Contacts of the helix formed by residues 280 - 294 (chain A) in PDB entry 5EGO
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 PRO 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ALA 4.5 1.3 - - - +
279A PHE* 1.3 96.4 - - + +
281A LYS* 1.3 65.8 + - - +
282A VAL* 4.3 14.1 - - + -
283A ALA* 3.0 29.3 + - + +
284A THR* 3.4 8.5 + - - -
312A THR 4.8 7.2 - - - +
314A LEU* 4.4 5.6 - - + -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE 3.4 4.3 + - - -
280A PRO* 1.3 72.5 - - - +
282A VAL* 1.3 76.5 + - + +
284A THR* 3.4 8.6 + - - -
285A ASN* 3.1 38.2 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PRO* 4.3 15.0 - - + -
281A LYS* 1.3 95.4 - - + +
283A ALA* 1.3 66.1 + - + +
285A ASN* 3.6 9.2 + - + +
286A ILE* 3.3 38.3 + - + +
311A ASP 5.7 1.1 - - - +
312A THR* 5.6 3.6 - - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 4.8 1.1 - - + -
280A PRO* 3.0 27.8 + - + +
282A VAL* 1.3 79.4 - - - +
284A THR* 1.3 65.9 + - - +
286A ILE* 4.6 0.4 - - - -
287A MET* 3.4 28.9 + - - +
312A THR* 3.6 37.8 - - - +
314A LEU* 3.9 16.2 - - + -
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 4.2 13.5 + - - +
280A PRO 3.4 6.4 + - - -
281A LYS* 3.5 14.2 - - - -
283A ALA* 1.3 75.8 - - - +
285A ASN* 1.3 66.4 + - - +
287A MET* 3.1 12.3 + - - +
288A ARG* 2.8 61.5 + - + +
322A TRP* 4.4 12.9 + - + +
23D G 4.5 8.1 + - - -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS* 3.1 30.3 + - - +
282A VAL* 3.8 9.6 - - + +
283A ALA 3.5 0.2 - - - -
284A THR* 1.3 86.4 - - - +
286A ILE* 1.3 58.3 + - + +
288A ARG* 3.8 10.4 + - - +
289A ALA* 2.8 31.9 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A VAL* 3.3 33.8 + - + +
283A ALA 3.8 3.8 - - - +
284A THR 3.2 0.2 - - - -
285A ASN* 1.3 77.2 - - + +
287A MET* 1.3 58.4 + - - +
289A ALA* 3.3 7.3 + - - +
290A TRP* 2.9 25.5 + - - +
308A LEU* 3.9 22.6 - - + +
311A ASP* 3.7 39.3 - - + +
312A THR* 4.1 13.7 - - + -
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 4.6 2.5 - - + -
283A ALA 3.4 18.1 + - - +
284A THR* 3.1 7.4 + - - +
286A ILE* 1.3 74.4 - - + +
288A ARG* 1.3 56.7 + - - +
290A TRP* 3.2 7.8 + - - +
291A LEU* 2.7 34.7 + - - +
308A LEU* 4.8 6.3 - - + -
312A THR* 3.9 11.9 - - + -
314A LEU* 3.3 33.9 - - + -
319A VAL* 4.3 15.5 - - - -
322A TRP* 3.5 58.8 - - + +
323A PHE* 4.0 18.6 - - + -
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A THR* 2.8 41.3 + - - +
285A ASN* 3.8 9.9 + - - +
287A MET* 1.3 75.3 - - - +
289A ALA* 1.3 58.8 + - - +
291A LEU* 3.1 1.7 + - + -
292A PHE* 2.9 62.0 + - + -
322A TRP* 3.7 16.7 - - + -
330A ILE* 3.8 25.2 - - + +
22D T 4.5 13.9 + - - -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN 2.8 19.2 + - - +
286A ILE* 3.5 7.2 - - - +
288A ARG* 1.3 76.6 - - - +
290A TRP* 1.3 62.1 + - - +
292A PHE* 3.8 4.4 + - - +
293A GLN* 3.3 25.8 + - - +
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Residues in contact with TRP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ILE 2.9 14.1 + - - +
287A MET* 3.4 9.0 - - - +
288A ARG 3.2 0.2 - - - -
289A ALA* 1.3 74.2 - - - +
291A LEU* 1.3 67.1 + - - +
293A GLN* 3.1 6.8 + - - -
294A HIS* 2.6 73.2 + + + -
297A HIS 4.7 1.6 - - - -
298A PRO* 4.2 3.1 - - + -
299A TYR 3.9 12.1 - - - -
300A PRO* 3.6 36.8 - - + -
304A GLN* 3.5 40.5 - - - +
308A LEU* 4.0 32.4 - - + +
323A PHE* 3.6 18.2 - + + -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A MET 2.7 21.2 + - - +
288A ARG* 3.4 10.3 - - - +
290A TRP* 1.3 78.9 - - - +
292A PHE* 1.3 77.0 + - + +
294A HIS 3.3 4.9 + - - -
295A LEU* 3.3 29.8 + - + -
298A PRO* 3.7 24.7 - - + +
322A TRP* 4.1 13.0 - - + -
323A PHE* 3.9 20.9 - - + -
326A ALA* 4.5 10.8 - - + -
327A ARG* 5.0 3.1 - - + -
330A ILE* 4.4 10.5 - - + -
331A VAL* 3.8 25.4 - - + -
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ARG* 2.9 53.7 + - + +
289A ALA* 4.4 4.7 - - - +
291A LEU* 1.3 82.1 - - + +
293A GLN* 1.3 64.1 + - - +
294A HIS 3.2 1.9 + - - -
295A LEU* 3.7 31.6 + - + +
330A ILE* 4.0 28.9 - - + -
334A MET* 3.9 24.2 - - + -
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ALA 3.3 20.2 + - - +
290A TRP* 3.1 6.7 + - - +
292A PHE* 1.3 77.3 - - - +
294A HIS* 1.3 80.6 + - + +
295A LEU 3.6 1.0 + - - -
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Residues in contact with HIS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A TRP* 2.6 86.2 + + + +
291A LEU 3.4 3.8 - - - -
292A PHE 3.2 0.2 - - - -
293A GLN* 1.3 103.1 - - + +
295A LEU* 1.3 62.9 + - - +
296A THR* 3.3 4.5 - - - -
297A HIS 3.0 11.3 - - - +
298A PRO* 2.9 20.8 - - - +
304A GLN* 4.5 6.1 + - - -
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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