Contacts of the helix formed by residues 327 - 337 (chain O) in PDB entry 5MQF
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 ALA 327 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182N MET* 5.7 4.7 - - + -
184N ILE 5.3 3.6 - - - +
185N ASP* 4.9 21.3 - - + +
324O GLY* 3.4 13.1 + - - +
325O ASN 3.2 0.4 - - - -
326O VAL* 1.3 77.9 - - - +
328O GLY* 1.3 59.9 + - - +
330O ARG* 3.1 6.5 + - - +
331O GLN* 2.9 31.1 + - - +
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Residues in contact with GLY 328 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316O TYR* 5.4 1.5 - - - +
320O GLU* 4.3 17.8 - - - +
323O LEU 5.3 0.4 - - - -
324O GLY* 2.5 23.5 + - - -
327O ALA* 1.3 73.1 - - - +
329O ALA* 1.3 55.9 + - - +
331O GLN* 3.9 3.8 - - - +
332O VAL* 2.9 32.5 + - - +
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Residues in contact with ALA 329 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320O GLU* 4.6 5.3 - - + +
325O ASN 3.0 19.9 + - - +
326O VAL* 4.4 2.9 - - - +
328O GLY* 1.3 75.9 - - - +
330O ARG* 1.3 57.0 + - - +
332O VAL* 4.2 5.3 - - - +
333O PHE* 2.9 30.9 + - - +
353O GLU* 5.1 17.3 - - + -
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Residues in contact with ARG 330 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N GLU 5.3 5.2 - - - +
178N GLU 6.2 0.2 - - - -
179N ILE 5.1 0.2 - - - +
180N ASP* 3.2 42.7 - - - +
182N MET* 5.6 2.0 - - + -
326O VAL 3.1 20.3 + - - +
327O ALA* 3.1 9.0 + - - +
329O ALA* 1.3 75.2 - - - +
331O GLN* 1.3 59.4 + - - +
333O PHE* 3.4 1.2 + - - +
334O GLU* 2.9 29.6 + - - +
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Residues in contact with GLN 331 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N ASP 4.5 2.4 + - - -
182N MET* 6.3 3.6 - - + -
327O ALA 2.9 14.5 + - - +
328O GLY* 4.3 4.0 - - - +
330O ARG* 1.3 76.5 - - - +
332O VAL* 1.3 57.9 + - - +
334O GLU* 3.8 5.8 - - - +
335O ARG* 2.9 30.5 + - - +
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Residues in contact with VAL 332 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316O TYR* 4.4 25.4 - - + +
320O GLU* 6.0 1.1 - - + -
328O GLY 2.9 22.0 + - - +
329O ALA* 4.2 4.9 - - - +
331O GLN* 1.3 75.6 - - - +
333O PHE* 1.3 59.7 + - - +
335O ARG* 4.1 4.2 - - - +
336O TRP* 2.9 32.1 + - - +
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Residues in contact with PHE 333 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N ASP* 5.2 5.8 - - + -
329O ALA 2.9 21.4 + - - +
330O ARG* 3.8 5.2 - - - +
332O VAL* 1.3 75.5 - - - +
334O GLU* 1.3 59.5 + - - +
336O TRP* 4.3 3.1 - - - +
337O MET* 2.9 32.4 + - - +
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Residues in contact with GLU 334 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N ASP* 4.5 12.2 - - + +
181N ARG* 5.0 9.2 - - + +
330O ARG 2.9 17.8 + - - +
331O GLN* 3.9 7.2 - - - +
332O VAL 3.3 0.2 - - - -
333O PHE* 1.3 75.3 - - - +
335O ARG* 1.3 59.6 + - - +
337O MET* 3.5 5.3 + - - +
338O GLU* 3.0 28.4 + - - +
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Residues in contact with ARG 335 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303O ILE* 6.1 4.9 - - + -
331O GLN 2.9 18.9 + - - +
332O VAL* 4.1 4.5 - - - +
334O GLU* 1.3 75.8 - - - +
336O TRP* 1.3 60.4 + - - +
338O GLU* 3.0 24.4 + - - +
339O TRP* 3.4 10.2 + - - +
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Residues in contact with TRP 336 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332O VAL 2.9 20.1 + - - +
333O PHE* 4.3 3.8 - - - +
335O ARG* 1.3 76.5 - - - +
337O MET* 1.3 56.0 + - - +
338O GLU 3.2 0.4 - - - -
339O TRP 5.0 1.8 - - - -
340O GLN 2.8 26.7 - - - +
341O PRO* 4.4 5.0 - - - +
342O GLU* 5.4 8.9 + - + -
346O TRP* 6.2 4.9 - - + -
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Residues in contact with MET 337 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333O PHE 2.9 23.0 + - - +
334O GLU* 3.6 6.3 - - - +
335O ARG 3.2 0.2 - - - -
336O TRP* 1.3 75.4 - - - +
338O GLU* 1.3 61.8 + - - +
340O GLN 5.1 0.7 - - - -
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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