Contacts of the helix formed by residues 341 - 345 (chain C) in PDB entry 1MPX
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 SER 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C SER* 2.8 35.2 + - - -
174C SER* 4.5 1.9 - - - -
198C SER* 4.3 5.8 + - - -
339C ARG* 3.2 7.6 + - - -
340C HIS* 1.3 93.3 + - - +
342C GLN* 1.3 60.2 + - - +
343C VAL* 3.1 12.0 + - - +
344C ASN* 3.2 14.6 + - - +
345C TYR* 3.2 19.4 - - - -
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Residues in contact with GLN 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C PRO 3.9 3.4 + - - +
338C TRP* 3.3 22.0 - - + +
339C ARG* 3.1 64.8 + - - +
340C HIS 3.2 2.6 + - - -
341C SER* 1.3 76.5 - - - +
343C VAL* 1.3 63.1 + - - +
344C ASN 3.1 0.4 - - - -
345C TYR* 3.1 15.0 + - - -
346C ASP 2.9 26.0 + - - +
347C GLY* 3.5 6.3 - - - -
349C ALA 2.7 29.5 + - - -
350C LEU* 3.8 8.1 - - - +
360C ALA* 3.4 10.4 - - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C SER* 5.0 0.4 - - - +
197C GLU* 3.7 31.2 - - + +
198C SER* 6.1 0.2 - - - +
302C LEU* 3.9 13.0 - - + -
338C TRP* 3.7 34.0 - - + -
341C SER* 3.1 10.0 - - - +
342C GLN* 1.3 77.8 - - - +
344C ASN* 1.3 65.6 + - - +
345C TYR 3.4 0.4 - - - -
360C ALA* 3.5 9.4 - - - +
363C PHE* 3.4 38.6 - - + -
364C ARG* 2.9 26.6 + - + +
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Residues in contact with ASN 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 5.6 7.0 - - - +
101C SER* 5.7 1.9 - - - +
102C ALA* 3.5 7.1 + - - +
103C GLY* 3.2 39.3 + - - +
171C ILE* 5.7 1.7 - - - +
172C GLY* 5.9 0.2 - - - -
173C SER* 4.0 15.0 - - - +
197C GLU* 3.2 28.5 + - - +
341C SER* 3.2 10.3 + - - +
342C GLN 3.1 1.2 - - - -
343C VAL* 1.3 89.4 - - - +
345C TYR* 1.3 74.7 + - + +
364C ARG* 3.8 10.6 - - - +
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Residues in contact with TYR 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ARG* 5.1 8.8 + - - -
101C SER* 6.1 3.8 - - - -
102C ALA* 4.7 17.7 - - + -
339C ARG* 3.9 31.2 - - - +
341C SER* 3.2 34.1 - - - -
342C GLN* 3.1 7.6 + - - +
344C ASN* 1.3 90.7 - - + +
346C ASP* 1.3 63.6 + - - +
358C ASP* 4.0 2.6 - - - +
360C ALA* 3.2 8.5 - - - +
364C ARG* 3.2 21.2 + - - -
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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