Contacts of the helix formed by residues 251 - 263 (chain C) in PDB entry 4H0N
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 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C TYR* 4.0 1.1 - - + -
249C ASP 3.6 3.3 - - - +
250C LYS* 1.3 91.8 - - + +
252C ARG* 1.3 67.2 + - - +
253C GLU 4.3 2.0 - - - +
254C VAL* 3.0 29.4 + - + +
255C VAL* 3.4 8.8 + - - +
23D GLY 4.8 6.1 - - - +
24D LEU 5.5 0.2 - - - -
25D ASP* 3.7 42.8 - - + +
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Residues in contact with ARG 252 (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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221C ILE 5.5 0.2 + - - -
223C TYR* 3.2 59.2 - - + +
225C THR* 3.9 21.0 - - - +
226C SER* 4.0 7.7 + - - +
251C PRO* 1.3 70.9 - - - +
253C GLU* 1.3 58.6 + - - +
255C VAL* 2.8 21.4 + - - +
256C GLN* 3.0 36.3 + - + +
22D SER 3.6 22.0 + - - -
23D GLY 4.0 15.6 + - - +
24D LEU* 6.3 0.4 - - - +
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Residues in contact with GLU 253 (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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251C PRO* 3.2 1.4 - - - +
252C ARG* 1.3 78.7 - - - +
254C VAL* 1.3 60.6 + - + +
256C GLN* 3.8 10.6 + - + +
257C LYS* 3.3 21.3 + - - +
3D HIS* 3.3 29.0 + - - -
23D GLY 5.1 1.4 + - - -
24D LEU* 4.5 20.8 - - + +
25D ASP* 3.4 35.8 + - + +
113D TYR* 5.6 0.3 + - - -
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Residues in contact with VAL 254 (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* 4.2 18.2 - - + -
251C PRO* 3.0 36.7 + - + +
253C GLU* 1.3 75.0 - - + +
255C VAL* 1.3 66.9 + - - +
257C LYS* 3.3 9.5 + - + +
258C CYS* 3.1 21.0 + - + +
279C LEU* 4.2 8.1 - - + -
25D ASP* 4.4 11.0 - - - +
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Residues in contact with VAL 255 (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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221C ILE* 3.8 18.2 - - + -
223C TYR* 3.6 27.8 - - + +
248C THR* 4.0 13.5 - - + -
250C LYS* 4.6 1.6 - - + -
251C PRO 3.8 9.6 - - - +
252C ARG 2.8 7.6 + - - +
254C VAL* 1.3 77.4 - - - +
256C GLN* 1.3 67.3 + - - +
258C CYS* 3.1 5.0 + - - +
259C TYR* 3.0 45.8 + - + -
279C LEU* 3.8 29.4 - - + -
281C LEU* 5.5 0.2 - - + -
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Residues in contact with GLN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C TYR* 4.6 1.6 + - - -
252C ARG* 3.0 41.2 + - + +
253C GLU* 4.0 10.1 - - + +
254C VAL 3.3 0.2 - - - -
255C VAL* 1.3 85.3 - - - +
257C LYS* 1.3 64.8 + - - +
259C TYR* 3.4 12.6 + - - +
260C ALA* 3.2 24.8 + - - +
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Residues in contact with LYS 257 (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 GLU 3.3 12.9 + - - +
254C VAL* 3.3 14.3 + - + +
255C VAL 3.2 0.6 - - - -
256C GLN* 1.3 78.6 - - - +
258C CYS* 1.3 62.5 + - - +
260C ALA* 3.6 5.2 + - - +
261C ALA* 3.2 27.0 + - - +
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Residues in contact with CYS 258 (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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254C VAL* 3.1 11.8 + - + +
255C VAL 3.1 9.5 + - - +
257C LYS* 1.3 76.5 - - - +
259C TYR* 1.3 59.3 + - - +
261C ALA* 3.1 7.7 + - - +
262C ALA* 2.9 26.7 + - - +
275C LEU* 3.1 43.1 - - - +
276C PHE* 3.6 24.2 - - - -
278C GLU* 4.7 4.3 - - - +
279C LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 259 (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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216C ALA* 2.7 36.0 + - - +
217C LYS* 4.3 20.0 - - + -
219C PHE* 4.0 9.0 + - - +
221C ILE* 4.0 18.6 - - + +
255C VAL* 3.0 44.5 + - + +
256C GLN* 3.9 14.4 - - - +
257C LYS 3.4 0.6 - - - -
258C CYS* 1.3 76.6 - - - +
260C ALA* 1.3 56.9 + - - +
262C ALA* 3.2 2.6 + - - +
263C ALA* 2.9 30.1 + - - +
276C PHE* 3.6 35.2 - + - -
281C LEU* 5.9 0.2 - - - +
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Residues in contact with ALA 260 (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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256C GLN 3.2 15.7 + - - +
257C LYS* 4.1 4.9 - - - +
259C TYR* 1.3 78.9 - - - +
261C ALA* 1.3 61.0 + - - +
263C ALA* 3.8 11.5 + - - +
264C GLN* 3.5 20.1 - - - +
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Residues in contact with ALA 261 (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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257C LYS* 3.2 19.0 + - - +
258C CYS* 3.1 12.3 + - - +
259C TYR 3.1 0.4 - - - -
260C ALA* 1.3 75.5 - - - +
262C ALA* 1.3 63.6 + - - +
263C ALA 3.1 1.3 - - - -
264C GLN* 3.0 19.3 + - - +
265C ASN* 2.9 21.1 + - - -
275C LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 262 (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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258C CYS 2.9 13.4 + - - +
259C TYR* 3.2 4.5 + - + +
261C ALA* 1.3 71.1 - - - +
263C ALA* 1.3 57.0 + - - +
264C GLN 3.0 5.6 - - - -
265C ASN* 3.0 32.3 + - - +
272C PHE* 3.5 25.2 - - + +
275C LEU* 3.8 11.6 - - + +
276C PHE* 3.5 33.9 - - + -
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LYS* 5.3 15.0 - - - +
259C TYR 2.9 17.0 + - - +
260C ALA* 3.8 12.6 - - - +
261C ALA 3.1 0.6 - - - -
262C ALA* 1.3 75.1 - - - +
264C GLN* 1.3 59.4 + - + +
265C ASN 3.3 5.6 + - - +
272C PHE* 5.8 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