Contacts of the helix formed by residues 304 - 316 (chain I) 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 304 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H VAL* 4.7 2.8 - - - +
259I TYR 4.5 0.9 - - - +
260I LEU* 3.3 13.5 - - + +
261I GLY* 2.6 36.7 + - - -
262I ASP 4.0 3.6 + - - -
263I GLY 4.7 2.3 + - - +
264I PRO* 4.9 2.4 - - - +
298I ASN* 4.9 6.3 - - - +
299I SER 3.7 11.7 - - - +
300I GLY* 3.1 29.3 + - - +
303I ARG* 1.3 78.0 - - - +
305I ILE* 1.3 69.2 + - + +
306I GLN 3.1 1.8 - - - -
307I ARG* 3.0 32.1 + - - +
308I THR* 3.1 21.3 + - - +
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Residues in contact with ILE 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I ILE* 4.4 20.9 - - + -
290I ILE* 2.6 47.6 - - + +
291I GLY* 4.8 4.3 - - - +
293I LYS 3.9 18.8 - - - +
294I ARG* 5.5 2.9 - - - -
295I TYR 5.9 1.1 - - - +
298I ASN* 4.1 13.7 - - - +
301I GLY 3.7 20.2 - - - +
302I GLU* 3.9 13.8 + - + +
304I GLU* 1.3 78.5 - - + +
306I GLN* 1.3 52.8 + - - +
308I THR* 3.1 11.5 - - - -
309I MET* 2.8 35.2 + - + +
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Residues in contact with GLN 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H ARG* 5.3 9.6 + - - -
302I GLU 3.5 16.1 + - - +
303I ARG* 4.5 8.5 - - - +
305I ILE* 1.3 79.2 - - - +
307I ARG* 1.3 54.8 + - - +
309I MET* 2.9 17.2 + - - +
310I LEU* 2.6 46.8 + - + +
338I ASP* 3.5 24.3 + - - +
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Residues in contact with ARG 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H GLY 5.6 0.7 - - - +
243H SER* 4.5 6.0 + - - -
246H VAL* 4.2 14.9 - - + +
278H ASP 4.7 3.8 + - - -
279H ALA* 2.6 48.2 + - + +
280H ILE 4.6 0.2 - - - -
281H GLY* 5.2 1.4 - - - -
292H ASP* 3.2 16.1 + - - -
295H VAL* 3.2 35.1 - - - +
260I LEU* 5.9 0.4 - - - +
264I PRO* 5.1 9.2 - - + -
303I ARG* 2.6 36.7 + - - +
304I GLU* 3.0 22.3 + - - +
306I GLN* 1.3 83.5 - - - +
308I THR* 1.3 54.3 + - - +
310I LEU* 2.5 16.6 + - - +
311I GLU* 2.3 38.1 + - - +
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Residues in contact with THR 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I LEU* 3.7 31.0 + - + +
256I ILE* 6.0 0.4 - - + -
263I GLY* 3.2 42.2 + - - +
264I PRO* 3.9 5.0 - - - +
267I VAL* 4.2 1.4 - - - +
290I ILE* 5.2 6.7 - - + -
304I GLU* 3.1 17.3 + - - +
305I ILE* 3.1 13.3 - - - -
307I ARG* 1.3 77.0 - - - +
309I MET* 1.3 56.7 + - - +
311I GLU* 3.3 9.7 - - - +
312I LEU* 2.9 27.9 + - - +
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Residues in contact with MET 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I ILE* 4.5 8.3 - - + +
290I ILE* 3.7 44.2 - - + +
291I GLY* 5.7 2.0 - - - -
305I ILE* 2.8 22.0 + - + +
306I GLN* 3.0 21.5 - - - +
308I THR* 1.3 72.4 - - - +
310I LEU* 1.4 52.9 - - - +
312I LEU* 2.9 9.8 + - + +
313I LEU* 2.6 39.0 + - + +
337I LEU* 4.7 5.6 - - + -
338I ASP* 4.7 13.5 - - - +
341I LEU* 3.1 44.0 - - + +
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Residues in contact with LEU 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H SER* 4.3 6.5 - - - +
276H GLU* 3.3 48.2 - - + +
278H ASP* 4.7 8.3 - - + +
279H ALA* 3.1 41.7 - - + +
