Contacts of the helix formed by residues 340 - 351 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 4.6 2.1 + - - -
339B ILE* 1.3 94.2 - - - +
341B LYS* 1.3 63.0 + - - +
342B GLU* 3.1 14.0 + - - +
343B GLY 3.3 1.9 + - - -
344B ILE* 3.2 5.2 + - - +
369B TYR* 3.6 24.9 - - - -
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B SER* 6.1 0.7 - - - -
340B SER* 1.3 73.1 - - - +
342B GLU* 1.3 60.0 + - + +
344B ILE* 3.8 9.1 - - - +
345B ASP* 2.9 27.3 + - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B SER* 3.1 9.6 + - - +
341B LYS* 1.3 80.2 - - + +
343B GLY* 1.3 55.9 + - - +
345B ASP* 2.9 6.6 + - + +
346B LEU* 2.8 31.0 + - - +
367B HIS* 3.2 22.0 - - + -
368B PRO* 3.2 39.1 - - + +
369B TYR* 4.2 9.2 - - + +
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PHE* 3.9 6.0 - - - -
339B ILE* 3.5 11.4 - - - -
340B SER* 3.3 3.0 + - - -
342B GLU* 1.3 77.8 - - - +
344B ILE* 1.3 61.3 + - - +
346B LEU* 3.1 5.1 + - - +
347B LEU* 2.9 22.6 + - - +
369B TYR* 3.2 42.3 - - - -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 5.5 0.2 - - + -
332B LEU* 3.6 21.8 - - + +
333B SER* 3.9 25.4 - - - +
336B TYR* 3.6 26.0 - - + +
339B ILE* 3.2 27.3 - - + +
340B SER 3.2 11.5 + - - +
341B LYS* 3.9 8.1 - - - +
343B GLY* 1.3 73.6 - - - +
345B ASP* 1.3 57.5 + - - +
347B LEU* 3.6 9.3 - - + +
348B GLU* 2.8 56.3 + - + +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B LYS 2.9 20.6 + - - +
342B GLU* 2.9 10.7 + - + +
344B ILE* 1.3 75.7 - - - +
346B LEU* 1.3 61.3 + - - +
348B GLU* 3.7 6.7 + - - +
349B SER* 2.9 41.1 + - - -
352B ARG* 4.5 7.6 + - - -
367B HIS* 2.8 25.1 + - - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.9 18.4 - - + -
247B PHE* 4.1 6.7 - - + -
342B GLU 2.8 14.8 + - - +
343B GLY* 3.3 8.5 - - - +
345B ASP* 1.3 70.4 - - - +
347B LEU* 1.3 66.7 - - - +
349B SER* 3.1 4.7 + - - -
350B MET* 3.1 38.2 + - + +
359B ILE* 3.7 16.8 - - + -
364B ALA* 4.1 8.1 - - - -
367B HIS* 3.5 35.4 + - + +
369B TYR* 4.0 20.0 - - + -
370B LEU* 3.9 26.0 - - + -
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLY* 3.4 26.5 - - - +
247B PHE* 3.5 28.2 - - + -
248B ALA* 4.2 8.7 - - + +
251B LEU* 4.3 8.5 - - + -
267B LEU* 5.4 0.2 - - + -
332B LEU* 3.9 24.9 - - + -
336B TYR* 4.1 28.7 - - + -
343B GLY 2.9 12.1 + - - +
344B ILE* 3.6 13.5 - - + +
346B LEU* 1.3 77.3 - - - +
348B GLU* 1.3 63.8 + - + +
349B SER 3.2 1.0 + - - -
350B MET* 3.4 3.5 + - - +
351B LEU* 3.3 33.3 + - + +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ILE 5.5 0.3 - - - +
331B ASP* 5.3 1.7 - - - +
332B LEU* 3.9 34.9 + - + +
333B SER* 4.5 1.9 + - - -
344B ILE* 2.8 43.1 + - + +
345B ASP* 4.2 5.6 - - - +
347B LEU* 1.3 74.3 - - + +
349B SER* 1.3 58.9 + - - +
351B LEU* 3.5 12.7 + - - +
352B ARG* 3.0 39.3 + - - +
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B ASP* 2.9 30.7 + - - -
346B LEU* 3.1 5.4 + - - -
348B GLU* 1.3 73.8 - - - +
350B MET* 1.3 65.7 + - - +
351B LEU 3.2 1.3 - - - -
352B ARG* 3.4 32.4 + - - +
357B LYS 5.6 1.3 - - - -
358B ARG* 3.4 2.1 - - - -
359B ILE* 3.0 44.1 + - - -
367B HIS* 5.9 0.2 - - - -
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Residues in contact with MET 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.3 10.8 - - + -
141B LEU* 4.0 20.6 - - + -
240B ILE* 3.6 32.1 - - + +
241B TRP* 3.6 13.5 - - - -
243B THR* 3.6 22.4 - - + -
244B GLY* 3.7 25.8 - - - -
247B PHE* 4.1 14.4 - - - -
346B LEU* 3.1 36.8 + - + +
347B LEU 3.4 7.2 + - - +
349B SER* 1.3 77.9 - - - +
351B LEU* 1.3 57.5 + - - +
352B ARG 3.4 1.1 - - - -
358B ARG* 3.0 20.1 - - - +
359B ILE* 3.8 6.9 - - + +
364B ALA* 4.4 4.5 - - + -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B TRP* 3.4 56.6 - - + +
244B GLY* 3.9 6.7 - - - -
245B CYS 3.9 8.1 - - - +
267B LEU* 3.7 29.2 - - + -
268B PHE* 4.0 10.5 - - + -
301B ILE* 3.6 24.2 - - + +
332B LEU* 4.7 8.5 - - + -
347B LEU* 3.3 34.8 + - + +
348B GLU* 3.5 9.8 + - - +
349B SER 3.2 1.0 - - - -
350B MET* 1.3 77.3 - - - +
352B ARG* 1.3 63.5 + - - +
353B PHE 3.5 1.4 + - - -
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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