Contacts of the helix formed by residues 270 - 284 (chain A) in PDB entry 3H0G
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 HIS 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A MET* 6.5 1.1 - - + -
264A GLY* 5.7 0.2 - - - -
265A GLU* 3.7 28.6 + - + +
266A ASP 3.2 9.3 + - - -
267A ASP* 3.5 22.7 - - - +
268A LEU 2.3 13.1 + - - +
269A THR* 1.3 81.7 + - - +
271A LYS* 1.3 53.3 + - - +
273A SER* 2.3 47.5 + - - -
274A ASP* 3.2 5.3 + - - +
322A GLN* 4.2 9.0 - - + +
323A LYS* 4.8 14.4 + - - -
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Residues in contact with LYS 271 (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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268A LEU 3.0 3.6 + - - +
269A THR 2.3 10.1 + - - +
270A HIS* 1.3 73.6 - - - +
272A LEU* 1.3 54.2 + - - +
274A ASP* 2.5 36.1 + - + +
275A ILE* 2.9 16.9 + - + +
305A HIS* 4.2 25.4 + - + +
308A THR* 2.6 39.6 + - - +
309A TYR* 5.0 7.9 - - + -
320A ALA* 3.7 12.5 + - - +
321A LEU 5.7 0.6 + - - +
322A GLN* 2.7 31.8 + - - +
328A LEU* 2.4 47.9 - - + +
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Residues in contact with LEU 272 (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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245A LEU* 5.5 8.7 - - + -
247A VAL* 5.0 13.9 - - + -
248A PRO* 5.2 3.1 - - + -
253A ARG* 4.4 20.0 - - - +
269A THR* 2.2 37.3 + - - +
271A LYS* 1.3 68.1 - - - +
273A SER* 1.3 59.8 + - - +
275A ILE* 3.3 22.0 + - + +
276A ILE* 3.4 17.8 + - - +
309A TYR* 3.4 58.3 - - + +
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Residues in contact with SER 273 (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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40A PRO 3.7 22.8 - - - +
41A GLU* 4.5 7.2 - - - -
42A THR 5.1 1.3 - - - -
43A MET* 5.1 8.7 - - - +
55A LEU* 6.3 2.7 - - - -
269A THR 4.8 0.2 - - - -
270A HIS* 2.3 39.1 + - - +
272A LEU* 1.3 76.2 - - - +
274A ASP* 1.3 64.8 + - - -
276A ILE* 3.3 5.1 + - - +
277A LYS* 3.1 31.8 + - - +
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Residues in contact with ASP 274 (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 HIS* 4.2 2.9 - - - +
271A LYS* 2.5 32.3 + - + +
273A SER* 1.3 77.2 + - - +
275A ILE* 1.3 57.6 + - - +
277A LYS* 3.3 32.7 + - - +
278A ALA* 3.2 20.6 + - - +
305A HIS* 4.4 22.2 + - + +
322A GLN* 4.8 6.8 + - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 5.7 5.2 - - + -
245A LEU* 5.5 3.6 - - + -
271A LYS* 2.9 17.2 + - + +
272A LEU* 3.6 18.4 - - + +
273A SER 3.1 0.2 - - - -
274A ASP* 1.3 76.2 - - - +
276A ILE* 1.3 64.0 + - + +
277A LYS 3.1 0.2 - - - -
278A ALA* 3.0 4.2 + - - +
279A ASN* 2.9 24.7 + - + +
302A LEU* 3.3 26.0 - - + +
305A HIS* 3.2 26.2 - - + +
306A VAL* 3.1 50.3 - - + +
309A TYR* 4.7 8.3 - - + -
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Residues in contact with ILE 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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37A ILE* 3.4 37.2 - - + +
38A GLU* 5.5 0.2 - - - -
40A PRO* 2.4 69.0 - - + +
86A ILE* 3.4 27.1 - - + -
87A GLU* 5.8 2.0 - - - +
272A LEU 3.4 13.7 + - - +
273A SER* 3.3 3.9 + - - +
275A ILE* 1.3 74.3 - - + +
277A LYS* 1.3 59.0 + - - +
279A ASN* 4.1 10.1 - - + +
280A ALA* 2.9 30.0 + - + +
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Residues in contact with LYS 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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40A PRO* 3.5 4.2 - - + +
