Contacts of the helix formed by residues 349 - 354 (chain B) in PDB entry 1MOX
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 PRO 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B LEU* 1.3 89.6 - - + +
350B VAL* 1.3 64.4 + - + +
351B ALA 3.0 1.2 + - - -
352B PHE* 3.4 7.1 + - + +
353B ARG* 3.3 48.8 + - - +
384B GLN* 3.9 31.0 - - + +
385B ALA* 3.3 15.9 - - + -
18D HIS* 4.3 21.8 - - + +
44D GLU 5.3 0.7 - - - +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 5.5 1.3 - - + -
326B SER* 5.3 2.9 - - - -
328B ASN* 5.6 1.1 - - - +
348B LEU* 4.0 22.7 - - + -
349B PRO* 1.3 82.3 - - + +
351B ALA* 1.3 63.7 + - - +
353B ARG* 4.6 5.8 - - - +
354B GLY* 2.8 25.2 + - - +
355B ASP* 3.6 24.4 + - + +
360B THR* 5.7 1.5 - - + +
17D PHE* 3.2 58.8 - - + -
44D GLU* 5.5 0.4 - - + -
1H NAG 3.6 15.0 - - - +
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Residues in contact with ALA 351 (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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326B SER* 3.7 8.9 + - - +
327B ILE 3.2 27.1 - - - +
328B ASN* 4.6 9.4 - - - +
347B ILE* 4.8 4.0 - - + -
348B LEU 3.0 17.7 + - - +
349B PRO 3.0 0.2 + - - -
350B VAL* 1.3 82.9 - - - +
352B PHE* 1.3 69.3 + - + +
354B GLY* 3.6 4.3 + - - -
361B PRO 4.4 2.3 - - - +
362B PRO 4.0 1.7 - - - -
363B LEU* 3.4 31.9 + - + +
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Residues in contact with PHE 352 (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* 4.3 10.3 - - + -
348B LEU 4.6 0.9 - - - -
349B PRO* 3.4 5.6 + - + +
351B ALA* 1.3 73.9 - - + +
353B ARG* 1.3 63.5 + - - +
362B PRO* 3.7 16.3 - - - +
363B LEU* 3.7 31.2 + - + +
365B PRO* 3.8 25.1 - - + -
368B LEU* 3.8 22.2 - - + -
385B ALA* 3.7 18.8 - - + -
386B TRP* 3.5 31.2 - - - -
387B PRO* 3.4 35.9 - - + -
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Residues in contact with ARG 353 (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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349B PRO* 3.3 42.6 + - - +
350B VAL* 4.4 3.0 - - - +
352B PHE* 1.3 80.5 - - - +
354B GLY* 1.3 69.3 + - - +
362B PRO* 3.8 13.7 - - - +
13D THR* 6.5 1.1 - - - +
14D GLN* 3.1 35.6 - - - +
17D PHE* 4.2 26.4 + - - +
18D HIS* 5.3 7.1 + - - -
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Residues in contact with GLY 354 (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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350B VAL* 2.8 24.5 + - - +
351B ALA 4.1 1.1 - - - -
352B PHE 3.5 1.2 - - - -
353B ARG* 1.3 89.5 - - - +
355B ASP* 1.3 61.6 + - - -
356B SER* 4.2 0.9 + - - -
360B THR* 3.4 14.6 - - - -
361B PRO 4.2 0.4 - - - -
362B PRO* 4.1 12.6 - - - -
13D THR* 4.6 8.3 - - - -
17D PHE* 5.8 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