Contacts of the helix formed by residues 331 - 343 (chain E) 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 SER 331 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163E GLU* 2.7 30.5 + - - -
330E PHE* 1.3 74.3 - - - +
332E LEU* 1.3 56.0 + - - +
333E GLU* 3.0 24.6 + - - -
334E PHE* 3.1 10.2 + - - +
335E GLN* 2.9 25.5 + - - +
363E ARG* 3.2 15.9 + - - -
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Residues in contact with LEU 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E GLY 6.3 0.2 - - - +
330E PHE 4.2 2.9 - - - +
331E SER* 1.3 74.6 + - - +
333E GLU* 1.3 66.7 + - + +
335E GLN* 3.6 25.6 - - - +
336E ASP* 2.9 30.3 + - - +
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Residues in contact with GLU 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E SER* 3.0 14.1 + - - +
332E LEU* 1.3 84.2 + - + +
334E PHE* 1.3 58.8 + - - +
336E ASP* 4.6 1.6 - - - -
337E PHE* 2.9 24.6 + - - +
358E HIS* 3.3 15.3 - - - -
359E ALA* 3.9 20.2 - - + -
360E PHE* 3.7 24.2 - - - +
363E ARG* 3.6 23.0 + - + +
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Residues in contact with PHE 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLU* 3.2 42.8 - - + +
166E LEU* 3.9 28.7 - - + -
253E LEU* 4.5 14.6 - - + -
257E ALA* 4.1 13.7 - - + -
325E LEU* 3.5 22.2 - - + -
330E PHE* 3.8 15.3 - + - -
331E SER* 3.1 11.2 + - - +
333E GLU* 1.3 77.2 - - - +
335E GLN* 1.3 62.8 + - - +
337E PHE* 2.9 17.6 + + + +
338E VAL* 3.0 28.6 + - + +
360E PHE* 3.4 39.3 - + + -
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Residues in contact with GLN 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325E LEU* 3.9 22.9 - - + +
326E PRO 3.5 18.2 + - - +
327E SER* 4.0 10.4 - - - +
328E GLY 4.6 8.3 - - - +
330E PHE* 2.8 34.3 + - + +
331E SER 2.9 13.1 + - - +
332E LEU* 3.6 27.3 - - - +
334E PHE* 1.3 74.9 - - - +
336E ASP* 1.3 61.1 + - - +
338E VAL* 3.1 7.8 - - - +
339E ASN* 2.9 32.8 - - - +
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Residues in contact with ASP 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E LEU 2.9 18.8 + - - +
333E GLU* 3.9 4.0 - - - +
335E GLN* 1.3 74.1 - - - +
337E PHE* 1.3 65.7 + - - +
339E ASN* 3.4 9.2 + - - +
340E LYS* 3.0 62.2 + - - +
358E HIS* 2.6 28.1 + - + +
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Residues in contact with PHE 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E SER* 4.1 10.8 - - - -
174E ILE* 3.9 15.5 - - + -
249E MET* 3.9 22.2 - - + -
253E LEU* 4.0 18.2 - - + -
333E GLU 2.9 15.1 + - - +
334E PHE* 2.9 13.4 + + - +
336E ASP* 1.3 78.4 - - - +
338E VAL* 1.3 63.3 + - - +
340E LYS* 3.4 4.0 + - - +
341E CYS* 3.3 25.2 + - - -
355E LEU* 3.4 31.6 - - + -
358E HIS* 3.6 25.5 + + + -
360E PHE* 3.6 25.4 - + + -
361E ILE* 3.5 29.8 - - + -
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Residues in contact with VAL 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E GLY* 4.5 2.7 - - - +
253E LEU* 4.3 17.3 - - + -
254E VAL* 4.2 22.4 - - + -
324E LYS* 5.1 1.1 - - - -
325E LEU* 3.8 36.6 - - + +
334E PHE* 3.0 29.5 + - + +
335E GLN* 3.1 19.7 - - - +
337E PHE* 1.3 74.2 - - - +
339E ASN* 1.3 71.3 + - - +
341E CYS* 2.9 20.6 + - - +
342E LEU* 2.9 21.2 + - + +
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Residues in contact with ASN 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E PRO 5.1 1.2 - - - +
324E LYS* 4.1 20.9 - - - +
325E LEU 5.0 0.3 + - - -
335E GLN* 2.9 25.7 + - - +
336E ASP* 3.7 9.4 - - - +
337E PHE 3.3 0.2 - - - -
338E VAL* 1.3 86.0 - - - +
340E LYS* 1.3 57.6 + - + +
342E LEU* 3.1 6.3 + - - +
343E ILE* 3.1 34.2 + - - +
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Residues in contact with LYS 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E ASP* 3.0 50.7 + - - +
337E PHE* 3.8 5.2 - - - +
338E VAL 3.3 0.2 - - - -
339E ASN* 1.3 75.2 - - + +
341E CYS* 1.3 56.5 + - - +
342E LEU 3.4 0.4 - - - -
343E ILE* 3.9 17.9 - - + -
348E GLU 6.0 0.2 - - - +
349E ARG* 3.4 8.3 - - - +
350E ALA* 2.9 47.9 + - + +
354E GLN* 5.7 5.6 - - - +
355E LEU* 4.8 4.3 - - + -
358E HIS* 4.3 13.3 - - + -
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Residues in contact with CYS 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ILE* 3.7 24.7 - - - +
247E TRP* 3.3 17.2 + - - -
249E MET* 3.6 29.8 - - - -
250E GLY* 3.8 12.6 - - - -
253E LEU* 5.3 0.2 - - - -
337E PHE* 3.3 24.4 + - - -
338E VAL* 2.9 13.1 + - - +
340E LYS* 1.3 76.5 - - - +
342E LEU* 1.3 58.2 + - - +
343E ILE 3.5 0.7 - - - -
349E ARG* 3.0 19.8 - - - -
355E LEU* 4.1 14.6 - - - -
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Residues in contact with LEU 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E TRP* 3.3 61.6 - - + +
250E GLY* 4.1 7.4 - - - -
251E LEU* 3.7 11.7 - - + +
254E VAL* 4.1 22.7 - - + -
322E PRO* 3.3 24.0 - - + +
323E PRO* 3.4 34.5 - - + +
338E VAL* 2.9 20.3 + - + +
339E ASN* 3.1 6.4 + - - +
341E CYS* 1.3 80.0 - - - +
343E ILE* 1.3 65.7 + - - +
344E LYS 3.2 2.4 + - - -
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Residues in contact with ILE 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E PRO* 5.2 2.2 - - - -
339E ASN 3.1 15.7 + - - +
340E LYS* 3.9 29.8 - - + +
341E CYS 3.5 0.6 - - - -
342E LEU* 1.3 76.5 - - - +
344E LYS* 1.3 62.3 + - - +
345E ASN 3.3 21.8 - - - +
348E GLU* 3.3 36.3 - - + +
349E ARG* 2.8 41.2 + - - +
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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