Contacts of the helix formed by residues 370 - 379 (chain H) in PDB entry 4MNE
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 ASP 370 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368H GLU 4.5 0.2 + - - -
369H VAL* 1.3 73.4 - - - +
371H PHE* 1.3 54.9 + - - +
372H ALA* 4.3 7.1 + - - +
373H GLY* 3.3 24.8 + - - -
374H TRP* 2.6 36.2 + - - +
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Residues in contact with PHE 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H LEU* 5.0 6.5 - - + -
165H ILE* 3.5 27.4 - - + -
168H LYS* 5.9 9.0 - - + -
169H VAL* 5.2 2.2 - - + -
198H VAL* 3.7 29.4 - - + -
202H GLY* 3.4 27.1 - - - +
204H ILE* 3.4 34.5 - - + -
369H VAL* 2.9 16.3 + - + +
370H ASP* 1.3 67.8 + - - +
372H ALA* 1.3 61.2 + - - +
373H GLY 3.1 1.3 - - - -
374H TRP* 3.4 35.7 - + - -
375H LEU* 2.8 40.8 + - + +
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Residues in contact with ALA 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H ASN 5.1 0.4 - - - -
200H SER 3.4 24.2 - - - +
201H ARG* 4.2 2.9 - - - -
202H GLY* 3.8 21.6 - - - +
370H ASP* 4.3 7.4 + - - +
371H PHE* 1.3 77.3 - - - +
373H GLY* 1.3 57.8 + - - +
375H LEU* 3.6 5.4 - - - +
376H CYS* 3.0 33.9 + - - +
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Residues in contact with GLY 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370H ASP* 3.3 27.7 + - - -
371H PHE 3.1 0.4 - - - -
372H ALA* 1.3 78.5 - - - +
374H TRP* 1.3 60.9 + - - +
375H LEU 3.2 0.6 + - - -
376H CYS* 3.5 5.4 + - - -
377H SER* 2.9 25.6 + - - -
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Residues in contact with TRP 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H LEU* 5.6 1.3 - - + -
154H VAL* 3.8 30.1 - - + -
158H ALA* 4.8 5.4 - - + -
160H ARG 5.1 0.2 - - - -
161H ILE* 3.9 20.2 - - + -
162H PRO* 3.4 38.2 - - + +
164H GLN* 5.2 4.3 - - - -
165H ILE* 3.4 31.0 - - + -
369H VAL* 5.3 1.3 - - + -
370H ASP 2.6 21.2 + - - +
371H PHE* 3.1 34.7 + + - +
373H GLY* 1.3 72.6 - - - +
375H LEU* 1.3 66.9 + - + +
377H SER* 2.7 18.5 + - - -
378H THR* 3.1 36.1 - - + +
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Residues in contact with LEU 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H GLY* 4.7 3.6 - - - -
154H VAL* 3.9 22.2 - - + -
198H VAL* 3.6 26.5 - - + -
199H ASN 3.5 27.6 - - - +
200H SER* 4.9 2.7 - - - +
371H PHE* 2.8 25.8 + - + +
372H ALA* 3.6 5.4 - - - +
374H TRP* 1.3 91.4 - - + +
376H CYS* 1.3 60.4 + - - +
377H SER 3.1 4.7 - - - -
378H THR* 3.1 12.8 + - - +
379H ILE* 3.0 51.1 + - + +
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Residues in contact with CYS 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H SER* 4.4 26.2 - - - -
372H ALA 3.0 19.8 + - - +
373H GLY* 3.5 7.1 + - - +
375H LEU* 1.3 78.1 - - - +
377H SER* 1.3 55.7 + - - +
379H ILE* 3.0 17.5 - - - +
380H GLY* 3.7 20.9 - - - +
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Residues in contact with SER 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373H GLY 2.9 12.9 + - - -
374H TRP* 2.7 24.1 + - - -
376H CYS* 1.3 76.4 - - - +
378H THR* 1.3 64.7 + - - +
379H ILE* 3.2 2.7 + - - -
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Residues in contact with THR 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H VAL* 4.9 5.9 - - - +
157H LYS* 4.2 16.2 + - - +
158H ALA* 4.2 25.4 - - + -
374H TRP* 3.1 37.9 - - + +
375H LEU* 3.1 17.5 + - - +
377H SER* 1.3 80.1 - - - +
379H ILE* 1.3 73.4 + - - +
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Residues in contact with ILE 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ASP 5.1 3.8 - - - +
148H GLY* 4.1 21.3 - - - +
154H VAL* 4.8 7.0 - - + -
157H LYS* 3.4 41.7 - - + +
375H LEU* 3.0 38.6 + - + +
376H CYS* 3.0 32.5 - - - -
377H SER 3.2 2.2 - - - -
378H THR* 1.3 92.7 - - - +
380H GLY* 1.3 65.9 + - - +
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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