Contacts of the helix formed by residues 321 - 328 (chain A) in PDB entry 3MH4
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 PHE 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A THR 5.4 0.2 - - - -
271A GLU* 3.3 62.4 - - + +
272A LEU 4.9 0.7 - - - -
287A GLY 5.2 0.2 + - - -
288A ALA* 3.6 19.6 - - + +
289A PHE 4.9 6.1 - - - +
320A SER* 1.3 80.6 - - - +
322A ALA* 1.3 80.3 + - + +
323A ALA 3.1 1.8 - - - -
324A LEU* 3.4 8.9 + - - +
325A ARG* 3.3 18.5 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A SER* 3.4 5.9 + - - +
321A PHE* 1.3 91.5 - - + +
323A ALA* 1.3 59.1 + - - +
324A LEU 3.1 0.9 - - - -
325A ARG* 3.5 11.4 - - + +
326A ALA* 2.9 32.7 + - - +
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.1 8.5 - - + -
319A SER* 3.9 10.3 - - - +
320A SER* 3.2 37.0 + - - +
321A PHE 3.1 0.2 - - - -
322A ALA* 1.3 78.8 - - - +
324A LEU* 1.3 59.6 + - - +
326A ALA* 4.3 2.5 - - - +
327A GLN* 3.0 45.3 + - - +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ALA* 3.8 20.9 - - + +
290A VAL* 5.3 5.6 - - + -
310A ILE* 3.7 37.5 - - + -
312A SER 4.5 3.6 - - - +
313A LEU* 4.8 1.8 - - + -
318A ILE* 3.4 32.8 - - + -
320A SER 4.0 0.2 + - - -
321A PHE 3.4 9.9 + - - +
322A ALA 3.1 0.4 - - - -
323A ALA* 1.3 77.1 - - - +
325A ARG* 1.3 66.5 + - - +
326A ALA 3.0 3.6 + - - -
328A VAL* 3.0 50.8 + - + +
339A LEU* 4.7 9.2 - - + -
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLU* 5.0 3.8 - - - +
266A GLY* 4.9 20.2 - - - +
267A ILE 5.7 1.0 - - - +
268A MET* 3.6 28.9 - - - +
321A PHE 3.3 5.6 + - - +
322A ALA* 3.1 20.8 + - + +
324A LEU* 1.3 80.0 - - - +
326A ALA* 1.3 59.3 + - - +
328A VAL* 4.3 5.6 - - - +
329A GLY* 3.7 14.0 + - - -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ALA 2.9 15.2 + - - +
323A ALA* 4.3 3.1 - - - +
325A ARG* 1.3 77.4 - - - +
327A GLN* 1.3 68.4 + - + +
328A VAL 3.3 0.2 - - - -
329A GLY* 3.0 12.2 + - - -
330A THR* 3.2 16.0 + - - +
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LEU* 3.3 25.5 - - + +
316A LYS* 5.2 10.4 + - - +
317A PRO 5.4 2.3 - - - +
318A ILE* 3.2 27.9 - - - +
323A ALA* 3.0 26.2 + - - +
324A LEU 4.3 0.7 - - - +
326A ALA* 1.3 79.3 - - + +
328A VAL* 1.3 57.9 - - - +
329A GLY 3.4 0.5 + - - -
330A THR* 3.6 10.3 - - - +
331A MET* 3.2 24.6 - - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLY 3.6 17.0 - - - +
265A LEU* 4.3 29.2 - - + +
266A GLY* 4.8 3.6 - - - +
313A LEU* 3.5 29.2 - - + -
324A LEU* 3.0 41.1 + - + +
325A ARG* 4.3 6.3 - - - +
327A GLN* 1.3 75.0 - - - +
329A GLY* 1.3 60.1 + - - +
330A THR 3.6 0.4 - - - -
331A MET* 4.3 16.9 + - - +
337A LEU* 4.1 11.5 - - + +
339A LEU* 5.5 3.6 - - + -
352A LEU* 5.0 4.5 - - - +
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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