Contacts of the helix formed by residues 328 - 339 (chain Y) in PDB entry 2Q4G
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 CYS 328 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297Y ASP* 3.7 20.9 - - + +
300Y ALA* 3.5 32.5 - - + -
324Y PHE* 4.2 12.3 - - - -
325Y THR 3.3 10.6 + - - -
326Y ALA 3.0 0.6 - - - -
327Y ALA* 1.3 77.3 - - - +
329Y CYS* 1.3 72.5 + - - +
330Y SER* 3.3 2.9 - - - -
331Y HIS* 3.2 32.9 - - + +
332Y PHE* 3.3 20.1 + - - -
347Y ILE* 5.2 2.0 - - - -
352Y LEU* 5.3 0.2 - - - -
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Residues in contact with CYS 329 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325Y THR 3.8 15.9 - - - -
326Y ALA* 3.1 12.6 + - - +
328Y CYS* 1.3 79.9 - - - +
330Y SER* 1.3 66.7 + - - +
331Y HIS 3.1 1.3 - - - -
332Y PHE* 4.5 2.5 - - - +
333Y SER* 2.9 25.8 + - - -
347Y ILE* 6.0 1.3 - - - -
352Y LEU* 3.8 26.5 - - - -
356Y GLY* 3.8 25.8 - - - +
359Y GLU* 3.4 19.1 - - - +
360Y LEU* 4.0 12.2 - - + +
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Residues in contact with SER 330 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326Y ALA 4.4 0.8 + - - -
327Y ALA 5.3 2.5 + - - -
328Y CYS* 4.5 0.5 - - - +
329Y CYS* 1.3 74.8 - - - +
331Y HIS* 1.3 82.5 + - - +
333Y SER* 3.2 7.6 - - - -
334Y SER* 2.9 24.0 + - - -
359Y GLU* 3.0 26.3 + - - -
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Residues in contact with HIS 331 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297Y ASP 5.7 0.2 - - - -
300Y ALA 5.1 1.3 - - - +
301Y ARG* 3.7 51.6 + - + +
304Y CYS* 3.9 22.4 - - + +
305Y GLU* 6.1 1.4 - - + +
308Y LEU* 4.9 0.3 - - - +
327Y ALA 4.3 6.9 + - - -
328Y CYS* 3.2 26.4 + - + +
329Y CYS 3.1 0.6 - - - -
330Y SER* 1.3 89.3 + - - +
332Y PHE* 1.3 56.4 + - - +
334Y SER* 2.6 33.9 + - - -
335Y VAL* 3.1 9.4 + - - +
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Residues in contact with PHE 332 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300Y ALA* 3.8 25.8 - - + -
303Y LEU* 4.9 4.7 - - + -
304Y CYS* 3.4 30.2 - - - -
307Y LEU* 4.6 7.0 - - + -
317Y LEU* 3.9 20.4 - - + -
319Y VAL* 4.5 4.9 - - + -
324Y PHE* 4.4 4.5 - + - -
328Y CYS* 3.3 24.0 + - - +
329Y CYS* 4.3 2.0 - - - +
331Y HIS* 1.3 78.2 - - - +
333Y SER* 1.3 63.2 + - - +
335Y VAL* 2.9 21.0 + - + +
336Y LEU* 2.9 18.2 + - + +
342Y LEU* 5.6 2.0 - - + -
345Y LEU* 3.8 34.5 - - + -
347Y ILE* 3.9 23.8 - - + -
360Y LEU* 3.8 20.0 - - + -
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Residues in contact with SER 333 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329Y CYS 2.9 20.5 + - - -
330Y SER* 3.2 9.4 - - - -
332Y PHE* 1.3 76.3 - - - +
334Y SER* 1.3 62.1 + - - +
336Y LEU* 3.3 4.3 + - - +
337Y ALA 3.2 16.8 + - - -
359Y GLU* 2.6 35.2 + - - +
360Y LEU* 3.8 10.4 - - - +
362Y GLN* 4.4 1.6 - - - +
363Y GLY* 3.0 28.1 + - - -
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Residues in contact with SER 334 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308Y LEU* 4.4 8.7 - - - -
330Y SER* 2.9 14.5 + - - -
331Y HIS* 2.6 18.3 + - - -
333Y SER* 1.3 70.7 - - - +
335Y VAL* 1.3 56.8 + - - -
337Y ALA* 3.5 4.2 + - - +
338Y GLN* 2.8 51.3 + - - +
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Residues in contact with VAL 335 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304Y CYS* 3.7 34.3 - - + +
307Y LEU* 4.0 20.6 - - + -
308Y LEU* 3.5 32.3 - - + -
331Y HIS 3.1 2.4 + - - +
332Y PHE* 2.9 12.6 + - + +
334Y SER* 1.3 75.6 - - - +
336Y LEU* 1.3 64.4 + - + +
339Y ASN* 2.6 54.9 + - + +
342Y LEU* 4.5 13.2 - - + -
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Residues in contact with LEU 336 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332Y PHE* 2.9 18.4 + - + +
333Y SER* 3.3 7.2 + - - +
335Y VAL* 1.3 79.4 - - + +
337Y ALA* 1.3 59.6 + - - +
338Y GLN 3.6 0.2 + - - -
339Y ASN 4.3 7.0 - - - +
340Y ARG* 4.7 0.2 + - - -
342Y LEU* 4.9 8.3 - - + -
345Y LEU* 4.8 14.4 - - + -
360Y LEU* 3.9 39.3 - - + +
363Y GLY 3.9 2.8 - - - +
364Y LEU* 3.9 24.9 - - + +
369Y SER* 4.1 19.6 - - - -
370Y VAL* 4.7 2.3 + - - +
371Y LEU* 3.8 44.8 + - + -
374Y LEU* 5.7 4.7 - - + -
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Residues in contact with ALA 337 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333Y SER 3.2 5.8 + - - +
334Y SER* 4.0 6.5 - - - +
335Y VAL 3.2 0.6 - - - -
336Y LEU* 1.3 80.0 - - - +
338Y GLN* 1.3 64.8 + - + +
340Y ARG* 3.4 20.3 + - - -
363Y GLY* 3.0 28.3 - - - +
366Y GLN* 3.4 26.9 - - + +
367Y PRO 4.7 1.9 - - - +
368Y GLY 4.6 1.5 - - - +
369Y SER* 5.6 2.0 - - - +
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Residues in contact with GLN 338 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308Y LEU* 3.7 21.7 - - + +
334Y SER* 2.8 41.2 + - - +
337Y ALA* 1.3 86.1 - - + +
339Y ASN* 1.3 58.1 + - - +
340Y ARG* 3.0 21.5 + - - +
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Residues in contact with ASN 339 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307Y LEU* 2.8 41.9 + - - +
308Y LEU* 5.0 0.7 - - + -
312Y CYS* 5.6 2.2 + - - -
314Y LEU 5.7 0.6 + - - -
335Y VAL* 2.6 38.3 + - + +
336Y LEU* 4.3 4.5 - - - +
338Y GLN* 1.3 73.5 - - - +
340Y ARG* 1.3 68.4 + - - +
341Y PHE* 2.6 38.4 + - - +
342Y LEU* 2.6 26.5 + - + +
370Y VAL* 3.3 14.9 - - - +
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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