Contacts of the helix formed by residues 279 - 288 (chain C) in PDB entry 1H5R
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 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276C LEU* 2.8 24.4 + - - +
278C LYS* 1.3 83.9 - - - +
280C ASN* 1.3 64.1 + - - +
281C TYR* 3.0 9.7 + - - +
282C GLY 2.9 20.3 + - - -
283C GLN* 3.0 28.4 + - - +
15D THR* 3.5 31.3 + - + +
16D ARG* 4.6 7.9 - - - +
18D TYR* 3.5 32.0 - - - +
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Residues in contact with ASN 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 5.1 3.8 + - - +
279C ASN* 1.3 75.5 - - - +
281C TYR* 1.3 57.9 + - - +
283C GLN* 3.4 20.0 + - - +
284C TYR* 3.0 26.2 + - - +
16D ARG 5.1 6.4 + - - +
230D HIS* 6.3 3.1 - - + +
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Residues in contact with TYR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASP* 4.4 4.3 - - + -
34C LYS* 3.8 21.3 - - + -
38C TYR* 3.7 18.9 - + - -
250C LYS* 3.8 22.9 - - + +
253C CYS* 3.5 13.5 - - - -
254C PRO* 3.7 3.8 - - - +
255C GLU* 2.7 41.1 + - - -
279C ASN* 3.0 7.7 + - - +
280C ASN* 1.3 78.0 - - - +
282C GLY* 1.3 60.6 + - - +
284C TYR* 3.1 9.5 + - - +
285C LEU* 2.9 45.6 + - + +
18D TYR* 3.9 32.9 + + + +
19D PRO* 3.4 26.5 - - + -
230D HIS* 6.4 0.2 - + - -
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Residues in contact with GLY 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C ALA* 3.8 2.6 - - - +
276C LEU* 3.3 31.8 - - - +
277C ILE* 3.3 15.3 - - - +
279C ASN* 2.9 11.7 + - - -
281C TYR* 1.3 77.7 - - - +
283C GLN* 1.3 58.5 + - - +
285C LEU* 3.3 10.6 + - - +
286C TYR 2.9 24.4 + - - -
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Residues in contact with GLN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LEU 4.2 0.2 + - - -
277C ILE* 2.8 38.7 + - + +
278C LYS 3.9 4.2 + - - -
279C ASN* 3.0 26.0 + - - +
280C ASN* 3.6 23.8 + - - +
281C TYR 3.1 0.2 - - - -
282C GLY* 1.3 75.0 - - - +
284C TYR* 1.3 56.1 + - - +
286C TYR* 3.2 3.7 + - - +
287C LYS* 2.9 30.8 + - - +
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Residues in contact with TYR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ARG* 3.7 1.0 + - - -
248C GLY 3.7 23.1 - - - -
249C LEU* 3.5 11.7 - - + +
250C LYS* 2.9 58.3 + - + -
253C CYS* 4.2 7.2 - - - -
256C GLU* 2.8 37.8 + - - -
280C ASN 3.0 13.4 + - - +
281C TYR 3.1 8.3 + - - +
283C GLN* 1.3 75.8 - - - +
285C LEU* 1.3 73.4 + - + +
287C LYS* 3.1 24.7 + - + +
288C MET* 3.3 23.9 + - + +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C CYS* 3.9 19.5 - - - -
255C GLU* 3.6 38.1 - - + +
269C VAL* 3.5 16.4 - - + +
272C LEU* 4.6 8.1 - - + -
273C ALA* 3.8 16.2 - - + +
276C LEU* 4.1 19.5 - - + -
281C TYR* 2.9 43.8 + - + +
282C GLY* 3.6 7.9 - - - +
284C TYR* 1.3 76.0 - - + +
286C TYR* 1.3 63.7 + - - +
288C MET* 3.3 29.4 + - + +
289C THR* 3.7 0.3 - - - +
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ARG* 4.5 31.4 + - + -
273C ALA* 3.8 14.1 - - + -
274C VAL* 4.3 19.7 - - + -
277C ILE* 3.2 35.4 - - + -
282C GLY 2.9 7.1 + - - +
283C GLN* 3.5 3.4 - - - +
284C TYR 3.2 0.4 - - - -
285C LEU* 1.3 77.8 - - - +
287C LYS* 1.3 64.9 + - - +
289C THR* 2.8 28.8 + - - -
290C LYS* 3.8 38.3 + - + +
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Residues in contact with LYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B HIS* 5.6 7.2 - - - -
170B ASN* 4.1 20.7 + - - +
248C GLY 6.2 0.7 - - - +
249C LEU* 6.4 2.0 - - + -
283C GLN 2.9 17.0 + - - +
284C TYR* 3.1 17.0 + - + +
286C TYR* 1.3 77.5 - - - +
288C MET* 1.3 67.5 + - + +
290C LYS* 3.0 28.8 + - + +
291C ASP 4.6 18.3 - - - +
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Residues in contact with MET 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C GLU* 4.3 4.9 - - + +
256C GLU* 3.4 50.5 - - - +
259C PHE* 3.9 30.5 - - + -
260C ARG* 4.4 16.7 + - - +
269C VAL* 3.5 26.9 - - + -
284C TYR* 3.3 29.0 + - + +
285C LEU* 3.4 21.1 - - + +
286C TYR 3.1 0.4 - - - -
287C LYS* 1.3 80.6 - - + +
289C THR* 1.3 58.9 + - + +
290C LYS 3.2 9.1 + - - +
291C ASP 5.5 0.2 - - - -
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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