Contacts of the helix formed by residues 367 - 377 (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 VAL 367 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300C MSE 3.8 25.1 - - + -
334C VAL* 5.0 2.7 - - + -
363C PHE* 3.1 24.5 + - + +
366C ASP* 1.3 87.1 - - + +
368C LEU* 1.3 69.4 + - - +
369C ARG 3.5 1.1 - - - -
370C PRO* 3.5 3.6 - - - +
371C PHE* 3.2 24.4 + - - +
385C THR* 4.3 12.4 + - + +
386C PRO* 4.5 15.7 - - + -
389C PHE* 3.7 41.5 - - + -
400C ARG* 4.6 5.4 - - - +
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Residues in contact with LEU 368 (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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103C GLY 5.4 1.1 - - - +
106C VAL* 4.3 12.3 - - + -
107C PHE* 3.9 17.7 - - + -
171C ILE* 3.8 25.6 - - + -
195C VAL* 3.7 29.2 - - + -
197C GLU* 4.9 0.9 - - - +
300C MSE 4.9 3.1 - - - -
363C PHE* 3.0 36.8 + - + +
364C ARG* 3.4 18.8 - - + +
367C VAL* 1.3 78.0 - - - +
369C ARG* 1.3 64.0 + - - +
371C PHE* 3.3 5.2 + - + +
372C PHE* 3.0 34.8 + - + +
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Residues in contact with ARG 369 (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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106C VAL* 3.5 29.5 + - + +
107C PHE* 5.6 2.5 - - - -
109C GLU* 4.1 15.8 + - - +
110C GLY* 3.3 36.0 + - - +
112C TYR* 4.2 6.0 - - - -
364C ARG 3.0 18.4 + - - +
365C HIS* 3.7 16.6 + - + +
368C LEU* 1.3 77.6 - - - +
370C PRO* 1.3 65.7 - - + +
372C PHE* 3.4 3.9 + - - +
373C ASP* 2.9 67.8 + - - +
377C VAL* 5.9 1.0 - - - +
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Residues in contact with PRO 370 (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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365C HIS 3.4 13.0 - - - +
366C ASP* 3.5 17.5 - - - +
367C VAL* 3.5 13.0 - - - +
369C ARG* 1.3 97.9 - - + +
371C PHE* 1.3 55.2 + - - +
373C ASP* 3.7 8.7 - - + +
374C GLN* 3.0 29.3 + - - +
381C PRO 4.8 1.6 - - - +
383C ALA* 3.5 23.6 - - + +
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Residues in contact with PHE 371 (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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193C VAL* 3.2 28.0 - - + -
194C ALA 4.3 1.8 - - - -
195C VAL* 4.2 5.8 - - + -
298C PRO* 3.9 19.5 - - + -
300C MSE 3.5 39.7 - - + -
332C TYR* 3.9 31.6 - + - -
367C VAL 3.2 19.1 + - - +
368C LEU* 3.5 4.3 - - + +
369C ARG 3.3 0.2 - - - -
370C PRO* 1.3 79.9 - - - +
372C PHE* 1.3 69.2 + + - +
374C GLN* 3.6 7.3 + - - +
375C TYR* 3.3 45.9 - + - -
383C ALA* 4.1 1.7 - - - +
385C THR* 3.6 23.1 - - + +
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Residues in contact with PHE 372 (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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76C VAL* 3.8 26.7 - - + -
107C PHE* 3.4 31.4 - + + -
112C TYR* 3.3 12.3 - + + +
169C GLY* 4.2 3.1 - - - -
170C MSE 3.8 25.4 - - - -
171C ILE* 4.3 5.2 - - + -
193C VAL* 3.7 28.5 - - + -
195C VAL* 3.4 27.1 - - + -
368C LEU* 3.0 25.3 + - + +
369C ARG* 3.9 2.7 - - - +
371C PHE* 1.3 75.6 - + - +
373C ASP* 1.3 62.1 + - - +
375C TYR* 3.2 2.3 + - - -
376C LEU* 2.9 52.4 + - + +
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Residues in contact with ASP 373 (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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112C TYR* 2.6 28.0 + - - -
369C ARG* 2.9 59.0 + - - +
370C PRO* 3.7 8.8 - - + +
372C PHE* 1.3 77.3 - - - +
374C GLN* 1.3 64.1 + - - +
377C VAL* 3.0 36.4 + - - +
380C ALA* 3.2 24.1 - - + +
381C PRO* 5.6 1.3 - - + +
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Residues in contact with GLN 374 (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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370C PRO 3.0 16.3 + - - +
371C PHE* 3.6 7.6 - - - +
372C PHE 3.2 0.2 - - - -
373C ASP* 1.3 79.2 - - - +
375C TYR* 1.3 98.7 + - + +
377C VAL 4.8 3.1 - - - +
380C ALA* 4.5 7.2 - - - +
381C PRO 3.7 18.1 + - - +
382C LYS* 3.7 39.6 - - + +
383C ALA* 3.0 31.6 + - - +
385C THR* 4.6 3.8 + - - -
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Residues in contact with TYR 375 (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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167C LYS* 3.8 7.9 - - - +
192C LYS* 3.4 46.2 - - + +
193C VAL* 4.1 16.2 - - + -
298C PRO* 3.4 33.6 - - + +
329C THR* 3.8 17.0 + - - -
330C LEU* 5.3 0.7 - - - +
332C TYR* 5.3 1.2 + - - -
371C PHE* 3.3 33.5 - + - -
372C PHE 3.2 4.2 + - - +
374C GLN* 1.3 113.8 + - + +
376C LEU* 1.3 60.1 + - - +
382C LYS* 5.4 1.4 + - - -
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Residues in contact with LEU 376 (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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74C PRO* 3.4 19.5 - - + +
75C ILE 4.6 3.4 - - - +
112C TYR* 3.7 13.5 - - + -
165C ASN* 2.8 27.5 + - - -
167C LYS* 3.8 13.0 - - + +
168C VAL 3.5 38.1 - - - +
169C GLY* 3.9 9.2 - - - +
192C LYS* 3.9 9.0 - - + -
193C VAL* 3.6 14.4 - - + -
372C PHE* 2.9 48.0 + - + +
373C ASP 3.4 0.2 + - - -
374C GLN 3.6 0.2 - - - -
375C TYR* 1.3 86.9 - - - +
377C VAL* 1.3 57.9 + - - +
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Residues in contact with VAL 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PRO* 4.1 12.3 - - + -
110C GLY 5.0 6.1 - - - +
112C TYR* 3.6 19.3 - - + +
165C ASN* 4.7 0.4 - - - +
167C LYS* 5.4 0.9 - - - -
369C ARG* 5.9 0.9 - - - +
373C ASP* 3.0 37.8 + - + +
374C GLN 4.8 2.6 - - - +
375C TYR 5.6 0.2 - - - -
376C LEU* 1.3 78.4 - - - +
378C ASP* 1.3 75.8 - - - +
379C GLY 3.3 0.5 + - - -
380C ALA* 3.2 26.8 + - + +
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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