Contacts of the helix formed by residues 340 - 351 (chain A) in PDB entry 3NIE
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 SER 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 4.6 2.2 + - - -
339A ILE* 1.3 80.8 - - - +
341A LYS* 1.3 63.6 + - - +
342A GLU* 3.6 11.9 + - - +
343A GLY 3.1 17.5 + - - -
344A ILE* 3.3 20.7 + - - +
369A TYR* 3.5 14.2 - - - -
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Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A SER* 6.0 1.6 - - - +
340A SER* 1.3 70.8 - - - +
342A GLU* 1.3 61.0 + - + +
344A ILE* 3.4 9.0 + - + +
345A ASP* 2.8 29.2 + - + +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A SER* 3.2 11.1 + - - +
341A LYS* 1.3 77.5 - - + +
343A GLY* 1.3 63.4 + - - +
345A ASP* 2.9 18.9 + - - +
346A LEU 3.0 10.6 + - - -
367A HIS* 3.3 13.1 - - + -
368A PRO* 3.5 38.4 - - + +
369A TYR* 4.0 13.3 - - + +
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Residues in contact with GLY 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A PHE* 4.1 3.5 - - - -
339A ILE* 3.4 13.6 - - - +
340A SER* 3.1 13.1 + - - -
342A GLU* 1.3 72.6 - - - +
344A ILE* 1.3 57.2 + - - +
346A LEU* 3.1 5.5 + - - +
347A LEU* 3.0 27.5 + - - +
369A TYR* 3.1 36.4 - - - -
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LEU* 3.5 28.9 - - + +
333A SER* 3.4 30.7 - - - +
336A TYR* 3.5 16.8 - - + +
339A ILE* 3.2 23.6 - - + +
340A SER 3.3 14.6 + - - +
341A LYS* 3.7 11.4 - - + +
343A GLY* 1.3 70.8 - - - +
345A ASP* 1.3 62.0 + - - +
347A LEU* 3.6 9.0 - - + +
348A GLU* 2.7 54.4 + - + +
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Residues in contact with ASP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 2.8 16.7 + - + +
342A GLU* 2.9 12.8 + - + +
344A ILE* 1.3 77.5 - - - +
346A LEU* 1.3 51.6 + - - +
348A GLU* 3.2 7.0 + - - +
349A SER* 2.8 50.9 + - - -
352A ARG* 5.1 3.8 + - - -
367A HIS* 2.6 28.1 + - - +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.1 9.9 - - + -
247A PHE* 4.0 13.9 - - + -
342A GLU 3.0 10.6 + - - +
343A GLY* 3.4 9.2 - - - +
345A ASP* 1.3 71.8 + - - +
347A LEU* 1.3 67.1 + - - +
349A SER* 3.3 2.6 + - - -
350A MET* 3.1 39.3 + - + +
359A ILE* 3.9 16.2 - - + -
364A ALA* 4.2 12.8 - - + -
367A HIS* 3.7 33.4 - - + +
369A TYR* 3.9 25.4 - - + -
370A LEU* 4.0 22.2 - - + -
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY* 3.6 25.8 - - - +
247A PHE* 3.7 24.9 - - + -
248A ALA* 4.2 6.5 - - + +
251A LEU* 3.9 13.2 - - + -
267A LEU* 5.7 0.2 - - + -
332A LEU* 4.3 20.2 - - + -
336A TYR* 3.8 33.4 - - + -
343A GLY 3.0 11.7 + - - +
344A ILE* 3.7 13.7 - - + +
346A LEU* 1.3 79.3 - - - +
348A GLU* 1.3 60.2 + - - +
350A MET* 3.5 2.3 + - - +
351A LEU* 3.3 42.6 + - + +
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ILE 5.2 3.1 - - - +
331A ASP* 5.6 0.9 - - - +
332A LEU* 3.6 36.1 + - + +
333A SER* 5.1 1.5 + - - -
344A ILE* 2.7 43.9 + - + +
345A ASP* 4.0 5.0 + - - +
347A LEU* 1.3 74.0 - - - +
349A SER* 1.3 62.1 + - - +
351A LEU* 3.3 15.0 + - - +
352A ARG* 3.4 39.5 + - - +
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ASP* 2.8 36.3 + - - -
346A LEU 3.8 3.4 - - - -
347A LEU 3.3 0.2 - - - -
348A GLU* 1.3 77.8 - - - +
350A MET* 1.3 61.6 + - - +
351A LEU 3.3 0.7 + - - -
352A ARG* 3.4 27.8 + - - +
357A LYS 5.7 1.1 - - - -
358A ARG* 3.3 16.1 - - - +
359A ILE* 3.3 36.7 + - - +
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Residues in contact with MET 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.2 9.2 - - + -
141A LEU* 3.7 38.4 - - + -
240A ILE* 3.5 30.3 - - + +
241A TRP* 3.6 12.1 - - - -
243A THR* 3.7 13.2 - - + -
244A GLY* 3.9 27.8 - - - -
247A PHE* 4.1 16.4 - - - -
346A LEU* 3.1 26.4 + - + +
347A LEU 3.9 2.0 - - - +
348A GLU 3.3 0.2 - - - -
349A SER* 1.3 76.5 - - - +
351A LEU* 1.3 58.5 + - - +
352A ARG 3.4 0.2 - - - -
358A ARG* 3.2 22.3 - - - +
359A ILE* 3.7 7.6 - - + -
364A ALA* 4.2 10.3 - - + -
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TRP* 3.4 34.3 - - + +
244A GLY* 3.6 25.1 - - - -
245A CYS 3.7 4.9 - - - +
267A LEU* 3.8 25.6 - - + -
268A PHE* 4.2 15.9 - - + -
301A ILE* 3.4 29.9 - - + +
332A LEU* 4.7 8.5 - - + -
347A LEU* 3.3 38.3 + - + +
348A GLU* 3.3 10.9 + - - +
349A SER 3.1 0.8 - - - -
350A MET* 1.3 77.3 - - - +
352A ARG* 1.3 60.0 + - - +
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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