Contacts of the helix formed by residues 274 - 285 (chain A) in PDB entry 3H4B
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 GLY 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLU 3.1 12.1 + - - -
271A LYS 5.0 0.2 - - - -
272A GLU 3.8 0.6 - - - +
273A LEU* 1.3 79.2 - - - +
275A ILE* 1.3 55.3 + - - -
276A SER* 2.6 20.4 + - - -
277A VAL 3.3 2.2 + - - -
278A ALA* 2.9 21.0 + - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLU* 3.2 48.5 + - + +
274A GLY* 1.3 70.5 - - - -
276A SER* 1.3 61.6 + - - +
279A GLN* 2.9 51.1 + - - +
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Residues in contact with SER 276 (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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274A GLY* 2.6 7.4 + - - -
275A ILE* 1.3 77.3 - - - +
277A VAL* 1.3 76.2 + - - +
278A ALA 2.8 2.4 + - - -
279A GLN* 3.0 3.8 + - - +
280A ARG* 2.9 32.6 + - - +
847T T 5.1 8.8 + - - -
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Residues in contact with VAL 277 (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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246A THR* 4.3 24.0 - - + +
273A LEU* 3.7 35.4 + - + +
274A GLY 3.3 1.6 + - - -
276A SER* 1.3 82.9 + - - +
278A ALA* 1.3 57.7 + - - +
280A ARG* 3.7 26.2 - - - +
281A ILE* 2.9 42.9 + - + +
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Residues in contact with ALA 278 (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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266A PRO 5.3 0.4 - - - +
269A LEU* 3.5 21.5 - - + +
270A GLU* 3.3 33.9 - - + +
273A LEU* 4.4 3.5 - - + +
274A GLY 2.9 17.7 + - - +
275A ILE 4.2 0.4 - - - +
276A SER 2.8 3.8 + - - -
277A VAL* 1.3 79.1 - - - +
279A GLN* 1.3 64.1 + - - +
280A ARG 3.0 1.4 + - - -
281A ILE* 3.5 7.4 - - - +
282A GLN* 3.1 23.0 + - - +
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Residues in contact with GLN 279 (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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270A GLU* 5.3 8.0 - - - +
275A ILE* 2.9 38.9 + - + +
276A SER* 3.0 2.9 + - - +
278A ALA* 1.3 78.9 - - - +
280A ARG* 1.3 59.0 + - - +
282A GLN* 3.8 5.9 + - - +
283A LYS* 3.5 42.2 + - - +
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Residues in contact with ARG 280 (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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241A GLY* 4.2 20.6 + - - -
276A SER* 2.9 23.1 + - - +
277A VAL* 3.7 33.1 - - - +
279A GLN* 1.3 73.8 - - - +
281A ILE* 1.3 74.8 + - - +
282A GLN 3.1 1.6 - - - -
283A LYS* 3.1 11.5 + - - +
284A LEU* 3.1 33.5 + - + +
288A GLU 5.0 0.2 - - - +
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Residues in contact with ILE 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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241A GLY 4.8 3.1 - - - +
242A ILE* 3.9 26.5 - - + +
246A THR* 4.0 25.1 - - + -
250A LEU* 4.2 18.2 - - + -
261A LEU* 3.7 18.5 - - + +
269A LEU* 4.9 2.5 - - + -
273A LEU* 4.1 16.2 - - + -
277A VAL* 2.9 35.0 + - + +
278A ALA* 3.5 6.7 - - - +
280A ARG* 1.3 86.1 - - - +
282A GLN* 1.3 61.6 + - - +
284A LEU* 3.3 17.5 - - + +
285A SER 3.0 20.8 + - - -
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Residues in contact with GLN 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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261A LEU* 3.4 23.0 + - + +
262A GLN 4.5 4.5 - - - -
264A PHE 3.1 26.3 + - - -
266A PRO* 3.7 26.6 - - - +
269A LEU* 3.4 27.8 - - + +
278A ALA 3.1 16.6 + - - +
279A GLN* 4.2 6.0 - - - +
281A ILE* 1.3 77.3 - - - +
283A LYS* 1.3 63.8 + - - +
285A SER* 2.8 9.9 + - - -
286A PHE* 2.8 38.6 - - + -
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Residues in contact with LYS 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 GLN* 3.5 33.3 + - - +
280A ARG* 3.1 11.5 + - - +
282A GLN* 1.3 78.3 - - - +
284A LEU* 1.3 63.8 + - - +
286A PHE* 3.0 17.0 + - - +
288A GLU* 3.1 53.5 + - + +
289A ASP* 5.9 0.4 - - - -
290A ASN* 4.1 22.6 - - - +
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Residues in contact with LEU 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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204A LEU* 3.4 36.3 - - + +
230A ILE* 3.9 5.2 - - - +
239A ILE* 4.2 15.2 - - + +
240A PRO 3.7 20.6 - - - +
241A GLY* 4.5 8.5 - - - -
242A ILE* 4.9 0.9 - - + -
280A ARG* 3.1 25.5 + - + +
281A ILE* 3.3 32.1 - - + +
282A GLN 3.1 0.2 - - - -
283A LYS* 1.3 72.3 - - - +
285A SER* 1.3 52.3 + - - +
286A PHE 2.7 16.3 + - - -
287A GLY* 2.7 15.8 + - - -
288A GLU 3.4 13.2 + - - +
289A ASP* 4.0 12.8 - - + +
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Residues in contact with SER 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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230A ILE* 3.2 14.6 - - - +
239A ILE* 4.0 12.8 - - - -
258A VAL* 3.4 8.9 - - - +
261A LEU* 3.5 32.6 - - - +
262A GLN* 2.5 51.7 - - - +
281A ILE 3.0 7.4 + - - -
282A GLN* 2.8 20.1 + - - -
284A LEU* 1.3 74.0 - - - +
286A PHE* 1.3 52.4 + - - +
287A GLY 3.5 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