Contacts of the helix formed by residues 279 - 288 (chain L) in PDB entry 3Q3G
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 LYS 279 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L GLU* 4.8 4.1 - - - +
277L SER* 3.1 7.0 - - - +
278L GLU* 1.4 74.5 - - - +
280L SER* 1.4 62.5 + - - +
281L ARG 3.3 1.6 - - - -
282L GLN* 3.1 49.7 + - - +
283L GLU* 3.7 4.0 + - - +
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Residues in contact with SER 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L GLU* 3.7 25.2 + - - -
274L ALA 3.2 20.6 + - - -
275L PHE* 3.2 23.6 + - - -
277L SER* 2.6 48.0 + - - -
279L LYS* 1.4 69.6 - - - +
281L ARG* 1.4 62.7 + - - +
283L GLU* 3.1 20.6 + - - +
284L LEU 3.4 4.2 + - - -
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Residues in contact with ARG 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L PHE 3.3 17.5 + - - +
276L ARG* 2.8 39.5 + - - +
277L SER 3.2 6.7 + - - +
278L GLU* 3.3 43.7 + - - +
279L LYS 3.3 0.2 - - - -
280L SER* 1.4 73.4 + - - +
282L GLN* 1.4 60.4 + - - +
284L LEU* 3.2 11.6 + - + +
285L ASN* 3.0 36.4 + - - +
296L VAL* 5.6 0.2 - - - +
298L GLN* 3.5 27.6 + - - +
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Residues in contact with GLN 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278L GLU 3.3 18.2 - - - +
279L LYS* 3.1 46.4 + - - +
281L ARG* 1.4 73.5 - - - +
283L GLU* 1.4 55.9 + - - +
285L ASN* 3.3 15.5 + - - +
286L THR* 2.7 38.5 + - - +
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Residues in contact with GLU 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L THR* 4.9 0.3 + - - -
243L GLY 4.9 0.3 - - - +
244L GLU* 3.3 32.8 - - + +
245L LYS* 2.8 28.6 + - - +
252L TYR* 2.6 41.0 + - + +
275L PHE* 5.0 4.9 - - + -
279L LYS 3.7 3.1 + - - +
280L SER* 3.1 14.7 + - - +
282L GLN* 1.4 78.7 - - - +
284L LEU* 1.4 55.6 + - - +
286L THR* 3.2 9.4 + - - -
287L ILE* 3.1 38.2 + - + +
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Residues in contact with LEU 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241L THR* 4.2 4.9 - - + -
268L VAL* 3.2 42.1 - - + +
270L GLY* 3.8 26.0 - - - +
275L PHE* 3.7 35.9 - - + -
280L SER 3.4 1.9 + - - +
281L ARG* 3.2 13.5 + - + +
283L GLU* 1.4 77.7 - - - +
285L ASN* 1.4 55.7 - - - +
287L ILE* 3.4 5.1 + - + +
288L ALA* 3.0 25.3 + - - +
296L VAL* 3.9 15.0 - - + -
298L GLN* 3.8 33.2 - - + +
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Residues in contact with ASN 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L ARG* 3.0 22.7 + - - +
282L GLN* 3.3 16.7 + - - +
284L LEU* 1.4 72.4 - - - +
286L THR* 1.4 59.9 + - - +
288L ALA* 3.0 21.4 - - - +
289L SER 5.4 0.2 - - - -
290L LYS* 5.5 4.9 - - - +
292L PRO* 3.4 37.6 - - + +
296L VAL* 3.6 16.2 - - - +
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Residues in contact with THR 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252L TYR* 3.6 35.7 - - + -
256L ILE* 3.4 24.7 - - + +
282L GLN* 2.7 21.2 + - - +
283L GLU* 3.2 12.0 + - - -
285L ASN* 1.4 74.7 - - - +
287L ILE* 1.3 65.2 + - - +
288L ALA 3.9 2.8 - - - +
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Residues in contact with ILE 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L THR* 4.0 9.2 - - + -
215L ILE* 3.9 13.5 - - + -
239L VAL* 3.9 24.9 - - + -
241L THR* 4.6 9.9 - - + -
252L TYR* 3.5 38.4 - - + +
256L ILE* 3.7 7.5 - - - +
266L ARG* 3.0 32.6 + - + +
268L VAL* 3.8 29.2 - - + -
275L PHE* 6.0 0.4 - - + -
283L GLU* 3.1 26.0 + - + +
284L LEU* 3.8 7.6 - - + +
286L THR* 1.3 76.5 - - - +
288L ALA* 1.4 58.2 + - - +
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Residues in contact with ALA 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266L ARG* 3.4 19.5 + - - +
268L VAL* 3.7 11.4 - - + -
284L LEU 3.0 17.5 + - - +
285L ASN 3.0 18.4 - - - +
286L THR 3.9 2.8 - - - +
287L ILE* 1.4 78.6 - - - +
289L SER* 1.4 65.0 + - - +
290L LYS* 3.9 2.1 + - - +
292L PRO* 5.7 0.2 - - + -
295L HIS* 3.8 12.8 - - + +
296L VAL* 3.6 22.2 - - + -
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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