322H ASN* 5.1 7.4 - - - +
306I GLN* 2.6 23.8 + - + +
307I ARG* 2.5 23.5 + - - +
309I MET* 1.4 68.9 - - - +
311I GLU* 1.3 55.7 + - - +
313I LEU* 3.1 15.6 + - + +
314I ASN* 2.7 28.9 + - - +
338I ASP* 5.9 1.1 - - - +
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Residues in contact with GLU 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H ILE* 4.7 7.3 - - - +
243H SER* 2.6 40.9 + - - +
263I GLY 4.3 0.2 - - - +
264I PRO* 3.5 24.5 - - + -
267I VAL* 3.5 15.7 - - + -
268I ARG* 3.1 35.5 + - - +
307I ARG 2.3 25.6 + - - +
308I THR* 3.3 15.7 - - - +
310I LEU* 1.3 68.1 - - - +
312I LEU* 1.3 57.2 + - - +
314I ASN* 3.6 3.7 - - - +
315I GLN* 2.8 45.6 + - - +
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Residues in contact with LEU 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I LEU* 4.0 13.5 - - + -
267I VAL* 3.5 36.6 - - + -
270I LEU* 5.0 4.3 - - + -
271I PHE* 4.3 7.9 - - + -
284I ILE* 3.7 32.8 - - + -
287I ILE* 4.9 5.2 - - + -
290I ILE* 5.6 2.9 - - + -
308I THR 2.9 16.0 + - - +
309I MET* 2.9 13.9 + - + +
311I GLU* 1.3 73.5 - - - +
313I LEU* 1.3 55.3 + - - +
316I LEU* 2.7 46.1 + - + +
329I MET* 4.5 10.5 - - + -
341I LEU* 4.0 22.9 - - + -
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Residues in contact with LEU 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H GLU* 2.6 35.0 - - - +
322H ASN* 5.6 5.6 - - - +
501H ADP 4.9 3.4 - - - +
309I MET* 2.6 22.1 + - + +
310I LEU* 3.5 15.3 - - + +
312I LEU* 1.3 75.9 - - - +
314I ASN* 1.3 56.0 + - - +
316I LEU* 4.7 0.2 - - - -
317I ASP* 2.8 26.7 + - - +
338I ASP* 5.0 3.1 - - + +
340I ALA* 2.4 45.5 - - + -
341I LEU* 4.3 12.8 - - + +
346I ARG* 2.5 47.6 + - - +
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Residues in contact with ASN 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H THR* 5.4 0.5 + - - -
241H ILE* 3.4 42.1 - - + +
275H ASP* 4.3 11.0 - - - +
276H GLU* 3.4 31.1 + - - +
310I LEU 2.7 15.7 + - - +
311I GLU* 3.7 5.8 - - - +
313I LEU* 1.3 74.7 - - - +
315I GLN* 1.3 64.8 + - - +
317I ASP* 3.1 14.1 + - - +
318I GLY* 3.2 31.0 + - - +
319I PHE* 5.6 3.5 - - - +
320I ASP* 5.4 0.7 - - - +
346I ARG* 4.7 0.2 - - - +
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Residues in contact with GLN 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 3.9 14.8 - - + -
268I ARG* 3.6 18.5 - - + +
271I PHE* 2.5 59.8 - - + +
272I ARG* 4.0 0.7 + - - -
311I GLU* 2.8 37.4 + - - +
314I ASN* 1.3 71.0 - - - +
316I LEU* 1.3 57.4 + - - +
317I ASP 2.9 11.6 + - - -
320I ASP* 5.6 3.5 - - - +
322I ARG* 2.7 35.1 + - - +
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Residues in contact with LEU 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I PHE* 2.8 34.0 - - + -
282I VAL* 5.4 0.7 - - + -
284I ILE* 5.4 1.1 - - + -
312I LEU* 2.7 31.8 + - + +
313I LEU* 4.7 0.2 - - - -
315I GLN* 1.3 71.7 - - - +
317I ASP* 1.3 58.0 + - - +
322I ARG* 5.3 3.4 - - - -
327I VAL* 3.3 51.9 - - + +
329I MET* 4.1 17.5 - - + -
341I LEU* 5.2 4.5 - - + -
345I GLY 5.1 0.5 - - - +
346I ARG* 3.5 38.6 - - + +
347I ILE* 4.3 5.8 - - + -
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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