Contacts of the helix formed by residues 280 - 291 (chain A) in PDB entry 4HE2
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 GLU 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASP* 3.5 13.2 - - - +
121A ASP* 4.5 0.7 - - - -
135A ILE* 4.1 6.8 - - + +
248A MET* 3.6 19.1 - - + +
275A LEU* 3.4 21.4 - - + +
276A ARG* 2.7 46.0 + - - +
279A TYR* 1.3 87.2 - - + +
281A CYS* 1.3 67.5 + - - +
282A ASN 3.6 0.4 - - - -
283A PRO* 3.5 3.0 - - - +
284A VAL* 3.3 25.6 + - - +
402A PO3 4.1 1.4 + - - -
403A MG 2.2 8.5 - - - -
404A ZN 2.1 35.2 - - - -
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Residues in contact with CYS 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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275A LEU* 3.4 33.4 - - - -
276A ARG 2.9 18.6 + - - +
277A LEU* 4.0 2.2 - - - +
280A GLU* 1.3 71.7 - - - +
282A ASN* 1.3 61.2 + - - +
284A VAL* 3.4 8.7 + - - +
285A ALA* 2.8 31.7 + - - +
302A VAL* 3.9 12.1 - - + -
314A VAL* 3.7 30.1 - - + -
316A LEU* 4.0 22.3 - - + +
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Residues in contact with ASN 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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137A ALA* 5.3 0.2 - - + -
139A TYR* 3.6 21.1 + - - +
154A GLN 4.4 6.1 + - - -
156A GLY* 3.6 19.5 - - - +
159A ILE* 4.2 6.1 - - + -
277A LEU* 2.9 41.8 + - - +
278A LEU* 4.1 7.3 - - - +
281A CYS* 1.3 73.5 - - - +
283A PRO* 1.4 67.4 - - + +
285A ALA* 4.3 0.7 - - - -
286A TYR* 2.9 24.9 + - - +
302A VAL* 3.4 27.9 + - - +
303A LEU* 3.6 12.6 - - - +
305A VAL 5.2 0.8 + - - -
307A PRO* 4.7 4.0 - - - +
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Residues in contact with PRO 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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135A ILE* 3.4 30.1 - - + -
136A PHE 3.5 19.7 - - - +
137A ALA* 3.8 17.7 - - + +
162A ALA* 4.2 11.8 - - + +
163A GLY 4.3 3.8 - - - +
278A LEU 3.5 13.0 - - - +
279A TYR 3.8 9.6 - - - -
280A GLU 3.5 11.4 - - - +
282A ASN* 1.4 94.1 - - + +
284A VAL* 1.3 60.8 + - - +
286A TYR* 3.3 3.8 + - - +
287A ILE* 3.1 26.6 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 4.4 10.1 - - + -
164A TYR* 4.4 17.0 - - + -
248A MET* 3.7 24.5 - - + -
249A VAL* 5.7 2.0 - - - -
252A VAL* 4.0 20.0 - - + -
280A GLU 3.3 19.0 + - - +
281A CYS 3.5 5.8 - - - +
283A PRO* 1.3 74.3 - - - +
285A ALA* 1.3 62.6 + - - +
287A ILE* 3.3 6.5 + - - +
288A ILE* 2.9 34.8 + - - +
316A LEU* 4.0 14.6 - - + -
318A LEU* 3.7 19.7 - - + -
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Residues in contact with ALA 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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281A CYS 2.8 19.0 + - - +
282A ASN 3.7 3.1 - - - +
284A VAL* 1.3 77.5 - - - +
286A TYR* 1.3 57.5 + - - +
288A ILE* 3.9 1.0 - - - +
289A GLU* 2.9 35.3 + - - +
295A ALA* 3.5 29.3 - - + +
302A VAL* 3.8 20.2 - - + -
303A LEU* 3.9 14.6 - - + -
316A LEU* 5.1 0.7 - - + -
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Residues in contact with TYR 286 (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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156A GLY 4.2 6.3 - - - -
