Contacts of the helix formed by residues 216 - 229 (chain A) in PDB entry 3M6L
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 ASP 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ASN* 3.2 20.5 + - - +
214A GLY 3.5 1.0 - - - -
215A HIS* 1.3 76.1 - - - +
217A TYR* 1.3 65.8 + - - +
218A GLU* 3.3 11.6 + - - +
219A GLU* 3.0 47.1 + - - +
220A ILE* 2.9 24.6 + - - +
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Residues in contact with TYR 217 (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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1A MSE 5.2 0.7 - - - +
3A ILE* 4.2 34.5 - - + -
6A LEU* 3.7 36.3 - - + -
7A GLN* 3.5 35.9 - - + +
10A ALA* 3.6 3.0 - - + +
14A ARG* 4.6 1.6 + - - -
37A ASP* 2.5 48.9 + - + -
40A SER* 5.0 0.9 - - - -
41A VAL* 3.7 24.3 - - + +
215A HIS 4.6 7.2 - - - -
216A ASP* 1.3 74.6 + - - +
218A GLU* 1.3 58.4 + - - +
220A ILE* 3.3 3.5 + - + +
221A ASN* 2.9 29.6 + - - +
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Residues in contact with GLU 218 (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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3A ILE* 5.0 15.0 - - + +
216A ASP* 3.3 8.2 + - - +
217A TYR* 1.3 78.3 - - - +
219A GLU* 1.3 58.6 + - + +
221A ASN* 3.4 9.0 + - + +
222A LYS* 2.9 30.0 + - - +
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Residues in contact with GLU 219 (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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211A SER 5.0 0.5 - - - +
212A ILE* 3.7 16.9 - - + +
213A ASN* 2.9 43.4 + - - +
216A ASP* 3.0 35.9 + - + +
218A GLU* 1.3 73.9 - - + +
220A ILE* 1.3 66.7 + - - +
222A LYS* 3.4 5.5 + - - +
223A ALA* 2.9 26.2 + - - +
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Residues in contact with ILE 220 (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 ASP* 3.8 24.2 - - + +
38A ILE* 3.9 21.5 - - + +
41A VAL* 3.7 21.8 - - + -
212A ILE* 4.0 24.2 - - + -
213A ASN 4.1 4.3 - - - +
214A GLY* 3.4 26.0 - - - +
216A ASP 2.9 25.4 + - - +
217A TYR* 3.7 8.3 - - - +
219A GLU* 1.3 76.1 - - - +
221A ASN* 1.4 62.7 + - - +
223A ALA* 3.2 2.6 + - - +
224A LEU* 3.0 34.1 + - + +
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Residues in contact with ASN 221 (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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1A MSE 3.7 25.9 - - + +
41A VAL* 3.8 12.8 - - + +
45A HIS* 2.8 30.7 + - - -
217A TYR 2.9 17.9 + - - +
218A GLU* 3.7 10.0 + - - +
220A ILE* 1.4 78.6 - - - +
222A LYS* 1.4 63.0 + - - +
224A LEU* 3.3 2.6 + - - +
225A GLU* 3.0 29.8 + - - +
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Residues in contact with LYS 222 (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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218A GLU 2.9 19.9 + - - +
219A GLU* 3.9 6.7 - - - +
221A ASN* 1.4 75.1 - - - +
223A ALA* 1.3 58.6 + - - +
225A GLU* 3.3 8.4 + - + +
226A GLN* 3.0 42.7 + - + +
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Residues in contact with ALA 223 (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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210A LEU* 3.4 21.6 - - + +
212A ILE* 3.8 23.6 - - + -
219A GLU 2.9 18.2 + - - +
220A ILE 3.7 3.4 - - - +
221A ASN 3.2 0.2 - - - -
222A LYS* 1.3 77.6 - - - +
224A LEU* 1.3 52.5 + - - +
226A GLN* 3.3 2.8 + - - -
227A ALA* 2.7 37.4 + - - +
236A ILE* 4.1 17.0 - - + -
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Residues in contact with LEU 224 (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 ILE* 5.2 0.9 - - + +
41A VAL* 4.0 13.7 - - + -
42A LEU* 4.0 31.9 - - + -
45A HIS* 3.7 33.0 - - + +
147A TYR* 4.1 13.2 - - + +
176A ILE* 4.7 2.0 - - + -
178A ILE* 4.0 14.8 - - + -
220A ILE* 3.0 30.3 + - + +
221A ASN 3.9 3.1 - - - +
223A ALA* 1.3 78.9 - - - +
225A GLU* 1.3 61.6 + - - +
227A ALA* 3.8 2.5 - - - +
228A LYS* 3.0 33.2 + - + +
236A ILE* 3.9 20.4 - - + -
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Residues in contact with GLU 225 (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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45A HIS* 3.2 24.1 - - + -
221A ASN* 3.0 26.0 + - - +
222A LYS* 3.6 11.2 - - + +
224A LEU* 1.3 77.8 - - - +
226A GLN* 1.3 62.8 + - - +
228A LYS* 3.4 22.6 + - - +
229A LYS* 3.6 27.6 + - - +
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Residues in contact with GLN 226 (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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208A GLU* 4.0 16.7 + - - +
210A LEU* 3.8 31.9 - - + +
222A LYS* 3.0 35.3 + - + +
223A ALA* 3.8 5.1 - - - +
225A GLU* 1.3 75.4 - - - +
227A ALA* 1.3 65.2 + - - +
229A LYS* 3.1 25.0 + - - +
230A SER* 3.2 11.3 + - - -
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Residues in contact with ALA 227 (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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145A LYS* 4.8 1.7 + - - -
173A ASP 5.4 1.2 - - - +
176A ILE* 3.9 33.5 - - + +
208A GLU* 5.8 0.2 - - - -
210A LEU* 4.1 1.0 - - + +
223A ALA 2.7 22.1 + - - +
224A LEU* 3.8 4.3 - - - +
226A GLN* 1.3 74.2 - - - +
228A LYS* 1.3 61.7 + - - +
230A SER* 3.1 19.0 + - - -
234A CYS* 3.5 31.7 - - - +
236A ILE* 4.1 7.0 - - + -
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Residues in contact with LYS 228 (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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45A HIS* 2.8 44.5 + - + +
47A LYS* 5.1 6.5 - - - +
145A LYS* 3.1 37.3 + - - +
147A TYR* 3.6 27.1 - - + +
176A ILE* 3.9 9.9 - - + -
224A LEU* 3.0 24.6 + - + +
225A GLU* 3.7 18.0 + - - +
226A GLN 3.3 0.2 - - - -
227A ALA* 1.3 75.7 - - - +
229A LYS* 1.3 60.0 + - + +
230A SER 4.9 0.5 - - - +
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Residues in contact with LYS 229 (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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225A GLU* 3.6 23.1 + - - +
226A GLN* 3.1 17.2 + - - +
228A LYS* 1.3 78.8 - - + +
230A SER* 1.3 65.2 + - - +
231A THR* 3.7 6.1 + - - +
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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