Contacts of the helix formed by residues 347 - 356 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341D ASP 3.7 23.1 + - - -
342D TYR* 3.7 35.4 - + + -
343D THR 3.5 9.0 - - - +
344D TRP 3.4 1.6 + - - -
346D ASP* 1.3 92.6 + - - +
348D GLY* 1.3 68.1 + - - +
349D TYR 3.2 1.5 - - - +
350D SER* 3.1 14.8 + - - +
351D LEU* 3.0 23.9 + - - +
476D THR* 5.3 8.3 - - + -
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Residues in contact with GLY 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D TYR* 3.7 22.3 - - - -
343D THR 3.2 8.6 + - - -
344D TRP* 4.0 4.9 - - - -
347D HIS* 1.3 75.7 - - - +
349D TYR* 1.3 68.7 + - - +
351D LEU* 3.4 1.1 + - - +
352D ILE* 3.2 26.0 + - - +
469D LEU* 4.3 5.6 - - - -
472D LEU* 3.8 15.4 - - - +
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Residues in contact with TYR 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D TRP* 3.0 46.0 + + - +
345D GLU* 4.6 12.1 - - - +
347D HIS 5.2 0.2 - - - +
348D GLY* 1.3 77.6 - - - +
350D SER* 1.3 64.9 + - - +
351D LEU 2.9 2.3 + - - -
352D ILE* 3.1 0.9 + - - +
353D GLN* 2.9 50.1 + - + +
360D GLY* 3.6 30.5 - - - -
361D GLN* 3.8 18.9 + - - +
364D ASP* 2.8 31.8 + - + -
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Residues in contact with SER 350 (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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346D ASP* 4.7 2.4 - - - +
347D HIS* 3.1 22.0 + - - +
349D TYR* 1.3 79.1 - - - +
351D LEU* 1.3 58.7 + - - +
353D GLN* 3.8 23.6 + - - +
354D ARG* 3.4 27.6 + - - +
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Residues in contact with LEU 351 (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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342D TYR* 3.4 4.0 - - - +
347D HIS 3.0 15.2 + - - +
348D GLY 3.8 4.5 - - - +
349D TYR 2.9 0.2 + - - -
350D SER* 1.3 77.1 - - - +
352D ILE* 1.3 67.4 + - - +
354D ARG* 3.6 29.3 + - - +
355D LEU* 3.2 29.6 + - + +
472D LEU* 3.3 44.2 - - + +
475D ILE* 3.7 14.8 - - + -
476D THR* 3.3 19.3 - - + +
479D MET* 4.0 15.9 - - - -
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Residues in contact with ILE 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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195D ILE* 3.8 20.2 - - + -
198D LEU* 6.6 0.2 - - + -
199D VAL* 4.6 4.9 - - + -
344D TRP* 4.2 11.7 - - + -
348D GLY 3.2 13.7 + - - +
349D TYR 3.1 5.9 + - - +
351D LEU* 1.3 74.4 - - - +
353D GLN* 1.3 53.7 + - - +
354D ARG 3.0 0.2 - - - -
355D LEU* 2.7 11.5 + - - -
356D TYR* 2.6 46.8 + - + +
360D GLY* 3.4 31.6 - - - +
363D LEU* 4.4 8.7 - - + -
468D LEU* 4.5 14.6 - - + -
472D LEU* 3.4 32.5 - - + -
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Residues in contact with GLN 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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349D TYR* 2.9 53.9 + - + +
350D SER* 3.8 25.3 - - - +
352D ILE* 1.3 76.3 - - - +
354D ARG* 1.3 60.2 + - - +
356D TYR 4.3 1.3 - - - -
357D PRO* 3.3 36.6 - - + +
360D GLY* 4.7 2.7 - - - -
361D GLN 5.1 0.4 - - - +
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Residues in contact with ARG 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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350D SER 3.4 23.3 + - - +
351D LEU* 3.6 30.8 - - - +
352D ILE 3.0 1.2 - - - -
353D GLN* 1.3 80.2 - - - +
355D LEU* 1.3 72.9 + - - +
356D TYR 3.8 0.3 + - - -
357D PRO* 4.1 6.6 - - - +
479D MET* 3.7 24.7 - - - +
480D THR* 6.0 2.0 - - - +
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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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106D PRO* 6.0 0.7 - - - +
191D LEU* 3.8 38.4 - - + +
192D ALA* 4.1 21.8 - - - +
195D ILE* 3.8 35.7 - - + -
351D LEU* 3.2 35.2 + - + +
352D ILE 2.7 8.0 + - - +
354D ARG* 1.3 88.7 - - + +
356D TYR* 1.3 58.6 + - - +
357D PRO* 3.8 4.2 - - - +
475D ILE* 4.4 5.6 - - + -
479D MET* 4.5 5.6 - - + -
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Residues in contact with TYR 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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99D LEU* 3.6 23.3 - - + +
100D LEU* 3.5 25.8 - - + +
105D GLY* 5.8 0.7 - - - -
106D PRO* 4.8 11.0 - - + -
192D ALA 5.4 0.9 - - - +
195D ILE* 3.5 21.3 - - + -
196D GLN* 3.4 44.2 + - + -
199D VAL* 4.0 30.3 - - + -
352D ILE* 2.6 19.9 + - + +
355D LEU* 1.3 74.7 - - - +
357D PRO* 1.4 69.9 - - + +
358D GLU* 3.1 15.9 + - + -
359D GLY* 3.9 20.2 - - - -
360D GLY* 3.0 19.1 + - - -
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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