3.1 12.2 + - - +
383B LEU* 1.3 77.5 - - - +
385B ALA* 1.3 56.4 + - - +
386B GLY 3.2 1.6 + - - -
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Residues in contact with ALA 385 (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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347B ILE* 4.5 9.2 - - + -
350B ILE* 5.1 1.1 - - + -
351B GLU* 4.0 39.7 - - + +
354B VAL* 3.2 30.1 - - - +
381B LYS 3.1 9.5 + - - +
382B LEU* 3.5 14.1 - - - +
383B LEU 2.9 1.2 + - - -
384B LYS* 1.3 75.1 - - - +
386B GLY* 1.3 58.8 + - - +
387B VAL* 4.5 5.8 - - + -
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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