Contacts of the helix formed by residues 300 - 311 (chain D) in PDB entry 3K6G
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 ASP 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298D ALA* 2.8 10.5 - - + -
299D GLN* 1.3 87.7 + - + +
301D SER* 1.3 62.1 + - - +
302D GLU 3.2 4.0 + - - -
303D ALA* 3.2 15.5 + - - +
304D ALA* 3.0 29.2 + - + +
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Residues in contact with SER 301 (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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292D PHE* 3.4 6.4 - - - -
293D LYS* 3.7 43.0 + - - +
296D SER* 3.9 19.5 - - - -
298D ALA* 2.9 19.0 + - - +
299D GLN* 3.4 1.9 + - - -
300D ASP* 1.3 77.7 - - - +
302D GLU* 1.3 57.7 + - - +
304D ALA* 4.0 7.2 - - - -
305D PHE* 2.8 32.6 + - - +
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Residues in contact with GLU 302 (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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289D LYS* 2.6 40.8 + - - -
293D LYS* 2.9 33.4 + - - +
299D GLN 4.7 4.8 + - - +
300D ASP 3.2 1.4 + - - -
301D SER* 1.3 81.7 + - - +
303D ALA* 1.3 62.4 + - - +
305D PHE* 3.4 6.1 + - - +
306D ALA* 3.2 21.5 + - - +
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Residues in contact with ALA 303 (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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300D ASP* 3.2 20.2 + - - +
302D GLU* 1.3 77.8 - - - +
304D ALA* 1.3 66.0 + - - +
306D ALA* 3.2 9.1 + - - +
307D LYS* 3.0 22.5 + - - +
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Residues in contact with ALA 304 (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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292D PHE* 4.1 13.7 - - + -
300D ASP* 3.0 25.5 + - + +
301D SER* 3.6 9.9 - - - +
303D ALA* 1.3 76.9 - - - +
305D PHE* 1.3 62.4 + - - +
307D LYS* 3.3 9.2 + - - +
308D LEU* 3.1 28.1 + - + +
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Residues in contact with PHE 305 (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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333A THR* 3.9 22.7 - - + -
337A LEU* 3.7 30.2 - - + +
285D MSE 4.0 16.2 - - + -
286D MSE 4.4 7.4 - - + -
288D LEU* 4.1 4.5 - - + -
289D LYS* 3.6 56.8 - - + -
292D PHE* 3.8 29.3 - + + -
293D LYS* 5.6 0.2 - - + -
301D SER 2.8 17.6 + - - +
302D GLU* 3.7 5.6 - - - +
303D ALA 3.3 0.2 - - - -
304D ALA* 1.3 73.6 - - - +
306D ALA* 1.3 68.7 + - - +
308D LEU* 3.1 8.4 + - + +
309D ASP* 3.1 20.7 + - + +
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Residues in contact with ALA 306 (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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351B ALA 4.9 12.1 - - - +
302D GLU 3.2 10.8 + - - +
303D ALA* 3.2 12.8 + - - +
305D PHE* 1.3 83.0 - - - +
307D LYS* 1.3 57.7 + - - +
309D ASP* 3.4 6.9 + - - +
310D GLN* 3.0 30.6 + - - +
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Residues in contact with LYS 307 (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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303D ALA 3.0 12.6 + - - +
304D ALA* 3.5 12.1 - - - +
305D PHE 3.1 0.4 - - - -
306D ALA* 1.3 75.2 - - - +
308D LEU* 1.3 63.4 + - + +
310D GLN* 4.2 9.4 - - + -
311D LYS* 2.9 56.3 + - + +
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Residues in contact with LEU 308 (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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330A SER* 4.0 33.2 - - - +
333A THR* 4.2 13.2 - - + -
334A GLN* 3.1 37.5 + - + +
337A LEU* 3.9 13.1 - - + +
338A LYS* 2.9 21.8 + - - -
292D PHE* 3.8 31.6 - - + -
304D ALA* 3.2 14.6 - - + +
305D PHE* 3.1 9.7 + - - +
307D LYS* 1.3 80.8 - - + +
309D ASP* 1.3 57.4 + - - +
311D LYS 3.2 0.9 - - - +
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Residues in contact with ASP 309 (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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337A LEU* 3.7 20.6 - - + +
338A LYS* 3.0 16.5 + - - +
364A ARG* 4.2 13.6 + - - +
367A ASP* 4.9 4.9 - - - +
393A ARG* 4.8 1.4 + - - -
397A ARG* 2.7 42.9 + - - -
285D MSE 3.3 22.4 - - + +
305D PHE* 3.1 15.4 + - + +
306D ALA* 3.7 10.5 - - - +
307D LYS 3.2 0.2 - - - -
308D LEU* 1.3 76.8 - - - +
310D GLN* 1.3 61.1 + - - +
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Residues in contact with GLN 310 (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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364A ARG* 3.4 42.5 + - - +
324B LYS 3.1 20.8 + - - +
325B PHE* 3.2 40.5 - - - +
326B ASN* 2.6 29.9 + - + +
306D ALA 3.0 18.9 + - - +
307D LYS* 3.7 9.8 - - - +
309D ASP* 1.3 79.5 - - - +
311D LYS* 1.3 73.1 + - - +
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Residues in contact with LYS 311 (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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334A GLN* 3.0 21.2 + - - +
338A LYS* 2.8 22.7 + - - -
323B GLU 4.7 4.8 + - - -
324B LYS 5.3 0.6 + - - -
326B ASN* 2.8 34.6 + - - +
307D LYS* 2.9 50.1 + - + +
310D GLN* 1.3 85.3 - - + +
312D ASP* 1.3 64.0 + - - +
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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