Contacts of the helix formed by residues 298 - 313 (chain J) 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 298 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265J ALA* 5.9 5.5 - - - +
268J LEU* 5.6 2.0 - - - +
291J LEU* 5.5 1.4 - - - +
295J TYR* 3.3 23.1 + - + +
297J SER* 1.3 79.0 - - - +
299J PRO* 1.4 75.6 - - + +
300J VAL* 3.3 27.4 - - - +
301J SER* 3.0 42.8 + - - -
302J TRP* 3.7 7.7 - - - -
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Residues in contact with PRO 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297J SER 3.8 0.2 - - - -
298J ASN* 1.4 93.3 - - + +
300J VAL* 1.3 64.0 + - + +
302J TRP* 3.2 4.4 + - + -
303J PHE* 3.1 19.5 + - - +
326J ALA* 3.5 24.7 - - - +
329J LEU* 4.1 18.4 - - + -
330J GLU* 3.7 32.3 - - + +
333J TYR* 4.0 26.2 - - + -
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Residues in contact with VAL 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J ALA* 5.2 5.8 - - + +
268J LEU* 3.7 39.3 - - + -
269J PRO* 4.9 9.4 - - + -
272J ILE* 4.1 11.9 - - + -
291J LEU* 4.3 2.2 - - + -
298J ASN* 3.2 21.1 - - - +
299J PRO* 1.3 77.9 - - + +
301J SER* 1.3 57.4 + - - +
303J PHE* 3.1 7.3 + - + +
304J ALA* 2.9 27.4 + - - +
333J TYR* 3.1 32.5 - - + +
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Residues in contact with SER 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J LEU* 3.1 44.9 + - - +
292J VAL* 3.1 14.6 + - - +
295J TYR* 3.2 24.0 - - - -
296J PRO* 4.9 0.2 - - - -
298J ASN* 3.0 15.9 + - - -
299J PRO 3.3 0.4 - - - -
300J VAL* 1.3 75.0 - - - +
302J TRP* 1.3 65.6 + - - +
304J ALA* 3.3 5.0 + - - +
305J VAL* 3.1 23.6 + - - +
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Residues in contact with TRP 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292J VAL* 4.6 10.8 - - + -
296J PRO* 2.6 29.1 + - + +
298J ASN 3.7 11.9 - - - -
299J PRO* 3.2 4.7 + - + +
301J SER* 1.3 75.7 - - - +
303J PHE* 1.3 60.6 - - - +
305J VAL* 3.2 6.0 + - + +
306J GLY* 2.9 26.7 + - - -
322J TYR* 3.4 54.5 - + + +
325J LYS* 3.4 32.1 - - + +
326J ALA* 3.6 20.2 - - + -
329J LEU* 5.0 2.9 - - + -
31M ILE* 3.8 28.3 - - + -
32M PRO* 4.0 17.5 - - + -
35M GLU* 3.6 23.8 - - + +
36M LEU* 4.1 12.3 - - + -
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Residues in contact with PHE 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 5.4 7.4 - - - -
2G LEU* 5.4 8.3 - - + -
269J PRO* 4.7 13.5 - - + -
272J ILE* 3.6 35.4 - - + -
273J GLY* 5.3 1.1 - - - -
299J PRO 3.1 12.8 + - - +
300J VAL* 3.1 12.5 + - + +
302J TRP* 1.3 73.8 - - - +
304J ALA* 1.3 66.6 + - - +
306J GLY* 3.1 1.9 + - - -
307J CYS* 2.9 45.1 + - - +
323J LEU* 3.8 12.9 - - + +
326J ALA* 3.7 5.9 - - + +
333J TYR* 4.3 19.5 - + + -
335J PRO* 3.8 32.3 - - + -
336J ALA* 3.9 19.1 - - - -
339J ALA* 4.2 8.1 - - + -
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Residues in contact with ALA 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J ILE* 3.6 31.2 - - + -
284J LEU* 4.3 3.9 - - + +
287J LEU* 5.4 0.7 - - + -
288J SER* 2.9 22.3 + - - +
291J LEU* 3.9 15.3 - - + -
300J VAL 2.9 10.5 + - - +
301J SER 3.4 9.4 - - - +
303J PHE* 1.3 74.0 - - - +
305J VAL* 1.3 64.8 + - - +
307J CYS* 3.2 8.5 + - - +
308J TYR* 3.0 19.8 + - - +
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Residues in contact with VAL 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288J SER* 3.4 22.4 - - - +
292J VAL* 3.4 33.7 - - + -
301J SER 3.1 11.4 + - - +
302J TRP* 3.2 9.4 + - + +
304J ALA* 1.3 75.2 - - - +
306J GLY* 1.3 63.3 + - - +
308J TYR* 3.3 4.6 + - - +
309J TYR* 3.1 28.8 + - + -
322J TYR* 3.6 22.9 - - + -
29M VAL* 4.3 6.1 - - + -
31M ILE* 3.2 30.3 - - + -
