Contacts of the helix formed by residues 366 - 374 (chain D) in PDB entry 6B0Q
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 ARG 366 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D TYR* 3.5 13.9 - - - +
364D PHE* 3.8 5.5 - - - +
365D SER* 1.3 86.2 - - - +
367D SER* 1.3 65.3 + - - +
368D ASP* 3.0 34.5 + - - +
369D GLN* 3.5 24.3 + - - +
370D LEU 3.4 14.2 + - - -
9E A 3.6 25.9 + - - +
10E G 2.8 48.3 + - - -
11E T 3.4 17.1 + - - +
3F C 6.0 0.4 - - - -
4F A 3.7 2.1 - - - +
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Residues in contact with SER 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D TYR* 3.6 37.1 + - - -
366D ARG* 1.3 71.1 - - - +
368D ASP* 1.3 67.9 + - - +
370D LEU* 3.2 7.0 + - - +
371D LYS* 3.0 34.2 + - - +
2F A 3.4 33.5 + - - +
3F C 5.0 2.1 - - - -
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Residues in contact with ASP 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D ARG* 3.0 48.2 + - - +
367D SER* 1.3 78.7 + - - +
369D GLN* 1.3 63.0 + - - +
371D LYS* 3.9 8.5 - - - +
372D ARG* 3.0 28.6 + - - +
9E A 5.1 0.9 + - - -
3F C 4.1 17.5 - - + -
4F A 3.0 35.3 + - + +
5F C 4.1 3.6 + - - -
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Residues in contact with GLN 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D PHE* 4.0 16.0 - - + +
365D SER* 3.7 14.2 + - - -
366D ARG* 3.5 42.4 + - + +
367D SER 3.2 0.6 - - - -
368D ASP* 1.3 90.3 + - - +
370D LEU* 1.3 59.6 + - - +
372D ARG* 3.4 24.8 + - - +
373D HIS* 3.0 27.4 + - - +
7E G 5.0 1.0 + - + -
8E G 4.0 25.4 + - - +
9E A 2.9 39.7 + - - +
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Residues in contact with LEU 370 (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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353D TYR* 4.0 18.8 - - + -
354D GLN 3.5 23.1 - - - +
355D CYS* 3.6 33.0 - - + +
364D PHE* 3.7 29.7 - - + -
366D ARG 3.4 9.1 + - - +
367D SER* 3.2 9.9 + - - +
369D GLN* 1.3 78.8 - - - +
371D LYS* 1.3 61.4 + - + +
373D HIS* 3.1 4.4 + - + +
374D GLN* 2.9 49.5 + - + +
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Residues in contact with LYS 371 (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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377A HIS 4.9 5.9 + - - -
378A THR* 3.3 28.9 + - - +
379A GLY* 5.1 4.0 - - - -
380A VAL* 5.0 5.4 - - + +
367D SER* 3.0 25.4 + - - +
368D ASP* 4.0 7.0 - - - +
370D LEU* 1.3 82.0 - - + +
372D ARG* 1.3 60.5 + - - +
374D GLN* 3.8 19.5 + - - +
375D ARG* 3.6 21.4 + - - +
3F C 3.2 28.5 - - - +
4F A 6.1 0.9 - - - +
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Residues in contact with ARG 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D PHE* 6.1 0.6 - - - -
368D ASP 3.0 17.8 + - - +
369D GLN* 3.7 20.4 + - - +
370D LEU 3.2 0.2 - - - -
371D LYS* 1.3 76.5 - - - +
373D HIS* 1.3 64.5 + - - +
375D ARG* 3.2 44.9 + - - +
376D ARG* 4.5 1.9 + - - +
394D ARG* 3.5 48.3 - - - +
6E G 6.1 0.9 - - - +
7E G 3.6 26.9 + - - +
8E G 3.0 48.1 + - - -
9E A 4.0 11.7 - - - +
6F T 4.0 8.4 + - - +
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Residues in contact with HIS 373 (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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355D CYS* 3.5 10.4 - - - +
360D CYS* 3.3 11.2 - - - -
362D ARG* 4.3 10.1 - - - -
364D PHE* 3.4 34.2 - + + -
369D GLN 3.0 9.5 + - - +
370D LEU* 3.1 10.5 + - + +
372D ARG* 1.3 77.9 - - - +
374D GLN* 1.3 59.5 + - - +
376D ARG* 2.9 47.2 + - - +
377D HIS* 3.2 9.5 + + - -
502D ZN 2.0 36.5 - - - -
7E G 2.8 32.6 + - - +
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Residues in contact with GLN 374 (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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357A PHE* 4.0 21.9 - - + -
377A HIS 4.1 4.9 + - - +
378A THR* 3.8 32.8 - - + -
354D GLN 5.2 0.2 + - - -
355D CYS* 4.0 29.6 - - - +
356D ASP* 4.5 4.0 - - - +
370D LEU* 2.9 38.1 + - + +
371D LYS* 4.1 17.1 + - - +
372D ARG 3.3 0.4 - - - -
373D HIS* 1.3 73.4 - - - +
375D ARG* 1.3 59.3 + - - +
376D ARG 3.0 2.6 + - - -
377D HIS* 3.3 24.0 + - + +
378D THR* 3.5 16.2 + - - +
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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
------------------------------------------------------------
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