Contacts of the helix formed by residues 299 - 310 (chain P) in PDB entry 5G04
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 ASN 299 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264P TYR* 5.6 2.6 - - - -
267P SER* 2.6 31.7 + - - +
268P GLN* 5.8 1.0 + - - -
271P VAL* 4.4 6.7 - - + -
286P PHE* 4.1 5.9 - - + -
289P LEU* 3.9 14.3 - - - +
296P ARG* 2.8 33.4 + - - +
297P ILE 3.3 0.2 - - - -
298P GLU* 1.3 86.7 - - + +
300P MET* 1.3 66.7 + - - +
301P ASP* 3.1 4.3 - - - +
302P THR* 3.0 34.3 + - + +
303P PHE* 3.4 5.7 + - - +
364P TYR* 5.3 0.4 - - - -
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Residues in contact with MET 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286P PHE* 5.6 0.9 - - - -
289P LEU* 4.2 17.5 - - + -
290P ARG* 3.4 40.8 - - + +
296P ARG* 4.0 18.2 - - + +
297P ILE* 3.3 18.3 + - + +
299P ASN* 1.3 87.2 - - - +
301P ASP* 1.3 64.7 + - - +
303P PHE* 3.4 18.3 - - + +
304P SER* 2.9 26.5 + - - -
319P LEU* 3.7 21.0 - - + +
323P LEU* 3.8 28.7 - - + -
332P GLU* 5.0 0.4 - - + -
336P VAL* 3.4 4.8 - - + +
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Residues in contact with ASP 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299P ASN 4.7 1.3 - - - -
300P MET* 1.3 78.7 - - - +
302P THR* 1.3 68.0 + - + +
304P SER* 3.5 3.8 - - - -
305P ASN* 3.2 32.2 + - - +
332P GLU* 4.3 10.6 - - + +
335P CYS* 3.5 28.6 - - - -
336P VAL* 4.3 1.9 - - - +
339P ASN* 4.2 1.0 + - - -
364P TYR* 2.9 44.8 + - + +
365P LEU* 4.4 9.0 - - - +
366P GLY* 4.8 11.2 - - - -
370P LEU* 5.0 1.2 - - - +
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Residues in contact with THR 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271P VAL* 3.4 37.1 - - + +
274P HIS* 3.6 25.6 - - - +
286P PHE* 3.8 10.8 - - + -
299P ASN* 3.0 23.8 - - + +
301P ASP* 1.3 78.0 - - + +
303P PHE* 1.3 65.6 + - - +
305P ASN* 3.2 21.4 + - - +
306P LEU* 3.3 12.8 + - - +
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Residues in contact with PHE 303 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283P LEU* 3.8 17.3 - - + -
286P PHE* 3.5 58.4 - + + -
287P ASN* 3.7 23.3 - - - -
290P ARG* 4.3 15.9 - - + -
299P ASN 3.4 4.8 + - - -
300P MET* 3.2 35.8 + - + +
302P THR* 1.3 76.5 - - - +
304P SER* 1.3 62.4 + - - +
306P LEU* 3.3 3.6 + - - +
307P LEU* 3.0 44.5 + - + +
319P LEU* 4.2 14.6 - - + -
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Residues in contact with SER 304 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300P MET 2.9 16.7 + - - -
301P ASP 3.5 2.9 - - - -
303P PHE* 1.3 74.5 - - - +
305P ASN* 1.3 59.9 + - - +
307P LEU* 3.3 4.3 + - - +
308P TYR* 2.8 31.0 + - - +
316P LEU* 3.8 7.6 - - - +
319P LEU* 4.0 13.6 - - - +
336P VAL* 3.5 23.1 - - - -
339P ASN* 2.7 37.8 + - - +
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Residues in contact with ASN 305 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274P HIS* 4.0 17.9 + - + +
301P ASP* 3.2 25.9 + - - +
302P THR* 3.2 14.2 + - - +
304P SER* 1.3 79.7 - - - +
306P LEU* 1.3 61.5 + - - +
308P TYR* 3.3 8.1 + - - +
309P VAL* 3.2 24.0 + - - +
339P ASN* 3.1 23.3 + - - +
366P GLY* 5.6 1.9 - - - -
370P LEU* 3.7 24.0 - - - +
400P ARG* 5.2 10.2 + - - -
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Residues in contact with LEU 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274P HIS* 3.2 37.5 - - + +
279P ILE* 4.0 29.0 - - + +
282P ALA* 3.9 19.5 - - + -
283P LEU* 3.5 37.0 - - + +
286P PHE* 3.7 28.9 - - + -
302P THR 3.3 1.4 + - - +
303P PHE 3.3 12.5 + - - +
305P ASN* 1.3 75.4 - - - +
307P LEU* 1.3 70.5 + - - +
309P VAL* 3.4 14.8 + - - +
310P ARG* 3.4 9.4 + - - +
312P MET* 4.6 0.2 - - - +
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Residues in contact with LEU 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283P LEU* 3.7 31.4 - - + -
303P PHE* 3.0 34.2 + - + +
304P SER* 3.3 6.9 + - - +
306P LEU* 1.3 80.0 - - - +
308P TYR* 1.3 60.3 + - - +
310P ARG 3.4 1.0 + - - -
311P SER 3.2 15.4 + - - -
312P MET* 3.5 36.8 + - + +
315P GLU* 3.7 22.9 - - + +
316P LEU* 3.6 36.1 - - + +
319P LEU* 4.0 10.5 - - + -
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Residues in contact with TYR 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P SER 2.8 18.6 + - - +
305P ASN* 3.4 9.4 - - - +
307P LEU* 1.3 76.6 - - - +
309P VAL* 1.3 69.0 + - + +
311P SER* 3.1 20.8 + - - -
316P LEU* 3.9 10.9 - - + +
339P ASN* 3.5 25.1 - - + -
342P SER* 3.5 20.3 + - - -
343P LEU* 3.3 50.2 - - + +
347P HIS* 5.2 2.8 + - - -
370P LEU* 6.2 3.8 - - + -
373P HIS* 6.6 0.4 - + - -
374P GLU* 5.3 2.6 + - - -
377P GLU* 5.6 2.1 + - - -
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Residues in contact with VAL 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274P HIS* 6.1 3.4 - - + -
277P ARG* 4.1 25.1 - - - +
279P ILE* 3.7 28.7 - - + -
305P ASN 3.2 14.8 + - - +
306P LEU* 3.8 9.4 - - - +
307P LEU 3.3 0.8 - - - -
308P TYR* 1.3 80.8 - - + +
310P ARG* 1.3 65.4 + - - +
311P SER* 3.1 14.5 + - - -
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Residues in contact with ARG 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279P ILE* 3.6 36.3 - - + +
306P LEU 3.4 8.0 + - - +
307P LEU 3.7 1.1 - - - -
309P VAL* 1.3 81.6 - - + +
311P SER* 1.3 67.5 + - - +
312P MET* 3.2 36.0 + - + +
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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