Contacts of the helix formed by residues 347 - 356 (chain E) in PDB entry 6N0M
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 HIS 347 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340E GLN 5.6 0.4 + - - -
341E ASP 4.0 20.3 + - - -
342E TYR* 3.8 32.0 - + + -
343E THR* 3.7 9.5 + - - +
344E TRP 3.7 1.2 + - - -
346E ASP* 1.3 81.7 + - - +
348E GLY* 1.3 59.6 + - - +
349E TYR 3.3 1.7 - - - +
350E SER* 3.1 12.8 + - - +
351E LEU* 2.8 36.7 + - - +
476E THR* 5.3 8.6 - - + +
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Residues in contact with GLY 348 (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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342E TYR* 3.9 13.8 - - - -
343E THR 3.4 8.8 + - - -
344E TRP* 3.8 11.9 - - - -
347E HIS* 1.3 79.1 - - - +
349E TYR* 1.3 57.6 - - - +
351E LEU* 3.6 2.3 - - - +
352E ILE* 2.9 33.3 + - - +
469E LEU* 4.5 0.9 - - - -
472E LEU* 3.7 22.2 - - - +
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Residues in contact with TYR 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E TRP* 2.8 52.7 + + + +
345E GLU* 4.3 12.8 - - - +
348E GLY* 1.3 73.7 - - - +
350E SER* 1.3 59.3 + - - +
352E ILE* 2.9 20.1 + - - +
353E GLN* 2.9 55.4 + - - +
360E GLY 3.6 16.4 - - - -
361E GLN* 3.9 20.8 + - - +
364E ASP* 3.4 35.0 + - + +
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Residues in contact with SER 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E ASP* 4.7 1.7 - - - -
347E HIS* 3.1 22.8 + - - +
349E TYR* 1.3 78.4 - - - +
351E LEU* 1.3 65.0 + - - +
353E GLN* 4.0 13.7 - - - +
354E ARG* 3.1 31.8 + - - +
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Residues in contact with LEU 351 (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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342E TYR* 3.5 7.2 - - - +
347E HIS 2.8 22.8 + - - +
348E GLY 3.6 3.6 - - - +
350E SER* 1.3 71.4 + - - +
352E ILE* 1.3 69.4 + - - +
354E ARG* 3.6 25.5 + - - +
355E LEU* 3.3 35.7 + - + +
472E LEU* 3.3 43.3 - - + +
475E ILE* 3.8 11.7 - - + -
476E THR* 3.4 17.5 - - - +
479E MET* 4.0 14.8 - - - -
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Residues in contact with ILE 352 (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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195E ILE* 3.9 19.1 - - + -
199E VAL* 4.6 4.5 - - + -
344E TRP* 4.0 13.2 - - + -
348E GLY 2.9 19.8 + - - +
349E TYR 3.4 6.5 - - - +
351E LEU* 1.3 75.5 - - - +
353E GLN* 1.3 51.4 + - - +
355E LEU* 2.8 7.7 + - - +
356E TYR* 2.5 44.5 + - + +
359E GLY 4.6 0.2 - - - -
360E GLY* 3.3 32.8 - - - +
363E LEU* 4.5 10.5 - - + -
468E LEU* 4.5 15.5 - - + -
472E LEU* 3.3 34.8 - - + -
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Residues in contact with GLN 353 (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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349E TYR* 2.9 74.2 + - - +
350E SER* 4.1 11.3 - - - +
352E ILE* 1.3 74.1 - - - +
354E ARG* 1.3 66.9 + - - +
355E LEU 3.2 0.2 - - - -
356E TYR 4.1 1.3 - - - -
357E PRO* 3.6 40.1 - - + +
360E GLY* 4.6 5.1 - - - -
361E GLN 5.0 1.1 - - - +
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Residues in contact with ARG 354 (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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350E SER* 3.1 21.4 + - - +
351E LEU* 3.8 31.3 - - - +
353E GLN* 1.3 79.4 - - - +
355E LEU* 1.3 67.0 + - + +
357E PRO* 5.0 2.8 - - - +
479E MET* 4.2 23.9 - - - +
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Residues in contact with LEU 355 (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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191E LEU* 3.9 39.3 - - + -
192E ALA* 4.0 21.9 - - - +
195E ILE* 3.6 37.5 - - + -
351E LEU* 3.3 35.2 - - + +
352E ILE 2.8 6.3 + - - +
354E ARG* 1.3 88.6 - - + +
356E TYR* 1.3 58.4 + - - +
357E PRO* 3.9 5.4 - - - +
475E ILE* 4.5 0.9 - - + -
479E MET* 4.6 11.0 - - + -
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Residues in contact with TYR 356 (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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99E LEU* 3.5 20.5 - - + +
100E LEU* 3.5 21.8 - - + +
105E GLY* 5.8 0.7 - - - -
106E PRO* 4.5 10.8 - - + -
192E ALA 4.9 2.7 - - - -
195E ILE* 3.5 22.4 - - + -
196E GLN* 3.3 45.2 + - + -
199E VAL* 4.1 28.7 - - + -
352E ILE* 2.5 17.5 + - + +
355E LEU* 1.3 76.3 - - - +
357E PRO* 1.3 67.3 - - + +
358E GLU* 3.4 5.6 - - + -
359E GLY* 3.3 29.6 + - - -
360E GLY* 2.9 26.9 + - - -
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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