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Residues in contact with GLY 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J TRP 2.9 11.9 + - - -
305J VAL* 1.3 76.2 - - - +
307J CYS* 1.3 62.9 + - - +
309J TYR* 3.3 2.9 + - - -
310J LEU* 3.2 15.9 + - - +
319J ALA* 3.3 18.1 - - - +
322J TYR* 3.9 13.0 - - - -
323J LEU* 3.7 28.9 - - - -
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Residues in contact with CYS 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LEU* 4.8 9.0 - - - -
272J ILE* 3.8 19.1 - - + -
276J VAL* 4.2 14.3 - - + +
284J LEU* 4.0 6.5 - - + -
303J PHE* 2.9 47.4 + - - +
304J ALA 3.4 8.7 - - - +
306J GLY* 1.3 78.5 - - - +
308J TYR* 1.3 62.5 + - - +
310J LEU* 3.0 28.5 + - - +
311J MET* 3.1 17.3 + - - +
323J LEU* 4.3 1.0 - - - +
339J ALA* 5.1 1.8 - - - -
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Residues in contact with TYR 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C HIS* 5.3 1.4 - - - -
281J ALA* 3.8 18.6 - - + -
284J LEU* 3.5 20.6 - - + +
285J PHE* 3.3 43.8 - + + +
288J SER* 4.0 6.1 - - - +
304J ALA 3.0 12.7 + - - +
305J VAL* 3.5 6.5 - - - +
306J GLY 3.2 0.2 - - - -
307J CYS* 1.3 76.8 - - - +
309J TYR* 1.3 76.8 + + - +
310J LEU 3.2 0.7 + - - -
311J MET* 3.2 12.1 + - + +
312J VAL* 3.3 27.6 + - + +
26M TYR* 3.9 8.2 - + - -
27M GLU* 2.6 45.4 + - - +
29M VAL* 3.8 22.9 - - + -
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Residues in contact with TYR 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305J VAL* 3.1 34.8 + - + -
306J GLY 3.3 6.7 + - - +
308J TYR* 1.3 88.5 - + - +
310J LEU* 1.3 59.2 - - - +
312J VAL* 3.9 5.3 - - + +
313J GLY 3.5 13.5 + - - -
315J LYS* 3.6 43.3 - - + +
316J ASN* 3.9 5.9 + - - -
318J HIS* 4.2 10.1 - + + -
319J ALA* 3.8 14.4 - - + +
322J TYR* 3.6 34.6 + + - -
27M GLU 4.3 4.0 - - - -
28M ASP* 3.1 37.4 - - - +
29M VAL* 3.0 32.4 + - + -
31M ILE* 4.7 0.2 - - + -
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Residues in contact with LEU 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LEU* 4.2 24.5 - - + -
276J VAL* 5.8 3.4 - - + -
306J GLY 3.2 12.2 + - - +
307J CYS* 3.0 19.8 + - - +
309J TYR* 1.3 75.9 - - - +
311J MET* 1.3 65.5 + - + +
313J GLY* 3.3 13.2 + - - -
316J ASN* 3.2 25.3 + - - +
319J ALA* 3.6 12.1 - - + -
323J LEU* 4.5 10.3 - - + -
339J ALA* 4.5 13.9 - - + +
342J HIS* 5.4 3.8 - - + -
343J SER* 4.2 23.1 - - - +
346J VAL* 5.5 3.1 - - + -
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Residues in contact with MET 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J LEU 3.6 13.2 - - - +
276J VAL* 3.5 40.6 - - + +
279J ASN* 3.8 19.4 - - - +
280J LYS 3.6 11.2 - - - +
281J ALA* 3.4 45.1 - - + +
284J LEU* 3.3 34.5 - - + -
307J CYS 3.1 4.3 + - - +
308J TYR* 3.2 6.5 + - - +
310J LEU* 1.3 77.6 - - - +
312J VAL* 1.3 64.0 + - - +
313J GLY* 3.5 0.5 + - - -
26M TYR* 5.5 2.1 - - - -
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Residues in contact with VAL 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281J ALA* 5.3 0.2 - - + -
308J TYR* 3.5 35.4 - - + +
309J TYR* 3.9 7.2 - - + +
311J MET* 1.3 79.5 - - + +
313J GLY* 1.3 70.3 + - - +
314J HIS* 4.1 6.6 - - - -
315J LYS* 4.1 18.2 - - + -
26M TYR* 3.6 61.8 - - + +
27M GLU 4.9 0.9 - - - +
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Residues in contact with GLY 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J TYR 3.5 3.7 + - - -
310J LEU 3.3 15.6 + - - -
311J MET 3.3 0.6 - - - -
312J VAL* 1.3 91.2 - - - +
314J HIS* 1.3 74.6 - - - +
315J LYS* 2.9 13.3 + - - +
316J ASN* 4.8 5.2 - - - -
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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