Contacts of the helix formed by residues 370 - 379 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D ILE* 5.0 1.3 - - - +
368D GLU 4.4 0.2 + - - -
369D VAL* 1.3 69.4 - - - +
371D PHE* 1.3 58.9 + - - +
372D ALA* 4.5 1.6 + - - +
373D GLY* 3.2 28.2 + - - -
374D TRP* 2.9 27.0 + - - +
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Residues in contact with PHE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 5.4 3.6 - - + -
165D ILE* 3.6 38.8 - - + -
168D LYS* 5.1 7.2 - - + -
169D VAL* 5.2 2.0 - - + -
198D VAL* 3.7 33.2 - - + -
199D ASN 4.5 3.8 - - - -
202D GLY* 3.2 41.7 - - - +
203D GLU 4.2 0.9 - - - -
204D ILE* 4.0 21.8 - - + -
369D VAL* 2.9 24.8 + - + +
370D ASP* 1.3 70.8 - - - +
372D ALA* 1.3 65.0 + - - +
374D TRP* 2.9 27.5 + + - +
375D LEU* 3.0 19.7 + - + +
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Residues in contact with ALA 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ASN 5.0 0.4 - - - -
200D SER 3.2 27.4 - - - +
201D ARG 4.1 3.1 - - - +
202D GLY* 3.9 15.4 - - - +
370D ASP* 3.5 1.7 + - - +
371D PHE* 1.3 83.8 - - - +
373D GLY* 1.3 62.4 + - - +
375D LEU* 3.4 4.7 + - - +
376D CYS* 3.1 31.0 + - - -
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Residues in contact with GLY 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D ASP* 3.2 30.3 + - - -
371D PHE 3.1 1.4 - - - -
372D ALA* 1.3 75.1 - - - +
374D TRP* 1.3 65.9 + - - +
376D CYS* 4.2 3.8 - - - +
377D SER* 3.1 24.6 + - - -
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Residues in contact with TRP 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 5.7 2.5 - - + -
154D VAL* 4.0 28.9 - - + -
158D ALA* 4.2 14.1 - - + -
161D ILE* 4.0 21.5 - - + -
162D PRO* 3.4 38.6 - - + +
165D ILE* 3.7 35.7 - - + -
370D ASP* 2.9 14.7 + - - +
371D PHE* 2.9 20.0 + + - +
373D GLY* 1.3 76.4 - - - +
375D LEU* 1.3 75.5 + - + +
377D SER* 3.1 11.6 + - - -
378D THR* 2.8 45.6 + - - -
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLY* 4.3 8.1 - - - -
151D LEU* 6.3 0.2 - - + -
154D VAL* 3.8 24.9 - - + -
198D VAL* 3.7 23.6 - - + -
199D ASN 3.2 31.9 - - - +
200D SER* 4.5 3.1 - - - +
371D PHE* 3.0 17.0 + - + +
372D ALA* 3.8 8.5 - - - +
374D TRP* 1.3 86.4 - - + +
376D CYS* 1.3 62.5 + - - +
377D SER 3.1 1.1 - - - -
378D THR* 2.7 25.1 + - - -
379D ILE* 3.0 39.0 + - + +
381D LEU* 6.5 0.4 - - + -
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Residues in contact with CYS 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D SER* 3.9 22.9 - - - -
372D ALA 3.1 20.0 + - - +
373D GLY* 4.3 4.0 - - - +
375D LEU* 1.3 80.1 - - - +
377D SER* 1.3 63.2 + - - +
379D ILE* 3.4 18.8 + - - +
380D GLY 3.8 2.3 + - - +
381D LEU* 3.8 43.1 - - + +
382D ASN* 3.7 17.3 + - + +
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Residues in contact with SER 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D GLY 3.1 15.8 + - - -
374D TRP* 3.1 19.3 + - - -
376D CYS* 1.3 80.0 - - - +
378D THR* 1.3 59.7 + - - +
379D ILE 4.2 3.1 - - - +
382D ASN* 4.5 20.2 + - - +
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Residues in contact with THR 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL* 4.4 10.8 - - + +
157D LYS* 4.1 21.0 - - + +
158D ALA* 3.7 38.3 - - + +
374D TRP* 2.8 38.6 + - - -
375D LEU* 2.7 18.7 + - - -
377D SER* 1.3 74.9 + - - +
379D ILE* 1.3 61.7 + - + +
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Residues in contact with ILE 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ASP 5.6 0.7 - - - +
148D GLY* 3.8 23.1 - - - +
153D GLN* 6.0 0.4 - - + -
154D VAL* 3.9 11.0 - - + -
157D LYS* 3.4 36.8 - - + +
375D LEU* 3.0 39.3 + - + +
376D CYS* 3.5 9.1 - - - +
377D SER 3.3 3.2 - - - +
378D THR* 1.3 87.1 - - + +
380D GLY* 1.3 67.6 + - - +
381D LEU* 6.2 0.9 - - + -
382D ASN* 4.6 6.9 - - - +
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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