Contacts of the helix formed by residues 280 - 293 (chain P) in PDB entry 5GJQ
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 280 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241P LEU* 5.6 7.4 - - + -
278P PRO* 3.2 11.3 + - + +
279P PHE* 1.3 85.1 - - - +
281P ASN* 1.3 70.2 + - - +
282P GLU 4.6 3.6 - - - +
283P GLN* 3.6 8.7 + - + +
284P SER* 3.4 19.9 + - - -
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Residues in contact with ASN 281 (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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280P ASP* 1.3 79.4 - - - +
282P GLU* 1.3 72.0 + - + +
284P SER* 3.1 14.8 + - - -
285P ASP* 3.4 11.3 + - - +
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Residues in contact with GLU 282 (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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241P LEU* 4.3 15.0 - - + -
280P ASP* 3.6 1.8 - - - +
281P ASN* 1.3 84.6 - - + +
283P GLN* 1.3 65.0 + - - +
285P ASP* 2.5 29.9 - - - +
286P LEU* 3.0 32.4 + - + +
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Residues in contact with GLN 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241P LEU* 4.7 13.2 - - + +
274P VAL* 3.6 21.0 + - + +
275P ILE* 4.9 3.0 + - - +
277P ALA* 3.1 17.0 + - + +
278P PRO 2.8 39.7 - - - +
279P PHE* 3.0 20.3 - - + +
280P ASP* 3.6 16.3 + - + +
281P ASN 3.2 0.8 - - - -
282P GLU* 1.3 78.4 - - - +
284P SER* 1.3 70.5 + - - +
286P LEU* 3.6 3.6 - - - +
287P VAL* 2.8 32.9 + - + +
309P PHE* 5.5 10.7 - - - +
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Residues in contact with SER 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279P PHE* 3.4 27.0 - - - -
280P ASP 3.4 3.1 + - - -
281P ASN 3.1 11.7 + - - -
283P GLN* 1.3 85.1 - - - +
285P ASP* 1.3 60.6 + - - +
287P VAL* 2.7 16.3 + - - -
288P HIS* 2.8 34.7 + - - -
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Residues in contact with ASP 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281P ASN* 3.4 7.6 + - - +
282P GLU* 2.5 42.3 - - - +
284P SER* 1.3 75.4 - - - +
286P LEU* 1.3 61.1 + - - +
288P HIS* 3.9 9.1 - - - +
289P ARG* 2.9 42.9 + - - +
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Residues in contact with LEU 286 (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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241P LEU* 3.7 26.9 - - + -
244P CYS* 5.9 1.6 - - + -
245P LYS* 4.4 17.0 - - + +
248P ARG* 5.5 11.7 - - + -
274P VAL* 4.9 13.2 - - + -
282P GLU* 3.0 28.6 + - + +
283P GLN* 3.6 3.1 - - - +
285P ASP* 1.3 88.5 + - - +
287P VAL* 1.3 57.5 + - - +
289P ARG* 3.2 25.4 + - - +
290P ILE* 2.9 38.4 + - + +
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Residues in contact with VAL 287 (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 VAL* 2.5 46.0 - - + +
283P GLN* 2.8 27.8 + - + +
284P SER* 2.7 12.9 + - - +
286P LEU* 1.3 72.4 - - - +
288P HIS* 1.3 61.5 + - + +
290P ILE* 3.2 8.0 + - - +
291P SER* 2.9 30.2 + - - -
306P LEU* 5.7 6.7 - - + +
309P PHE* 6.2 3.8 - - + -
310P THR* 5.0 11.3 + - - +
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Residues in contact with HIS 288 (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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284P SER* 2.8 53.8 + - - +
285P ASP* 3.9 8.1 - - - +
287P VAL* 1.3 78.1 - - + +
289P ARG* 1.3 61.5 + - - +
291P SER* 3.5 8.3 + - - -
292P GLY* 3.3 15.8 + - - -
310P THR* 4.1 30.7 + - + +
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Residues in contact with ARG 289 (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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285P ASP* 2.9 32.3 + - - +
286P LEU* 3.2 24.6 + - + +
288P HIS* 1.3 74.3 - - - +
290P ILE* 1.3 69.4 + - + +
292P GLY* 3.1 11.2 + - - +
293P ASP* 3.1 11.6 + - - +
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Residues in contact with ILE 290 (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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248P ARG* 5.9 7.9 - - + -
251P TYR* 6.4 2.7 - - + -
267P LEU* 5.3 13.0 - - + -
270P VAL* 5.0 15.0 - - + +
271P VAL* 4.7 19.1 - - + +
274P VAL* 4.9 13.7 - - + -
286P LEU* 2.9 26.8 + - + +
287P VAL* 3.2 9.6 + - - +
289P ARG* 1.3 77.2 - - + +
291P SER* 1.3 68.8 + - - +
293P ASP* 3.0 27.9 + - + +
296P LEU* 3.3 24.8 - - + +
306P LEU* 5.4 4.9 - - + -
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Residues in contact with SER 291 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287P VAL 2.9 15.7 + - - -
288P HIS* 3.6 10.1 - - - -
289P ARG 3.3 0.2 - - - -
290P ILE* 1.3 76.8 - - - +
292P GLY* 1.3 58.7 + - - +
293P ASP 4.1 4.2 - - - +
296P LEU* 3.8 14.8 - - - +
306P LEU* 5.4 7.8 - - - +
307P LYS* 5.8 5.2 - - - +
310P THR* 4.8 13.2 - - - +
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Residues in contact with GLY 292 (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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288P HIS 3.3 8.1 + - - -
289P ARG* 3.1 7.9 + - - -
290P ILE 3.0 1.0 - - - -
291P SER* 1.3 78.6 - - - +
293P ASP* 1.3 65.0 + - - +
294P LYS* 3.1 9.2 + - - +
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Residues in contact with ASP 293 (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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251P TYR* 2.7 34.2 + - - -
267P LEU* 4.1 9.9 - - - +
289P ARG 3.1 9.1 + - - +
290P ILE* 3.0 22.8 + - + +
291P SER 4.1 3.1 - - - +
292P GLY* 1.3 75.5 - - - +
294P LYS* 1.3 74.9 + - - +
295P LYS* 3.1 21.1 + - - +
296P LEU* 3.3 20.3 + - + +
297P GLU* 4.1 4.0 + - - +
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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