Contacts of the helix formed by residues 306 - 317 (chain O) 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 GLU 306 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302O ILE* 3.7 21.1 - - + -
303O THR* 4.0 10.3 - - - +
305O ASN* 1.3 96.2 - - - +
307O VAL* 1.3 54.5 + - - +
309O LEU* 2.3 46.5 + - + +
310O LEU* 2.8 12.1 + - + +
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Residues in contact with VAL 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O PHE* 3.9 46.7 - - + +
296O ILE* 3.6 44.0 - - + -
297O ALA* 4.9 4.3 - - - +
302O ILE* 4.5 6.8 - - + +
303O THR 4.1 2.6 + - - +
304O VAL* 4.0 20.2 - - + -
305O ASN* 3.7 9.5 - - - +
306O GLU* 1.3 75.0 - - - +
308O GLU* 1.3 59.3 + - + +
310O LEU* 3.4 9.5 + - - +
311O VAL* 3.0 33.3 + - + +
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Residues in contact with GLU 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O PHE* 4.4 21.6 - - + -
305O ASN* 3.3 13.7 - - - +
306O GLU 2.7 4.6 + - - -
307O VAL* 1.3 78.4 - - + +
309O LEU* 1.3 62.8 + - + +
311O VAL* 4.1 7.1 - - - +
312O MET* 2.9 36.2 + - + +
324O ILE* 4.1 14.8 - - + +
326O GLU* 4.8 5.8 - - - +
370P TYR* 3.0 36.5 + - - +
373P ILE* 5.6 0.2 - - - +
377P ARG* 2.9 41.2 + - - +
381P LEU* 4.7 5.5 - - + +
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Residues in contact with LEU 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305O ASN 4.8 2.5 - - - +
306O GLU* 2.3 40.3 + - + +
308O GLU* 1.3 70.0 - - + +
310O LEU* 1.3 57.2 + - - +
312O MET* 3.9 15.7 - - + +
313O LYS* 3.0 32.2 + - - +
313P GLU* 4.3 8.4 - - - +
314P LEU* 5.9 3.1 - - + -
377P ARG* 5.7 4.0 - - - +
381P LEU* 6.0 3.1 - - + -
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Residues in contact with LEU 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270O ARG* 4.5 8.1 - - + +
273O GLN* 3.4 56.8 - - + +
274O LEU* 4.1 13.9 - - + +
277O LEU* 4.1 17.5 - - + -
296O ILE* 4.4 17.9 - - + -
300O ALA* 4.5 2.7 - - + -
302O ILE* 5.5 0.9 - - + -
306O GLU* 2.8 14.6 + - + +
307O VAL* 3.5 11.4 - - - +
309O LEU* 1.3 75.4 - - - +
311O VAL* 1.3 57.1 + - - +
313O LYS* 3.8 4.8 - - + +
314O ALA* 2.9 26.7 + - + +
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Residues in contact with VAL 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277O LEU* 4.2 14.4 - - + -
293O PHE* 6.2 0.4 - - + -
296O ILE* 4.1 26.0 - - + -
307O VAL* 3.0 19.3 + - + +
308O GLU* 4.1 4.0 - - - +
310O LEU* 1.3 74.4 - - + +
312O MET* 1.3 67.6 + - - +
314O ALA* 2.9 19.3 + - + +
315O LEU* 3.0 21.8 + - + +
320O VAL* 6.1 2.7 - - + -
322O GLY 6.5 0.4 - - - -
323O SER 5.5 0.4 - - - +
324O ILE* 3.9 26.2 - - + -
331O VAL* 4.2 21.8 - - + -
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Residues in contact with MET 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308O GLU* 2.9 33.1 + - + +
309O LEU* 4.0 8.7 - - + +
311O VAL* 1.3 76.0 - - - +
313O LYS* 1.3 62.7 + - - +
315O LEU* 3.1 9.1 + - - +
316O SER* 3.0 22.7 + - - -
324O ILE* 3.9 15.9 - - + -
313P GLU* 3.7 31.9 - - - +
314P LEU* 3.8 26.7 - - + -
366P MET* 6.1 0.4 - - - -
369P TYR* 3.9 29.7 - - + -
370P TYR* 3.3 37.9 - - - +
381P LEU* 5.2 0.9 - - + -
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Residues in contact with LYS 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309O LEU 3.0 19.2 + - - +
310O LEU* 3.9 5.4 - - + +
312O MET* 1.3 75.2 - - - +
314O ALA* 1.3 66.0 + - - +
315O LEU 3.2 0.3 + - - -
316O SER* 3.3 23.5 + - - +
317O VAL* 3.5 18.8 + - + +
313P GLU* 4.5 8.9 + - + +
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Residues in contact with ALA 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274O LEU* 5.2 14.1 - - + -
277O LEU* 4.1 16.8 - - + -
278O MET* 5.8 1.1 - - - -
310O LEU 2.9 14.5 + - - +
311O VAL* 2.9 18.0 + - + +
313O LYS* 1.3 76.4 - - - +
315O LEU* 1.3 59.5 + - - +
317O VAL* 4.0 1.4 + - - +
319O LEU* 3.2 38.6 + - + +
320O VAL* 3.4 16.8 + - + -
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Residues in contact with LEU 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311O VAL* 3.0 23.6 + - + +
312O MET* 3.6 8.7 - - - +
314O ALA* 1.3 73.9 - - - +
316O SER* 1.3 53.3 + - - +
317O VAL 3.0 4.3 - - - -
318O GLY* 2.5 32.1 + - - -
320O VAL* 3.6 34.9 - - + +
321O LYS* 4.6 0.4 - - - -
322O GLY 4.5 20.0 - - - +
369P TYR* 4.4 21.1 - - + -
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Residues in contact with SER 316 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312O MET 3.0 9.5 + - - -
313O LYS* 3.3 21.2 + - - +
315O LEU* 1.3 75.5 - - - +
317O VAL* 1.3 61.5 + - - +
318O GLY 3.3 1.1 + - - -
312P MET* 3.8 17.9 + - - -
313P GLU* 5.0 1.1 + - - -
369P TYR* 3.6 24.0 - - - -
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Residues in contact with VAL 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O GLU* 6.5 0.9 - - + -
274O LEU* 6.3 0.9 - - + -
313O LYS* 3.5 24.0 + - + +
314O ALA 4.5 3.8 - - - +
315O LEU 2.8 1.4 + - - -
316O SER* 1.3 82.8 - - - +
318O GLY* 1.3 60.4 + - - +
319O LEU* 3.4 18.3 + - + +
337O GLN* 5.3 0.7 - - - +
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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