Contacts of the helix formed by residues 351 - 357 (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 351 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D ARG* 5.4 7.3 + - - +
243D GLN* 3.4 20.9 - - - +
246D ILE* 3.9 5.8 - - - -
349D ARG 3.7 0.6 + - - +
350D ALA* 1.3 73.3 - - - +
352D LEU* 1.3 64.2 + - - +
353D LYS* 3.6 11.0 + - - +
354D GLN* 2.9 46.1 + - - +
355D LEU* 3.0 26.7 + - - +
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Residues in contact with LEU 352 (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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174D ILE* 4.4 22.0 - - + +
177D LEU* 4.0 19.3 - - + +
178D THR* 3.9 38.1 + - + +
181D ARG* 3.9 32.2 - - - +
242D VAL* 3.8 27.1 - - + -
243D GLN* 4.5 0.2 + - - -
246D ILE* 3.9 21.2 - - + +
351D ASP* 1.3 73.7 - - - +
353D LYS* 1.3 66.0 + - - +
355D LEU* 3.4 3.0 + - + +
356D MET* 3.1 25.5 + - - +
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Residues in contact with LYS 353 (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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181D ARG* 5.3 1.8 - - - +
351D ASP* 3.4 12.3 + - - +
352D LEU* 1.3 79.1 - - - +
354D GLN* 1.3 66.8 + - + +
355D LEU 3.5 0.2 + - - -
356D MET* 3.5 15.3 + - - +
357D VAL* 3.7 17.4 + - + +
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Residues in contact with GLN 354 (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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349D ARG 4.5 2.5 + - - +
350D ALA* 3.7 12.9 - - + +
351D ASP* 2.9 42.1 + - - +
353D LYS* 1.3 79.9 - - + +
355D LEU* 1.3 66.2 + - - +
357D VAL* 3.7 10.8 + - - +
358D HIS* 3.4 19.2 + - - +
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Residues in contact with LEU 355 (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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174D ILE* 3.8 20.4 - - + -
246D ILE* 3.7 41.5 - - + -
249D MET* 4.2 9.9 - - + -
337D PHE* 3.4 27.4 - - + +
340D LYS* 4.9 4.0 - - + -
341D CYS* 3.9 14.1 - - - -
350D ALA* 3.5 22.0 - - + -
351D ASP 3.0 16.9 + - - +
352D LEU* 4.0 4.0 - - + +
354D GLN* 1.3 74.1 - - - +
356D MET* 1.3 68.6 + - - +
357D VAL 3.1 1.8 - - - -
358D HIS* 3.0 18.8 + - + +
361D ILE* 3.3 17.5 - - - +
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Residues in contact with MET 356 (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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171D ILE* 4.8 7.4 - - + -
174D ILE* 3.8 25.2 - - + +
175D LYS* 4.1 31.9 - - + -
178D THR* 5.5 2.0 - - - -
352D LEU 3.1 18.1 + - - +
353D LYS* 3.6 9.0 - - - +
355D LEU* 1.3 78.7 - - - +
357D VAL* 1.3 62.6 + - + +
361D ILE* 3.1 38.7 - - + +
362D LYS* 4.9 1.7 + - - +
365D ASP* 4.8 10.3 - - - +
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Residues in contact with VAL 357 (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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353D LYS* 3.7 17.0 + - + +
354D GLN* 3.7 13.5 - - - +
355D LEU 3.1 0.6 - - - -
356D MET* 1.3 83.5 - - + +
358D HIS* 1.3 69.1 + - - +
359D ALA 3.7 0.3 + - - -
362D LYS* 3.4 33.6 + - - +
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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