41A GLU* 3.5 44.1 + - + +
43A MET* 5.5 4.8 - - - +
273A SER* 3.1 22.9 + - - +
274A ASP* 3.3 32.1 + - - +
276A ILE* 1.3 79.6 - - - +
278A ALA* 1.3 58.8 + - - +
279A ASN 3.6 0.2 + - - -
280A ALA* 4.8 1.4 - - - +
281A ASN* 3.4 31.5 + - - +
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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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274A ASP 3.2 9.3 + - - +
275A ILE* 3.0 10.1 + - - +
277A LYS* 1.3 78.2 - - - +
279A ASN* 1.3 58.1 + - - +
281A ASN* 4.4 3.8 - - - -
282A VAL* 3.0 27.4 - - - +
298A TYR 4.7 2.2 - - - +
301A LEU* 4.9 19.3 - - + -
302A LEU* 4.0 18.3 - - + +
305A HIS* 5.1 7.9 - - + +
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Residues in contact with ASN 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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86A ILE* 4.8 6.4 - - + +
87A GLU* 3.0 36.2 + - - -
88A LEU* 3.5 24.9 + - - +
90A LYS* 3.9 14.0 - - - +
275A ILE* 2.9 14.5 + - + +
276A ILE* 3.1 10.0 + - - +
278A ALA* 1.3 78.0 - - - +
280A ALA* 1.3 62.6 + - - +
281A ASN 3.1 1.3 - - - -
282A VAL* 2.9 4.4 + - - +
283A ARG* 2.8 28.9 + - - +
302A LEU* 3.8 19.2 - - + +
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Residues in contact with ALA 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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38A GLU 5.5 0.7 - - - +
40A PRO* 3.8 19.7 - - + -
276A ILE* 2.9 16.4 + - + +
277A LYS* 4.8 1.1 - - - +
279A ASN* 1.3 79.7 - - - +
281A ASN* 1.3 65.3 + - - +
283A ARG* 4.2 10.1 - - - +
284A ARG* 3.4 27.7 + - - +
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Residues in contact with ASN 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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277A LYS* 3.4 21.3 + - - +
278A ALA* 4.8 4.3 - - - -
279A ASN 3.1 0.8 - - - -
280A ALA* 1.3 80.3 - - - +
282A VAL* 1.3 61.6 + - + +
284A ARG* 3.7 33.3 + - - +
285A CYS* 3.0 23.4 - - - -
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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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90A LYS* 2.3 52.7 - - + +
278A ALA 3.0 24.5 - - - +
279A ASN 2.9 6.3 + - - +
281A ASN* 1.3 83.1 - - + +
283A ARG* 1.3 63.3 + - - +
284A ARG 3.4 1.1 - - - -
285A CYS* 3.5 18.3 + - - +
286A GLU* 4.2 4.2 + - - +
295A VAL* 4.5 9.9 - - + +
298A TYR* 4.3 29.4 - - + +
299A GLU* 3.7 12.1 - - + +
302A LEU* 5.5 0.2 - - + -
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Residues in contact with ARG 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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87A GLU* 4.6 21.6 + - - +
88A LEU 4.1 6.8 + - - +
89A ALA* 3.1 35.3 - - + +
90A LYS* 4.9 7.2 - - + +
279A ASN* 2.8 22.7 + - - +
280A ALA* 3.6 9.2 + - - +
282A VAL* 1.3 75.1 - - - +
284A ARG* 1.3 65.7 + - - +
285A CYS 3.1 2.0 - - - -
286A GLU* 3.2 23.8 + - + +
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Residues in contact with ARG 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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280A ALA 3.4 17.0 + - - +
281A ASN* 3.7 41.3 + - - +
283A ARG* 1.3 80.2 - - - +
285A CYS* 1.3 66.4 + - - +
286A GLU* 3.1 4.3 + - - +
287A GLN* 4.2 12.8 + - - +
288A GLU* 5.6 1.4 - - - -
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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