Contacts of the helix formed by residues 229 - 244 (chain A) in PDB entry 3ELP
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 CYS 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.5 13.7 - - - -
227A VAL* 3.5 6.9 - - + +
228A ASN* 1.3 85.0 - - - +
230A GLU* 1.3 72.2 + - - +
231A SER* 3.5 23.1 - - - -
232A LEU* 3.5 29.6 - - + -
233A HIS* 3.6 6.8 + - - +
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Residues in contact with GLU 230 (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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82A LYS* 5.4 0.5 + - - -
83A TYR* 2.7 32.5 + - - -
228A ASN 3.6 1.0 + - - +
229A CYS* 1.3 75.2 - - - +
231A SER* 1.3 66.2 + - - +
233A HIS* 3.4 4.2 + - - +
234A ASN* 2.8 44.3 + - - +
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Residues in contact with SER 231 (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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229A CYS* 3.5 12.7 - - - -
230A GLU* 1.3 77.6 - - - +
232A LEU* 1.3 61.3 + - - +
234A ASN* 3.0 10.6 + - - +
235A ARG* 2.8 53.4 + - - +
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Residues in contact with LEU 232 (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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100A LEU* 3.9 17.0 - - + -
183A ILE* 3.8 28.7 - - + -
204A ASP* 3.8 20.2 - - + +
205A ILE* 3.8 17.7 - - + -
227A VAL* 3.5 25.8 - - + -
229A CYS* 3.5 23.5 - - + -
230A GLU 3.4 0.2 - - - -
231A SER* 1.3 81.0 + - - +
233A HIS* 1.3 57.8 + - - +
235A ARG* 3.6 17.0 + - - +
236A LEU* 3.0 38.2 + - + +
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Residues in contact with HIS 233 (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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83A TYR* 3.3 61.6 - + + +
84A CYS 4.8 3.8 - - - -
85A LEU* 4.0 25.3 - - + +
227A VAL* 4.1 10.9 - - + +
229A CYS 3.6 3.8 + - - +
230A GLU* 3.4 7.1 + - - +
231A SER 3.1 0.6 - - - -
232A LEU* 1.3 77.5 - - - +
234A ASN* 1.3 71.3 + - - +
236A LEU* 3.4 4.2 + - - +
237A ARG* 2.8 42.4 + - - +
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU* 2.8 36.2 + - - +
231A SER* 3.0 13.1 + - - +
233A HIS* 1.3 89.0 - - - +
235A ARG* 1.3 64.1 + - + +
237A ARG* 3.2 7.6 + - - +
238A PHE* 3.0 23.6 + - - +
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 2.8 56.8 + - + +
101A LEU* 5.8 1.2 - - - +
183A ILE* 5.0 5.9 - - - +
231A SER* 2.8 35.3 + - - +
232A LEU* 3.9 19.8 - - - +
234A ASN* 1.3 73.9 - - + +
236A LEU* 1.3 61.3 + - - +
238A PHE* 3.4 7.9 + - - +
239A LEU* 3.1 29.4 + - + +
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Residues in contact with LEU 236 (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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85A LEU* 3.0 31.0 - - + -
87A PHE* 4.4 5.4 - - + -
96A THR* 4.2 21.3 - - + +
97A ILE* 4.3 11.4 - - + -
100A LEU* 3.4 34.3 - - + -
205A ILE* 4.4 11.7 - - + -
225A VAL* 3.9 21.5 - - + -
227A VAL* 4.8 6.1 - - + -
232A LEU* 3.0 25.8 + - + +
233A HIS 3.7 0.4 - - - +
235A ARG* 1.3 73.5 - - - +
237A ARG* 1.3 59.6 + - - +
239A LEU* 3.3 7.1 + - + +
240A GLN* 2.8 28.8 + - - +
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Residues in contact with ARG 237 (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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65A ASN 5.6 0.4 - - - +
68A ARG* 2.8 25.1 - - - +
69A ASN* 4.3 12.9 + - - +
72A GLU* 2.9 33.1 + - - -
84A CYS 4.3 1.4 + - - -
85A LEU* 3.5 16.5 - - + +
233A HIS* 2.8 32.1 + - + +
234A ASN* 3.2 7.6 + - - +
236A LEU* 1.3 73.2 - - - +
238A PHE* 1.3 66.9 + - - +
240A GLN* 2.8 32.2 + - - +
241A ASN* 2.9 43.0 + - - +
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Residues in contact with PHE 238 (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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234A ASN 3.0 13.1 + - - +
235A ARG* 3.5 11.2 - - - +
237A ARG* 1.3 77.3 - - - +
239A LEU* 1.3 63.3 + - + +
241A ASN* 3.2 4.3 + - - +
242A SER* 2.5 67.2 + - - -
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Residues in contact with LEU 239 (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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96A THR* 3.5 38.1 - - + +
99A HIS* 3.9 19.3 - - + +
100A LEU* 3.6 26.0 - - + -
235A ARG 3.1 10.6 + - - +
236A LEU* 3.5 8.1 - - + +
238A PHE* 1.3 88.7 - - + +
240A GLN* 1.3 64.1 + - - +
242A SER* 4.2 4.0 - - - -
243A LEU* 2.9 49.7 + - + +
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Residues in contact with GLN 240 (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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68A ARG* 3.3 20.3 - - - +
72A GLU* 3.1 16.3 - - - +
85A LEU* 3.5 8.7 - - - +
86A ALA 3.0 19.2 + - - +
87A PHE* 3.8 25.5 - - + -
236A LEU 2.8 13.8 + - - +
237A ARG* 2.8 50.9 + - - +
239A LEU* 1.3 79.1 - - - +
241A ASN* 1.3 60.4 + - - +
244A GLY* 3.2 20.6 + - - -
245A ALA 4.3 1.7 + - - +
246A VAL* 3.7 20.1 - - + +
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Residues in contact with ASN 241 (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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64A GLY 4.8 2.1 + - - -
68A ARG* 3.2 27.4 + - - -
237A ARG* 2.9 44.6 + - - +
238A PHE* 4.0 4.4 - - + +
240A GLN* 1.3 77.8 + - - +
242A SER* 1.3 60.3 + - - +
244A GLY* 4.4 4.0 + - - -
246A VAL* 5.4 0.6 - - - +
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Residues in contact with SER 242 (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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238A PHE* 2.5 64.9 + - - -
239A LEU* 3.1 5.8 + - - -
241A ASN* 1.3 73.9 - - - +
243A LEU* 1.3 73.0 + - - +
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Residues in contact with LEU 243 (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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96A THR* 5.1 5.4 - - - +
99A HIS* 3.4 36.6 - - + +
239A LEU* 2.9 32.5 + - + +
242A SER* 1.3 89.8 - - - +
244A GLY* 1.3 60.6 + - - +
245A ALA* 3.5 8.9 + - + +
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Residues in contact with GLY 244 (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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240A GLN 3.2 13.9 + - - -
241A ASN* 4.4 3.2 + - - -
242A SER 3.7 1.6 - - - -
243A LEU* 1.3 78.6 - - - +
245A ALA* 1.3 55.5 + - - +
246A VAL* 2.9 20.6 + - - +
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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