Contacts of the helix formed by residues 350 - 354 (chain C) in PDB entry 2NMP
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 LEU 350 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C LEU* 3.6 24.5 - - + -
325C ALA* 4.1 12.8 - - + -
326C GLU* 4.8 2.0 - - + -
329C LEU* 3.9 25.5 - - + +
349C GLU* 1.3 75.7 - - - +
351C PRO* 1.3 67.5 - - - +
352C ALA* 3.2 11.2 - - + +
353C ILE* 3.0 41.0 + - + -
354C MET* 3.3 21.8 + - - +
371C ASP* 3.8 28.7 - - - +
373C LEU 3.9 13.7 - - - +
374C ILE* 5.0 1.3 - - + -
52D PRO* 4.3 5.6 - - + -
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Residues in contact with PRO 351 (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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162C PRO* 4.0 15.5 - - + -
349C GLU* 3.1 32.1 - - - +
350C LEU* 1.3 82.4 - - - +
352C ALA* 1.3 62.2 + - - +
353C ILE 3.1 1.2 + - - -
354C MET 3.3 3.1 + - - -
355C THR* 3.8 11.0 - - + -
356C HIS* 2.9 30.3 + - - +
369C ILE* 4.0 14.8 - - + -
373C LEU* 3.3 36.8 - - + +
375C ARG* 3.9 11.2 - - + +
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Residues in contact with ALA 352 (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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350C LEU* 3.0 5.4 + - + +
351C PRO* 1.3 79.2 - - - +
353C ILE* 1.3 70.3 + - + +
357C ALA* 3.9 6.9 - - - +
364C ARG* 3.4 42.3 + - - +
369C ILE* 3.7 17.1 - - + +
370C SER 3.7 25.5 + - - +
371C ASP* 4.4 6.3 - - - +
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Residues in contact with ILE 353 (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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322C LEU* 4.3 14.4 - - + -
326C GLU* 4.8 3.8 - - - +
350C LEU* 3.0 28.9 + - + +
352C ALA* 1.3 90.9 - - + +
354C MET* 1.3 63.7 + - + +
357C ALA* 4.1 12.2 - - - +
364C ARG* 5.8 1.8 - - - +
371C ASP* 4.2 13.2 - - - +
52D PRO* 3.3 40.2 - - + +
53D GLY* 3.8 17.2 - - - +
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Residues in contact with MET 354 (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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337C LEU* 3.4 31.4 - - + -
338C ALA 4.2 17.5 - - - -
339C GLU* 3.2 20.5 - - + +
349C GLU* 3.4 11.4 - - + +
350C LEU 3.5 26.9 - - - +
351C PRO 3.3 1.6 + - - -
352C ALA 3.6 0.2 - - - -
353C ILE* 1.3 86.4 - - + +
355C THR* 1.3 67.1 + - - +
356C HIS 3.2 2.7 + - - -
357C ALA* 3.4 14.7 + - - +
358C SER 5.1 0.2 + - - -
49D GLN* 3.6 31.9 - - - +
52D PRO* 4.0 12.3 - - - -
53D GLY* 3.9 14.8 - - - +
59D GLU* 5.5 0.3 - - - +
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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