Contacts of the helix formed by residues 296 - 308 (chain M) in PDB entry 6PSS
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 GLY 296 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290M LEU* 4.6 9.2 - - - -
295M LEU* 1.3 77.1 - - - +
297M LYS* 1.3 54.8 + - - -
298M LYS 3.4 2.2 - - - -
299M SER* 3.4 3.9 + - - -
300M LEU* 2.7 40.9 + - - +
67P T 3.4 24.5 - - - -
68P G 4.2 3.6 - - - -
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Residues in contact with LYS 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286M GLU* 5.8 5.5 + - - +
287M VAL* 6.0 2.6 - - - +
290M LEU* 3.6 26.6 - - - +
296M GLY* 1.3 69.5 - - - -
298M LYS* 1.3 61.7 + - - +
300M LEU* 3.3 19.1 + - + +
301M THR* 2.7 30.7 + - - +
67P T 4.8 1.4 - - - -
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Residues in contact with LYS 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296M GLY 3.4 0.2 - - - -
297M LYS* 1.3 76.5 - - - +
299M SER* 1.3 59.5 + - - +
301M THR* 3.2 10.5 + - - +
302M GLU* 2.9 38.8 + - + +
66P T 2.7 51.6 + - + +
67P T 3.3 33.9 + - - +
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Residues in contact with SER 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M ARG* 5.0 3.5 - - - +
266M SER* 3.7 21.7 + - - -
295M LEU* 3.3 30.0 - - - +
296M GLY 3.4 13.5 + - - -
297M LYS 3.4 0.2 - - - -
298M LYS* 1.3 75.5 - - - +
300M LEU* 1.3 60.3 + - - +
302M GLU* 3.2 18.5 + - - +
303M ILE* 2.9 31.9 + - - +
67P T 3.8 12.4 + - - -
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Residues in contact with LEU 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286M GLU* 4.3 29.6 - - + +
289M LEU* 5.3 3.8 - - + -
290M LEU* 3.7 22.2 - - + +
295M LEU* 3.7 21.5 - - + -
296M GLY 2.7 20.9 + - - +
297M LYS* 3.3 30.1 - - + +
298M LYS 3.2 0.2 - - - -
299M SER* 1.3 75.0 - - - +
301M THR* 1.3 59.7 + - - +
303M ILE* 3.3 19.5 + - + -
304M LYS* 2.9 30.3 + - + +
314M LEU* 5.7 3.8 - - + -
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Residues in contact with THR 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297M LYS* 2.7 18.4 + - - +
298M LYS* 3.2 14.3 + - - -
300M LEU* 1.3 74.1 - - - +
302M GLU* 1.3 59.1 + - - +
304M LYS* 3.7 11.6 - - + +
305M ASP* 2.9 34.1 + - + +
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Residues in contact with GLU 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M LEU* 5.3 2.8 - - + +
263M THR* 3.2 36.7 + - - +
265M ARG* 4.8 3.5 - - - +
266M SER* 3.8 17.1 + - - -
298M LYS* 2.9 21.7 + - + +
299M SER* 3.2 22.5 - - - +
301M THR* 1.3 76.4 - - - +
303M ILE* 1.3 57.1 + - + +
305M ASP* 3.9 2.4 - - - +
306M VAL* 2.9 33.7 + - - +
67P T 3.2 23.7 + - - -
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Residues in contact with ILE 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266M SER* 5.4 7.2 - - - -
270M LEU* 6.5 1.8 - - + -
289M LEU* 3.7 36.8 - - + -
295M LEU* 4.3 21.1 - - + -
299M SER* 2.9 27.0 + - - +
300M LEU* 3.3 21.1 + - + +
302M GLU* 1.3 73.8 - - + +
304M LYS* 1.3 58.2 + - - +
306M VAL* 3.3 10.9 - - + +
307M LEU* 3.0 47.4 + - + +
314M LEU* 4.5 7.0 - - + -
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Residues in contact with LYS 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300M LEU* 2.9 18.2 + - + +
301M THR* 3.7 12.8 - - + +
302M GLU 3.3 0.2 - - - -
303M ILE* 1.3 78.1 - - - +
305M ASP* 1.3 57.9 + - - +
307M LEU* 3.5 1.9 + - - +
308M ALA* 2.9 33.2 + - + +
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Residues in contact with ASP 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301M THR* 2.9 20.3 + - + +
302M GLU* 4.2 2.7 - - - +
304M LYS* 1.3 75.9 - - - +
306M VAL* 1.3 59.3 + - - +
308M ALA* 3.6 7.1 - - - +
309M SER* 2.9 42.3 + - - -
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Residues in contact with VAL 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M LEU* 3.3 50.7 - - + +
261M GLU 4.7 5.2 - - - +
262M LEU* 4.7 15.9 - - + -
302M GLU 2.9 18.6 + - - +
303M ILE* 3.3 21.3 - - + +
305M ASP* 1.3 80.0 - - - +
307M LEU* 1.3 59.9 + - + +
309M SER* 3.8 7.4 + - - -
310M ARG* 2.4 38.2 + - - +
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Residues in contact with LEU 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260M LEU* 3.8 14.4 - - + -
278M ILE* 5.5 2.9 - - + -
281M LEU* 3.6 34.8 - - + +
282M VAL* 3.9 15.5 - - + -
289M LEU* 5.7 0.2 - - + -
303M ILE* 3.0 34.8 + - + +
304M LYS* 4.4 2.2 - - - +
306M VAL* 1.3 80.7 - - + +
308M ALA* 1.3 57.0 + - - +
309M SER 3.2 4.3 - - - -
310M ARG* 3.7 11.9 + - + +
311M GLY* 3.0 17.8 + - - -
312M LEU* 2.9 35.9 + - + +
313M SER* 5.2 1.3 - - - -
314M LEU* 4.1 18.4 - - + -
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Residues in contact with ALA 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304M LYS* 2.9 21.6 + - + +
305M ASP* 3.4 9.2 + - - +
307M LEU* 1.3 76.1 - - - +
309M SER* 1.3 61.4 + - - +
310M ARG 3.2 2.1 + - - -
311M GLY* 3.9 9.1 + - - +
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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