157A ARG* 5.5 3.6 - - - -
159A ILE* 3.7 54.8 + - + -
160A VAL 4.2 2.0 + - - -
162A ALA* 3.7 17.0 - - + -
176A SER* 3.3 36.3 - - - -
177A THR 3.8 2.3 - - - -
178A GLY* 3.2 27.7 + - - -
282A ASN 2.9 16.8 + - - +
283A PRO 3.5 4.7 - - - +
285A ALA* 1.3 77.3 - - - +
287A ILE* 1.3 57.7 + - - +
289A GLU* 4.0 0.9 - - - +
290A GLN* 2.9 50.0 + - + +
303A LEU* 3.8 16.3 - - + +
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Residues in contact with ILE 287 (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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162A ALA 3.6 22.4 - - - +
163A GLY* 3.9 16.6 - - - +
164A TYR* 4.0 27.4 - - + +
174A ALA* 4.2 6.7 - - + +
175A LEU 4.1 4.9 - - - +
176A SER* 3.8 22.2 - - - +
181A VAL* 3.3 28.0 - - + +
256A LEU* 4.3 13.2 - - + -
283A PRO 3.1 14.4 + - - +
284A VAL 3.3 7.4 + - - +
286A TYR* 1.3 76.4 - - + +
288A ILE* 1.3 68.8 + - + +
290A GLN* 3.3 1.2 + - - -
291A ALA* 3.0 19.2 + - - +
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Residues in contact with ILE 288 (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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202A ILE* 4.2 14.1 - - + +
252A VAL* 4.3 11.9 - - + -
255A THR 5.0 0.2 - - - -
256A LEU* 4.1 32.8 - - + +
284A VAL 2.9 20.7 + - - +
285A ALA* 4.0 4.5 - - - +
287A ILE* 1.3 79.8 - - + +
289A GLU* 1.3 60.5 + - - +
291A ALA* 3.2 11.5 + - - +
292A GLY 3.3 0.3 + - - -
293A GLY* 2.8 26.8 + - - -
294A LEU 3.6 33.7 - - - +
318A LEU* 3.9 27.8 - - + -
319A GLY 3.9 11.2 - - - +
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Residues in contact with GLU 289 (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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157A ARG* 2.8 43.4 + - - -
285A ALA 2.9 22.5 + - - +
286A TYR* 4.1 2.2 - - + +
288A ILE* 1.3 71.6 - - - +
290A GLN* 1.3 59.6 + - + +
292A GLY* 3.0 19.6 + - - -
293A GLY 3.5 17.7 - - - +
294A LEU* 5.3 6.7 - - - +
295A ALA* 4.5 18.7 + - + +
301A PRO* 4.1 10.7 - - - +
303A LEU* 3.7 14.1 - - + +
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Residues in contact with GLN 290 (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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176A SER* 2.8 26.1 + - - +
178A GLY* 3.1 22.8 + - - -
180A GLY* 2.8 31.7 + - - -
181A VAL* 3.7 16.4 - - + -
201A LYS* 2.9 23.9 + - - -
286A TYR* 2.9 42.9 + - + +
287A ILE* 3.6 5.2 - - - +
289A GLU* 1.3 76.6 - - + +
291A ALA* 1.3 57.1 + - - +
292A GLY 3.2 0.7 + - - -
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Residues in contact with ALA 291 (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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181A VAL* 3.9 5.1 - - + +
200A VAL 3.3 22.0 - - - +
201A LYS* 3.3 12.9 - - - +
202A ILE* 2.8 31.1 + - + +
256A LEU* 3.4 30.5 - - + -
287A ILE 3.0 13.8 + - - +
288A ILE* 3.7 4.7 - - - +
289A GLU 3.2 0.6 - - - -
290A GLN* 1.3 75.0 - - - +
292A GLY* 1.3 59.5 + - - +
293A GLY 3.4 0.7 - - - -
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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