Contacts of the helix formed by residues 214 - 226 (chain B) in PDB entry 2XFN
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 SER 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.9 1.9 - - - +
43B THR* 3.6 14.5 + - - -
44B TYR 4.9 0.3 + - - -
55B ASP* 3.0 15.6 + - - -
58B GLY 2.7 27.5 + - - -
59B SER* 4.6 1.6 - - - -
210B PHE* 4.0 22.5 - - - +
213B GLY* 1.3 68.7 - - - -
215B GLY* 1.3 63.8 + - - +
216B GLN 3.0 5.2 - - - -
217B VAL* 3.0 22.8 + - - +
218B SER 4.4 0.5 + - - -
436B MET* 3.7 24.7 - - - -
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY* 5.5 1.7 - - - -
43B THR* 4.2 14.3 - - - -
44B TYR* 5.0 1.6 - - - -
45B THR* 2.9 27.6 + - - -
47B ARG* 5.1 0.2 - - - -
214B SER* 1.3 79.4 + - - +
216B GLN* 1.3 57.0 + - - +
217B VAL 3.2 0.5 + - - -
218B SER* 3.3 6.4 + - - -
219B GLU* 3.0 40.2 + - - +
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 4.6 0.2 + - - -
47B ARG* 3.5 22.7 + - - +
77B LEU* 3.6 25.9 - - + +
210B PHE* 4.9 0.6 - - - +
211B VAL 2.9 26.8 + - - +
212B GLY* 3.1 16.5 - - - +
213B GLY 2.9 21.8 + - - +
214B SER 3.0 1.0 - - - -
215B GLY* 1.3 74.9 - - - +
217B VAL* 1.3 60.3 + - - +
219B GLU* 3.4 9.2 - - - +
220B ARG* 2.9 60.2 + - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.1 23.1 - - + -
68B ILE* 4.3 19.5 - - + -
71B LEU* 4.0 21.5 - - + -
72B ALA* 4.3 9.9 - - + -
75B LEU* 3.6 19.9 - - + +
77B LEU* 3.7 19.3 - - + -
210B PHE* 4.4 10.1 - - + -
214B SER 3.0 17.2 + - - +
216B GLN* 1.3 80.3 - - - +
218B SER* 1.3 62.6 + - - +
221B ILE* 3.2 26.6 + - + +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY 3.7 2.1 - - - -
14B ILE* 3.5 29.8 + - - +
17B MET* 3.9 17.2 - - - +
39B VAL* 3.7 9.1 - - - +
40B GLY* 3.5 37.5 - - - -
43B THR* 4.4 1.1 + - - -
214B SER 4.4 0.4 + - - -
215B GLY 3.3 6.6 + - - -
217B VAL* 1.3 78.2 - - - +
219B GLU* 1.3 57.4 + - - +
221B ILE* 3.3 1.6 + - - +
222B MET* 2.9 29.3 + - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.9 20.7 - - + +
45B THR* 4.7 1.9 + - - +
47B ARG* 2.9 43.9 + - - -
215B GLY* 3.0 24.1 + - - +
216B GLN* 3.4 12.9 - - - +
218B SER* 1.3 78.0 - - - +
220B ARG* 1.3 60.3 + - + +
222B MET* 3.2 13.0 + - + +
223B ASP* 2.8 35.6 + - - +
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Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 2.9 43.6 + - + +
76B GLY* 3.5 14.1 + - - -
77B LEU* 3.4 27.5 - - - +
216B GLN* 2.9 44.1 + - + +
217B VAL 4.2 1.3 - - - +
219B GLU* 1.3 76.4 - - + +
221B ILE* 1.3 65.5 + - - +
223B ASP* 3.2 17.5 + - + +
224B LEU* 3.1 26.3 + - - +
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE 5.3 0.7 - - - +
17B MET* 3.5 47.8 - - + +
18B ALA* 4.2 1.8 - - - +
21B LYS* 4.0 17.3 - - + -
71B LEU* 4.0 29.8 - - + -
75B LEU* 3.8 20.2 - - + -
217B VAL* 3.2 22.7 + - + +
218B SER 3.9 3.1 - - - +
219B GLU 3.3 0.2 - - - -
220B ARG* 1.3 73.1 - - - +
222B MET* 1.3 66.7 + - - +
224B LEU* 3.1 9.5 + - + +
225B LEU* 2.9 39.5 + - + +
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B MET* 3.9 9.8 - - + +
38B ARG* 6.1 0.4 - - - -
39B VAL* 3.6 35.7 - - + +
218B SER 2.9 13.5 + - - +
219B GLU* 3.3 18.2 - - + +
221B ILE* 1.3 76.3 - - - +
223B ASP* 1.3 63.5 + - - +
225B LEU* 3.2 0.9 + - - +
226B GLY* 2.9 31.2 + - - +
229B VAL* 4.0 31.2 - - + -
231B LEU* 4.4 16.4 - - + -
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Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLU* 2.8 24.4 + - - +
220B ARG* 3.4 23.5 - - - +
221B ILE 3.1 0.2 - - - -
222B MET* 1.3 86.4 - - - +
224B LEU* 1.3 64.3 + - + +
226B GLY* 3.6 8.4 + - - -
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 4.0 34.3 - - + -
24B HIS* 5.0 11.0 + - + +
25B ASP* 5.9 1.1 - - - +
75B LEU* 4.0 17.5 - - + -
220B ARG 3.1 13.3 + - - +
221B ILE* 3.1 9.6 + - + +
223B ASP* 1.3 79.2 - - + +
225B LEU* 1.3 66.9 + - + +
226B GLY* 3.5 0.5 + - - -
228B ARG* 4.2 6.2 + - - -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B MET* 4.5 2.2 - - - -
20B ALA* 3.8 29.4 - - + +
21B LYS* 4.8 3.6 - - + -
24B HIS* 3.7 43.1 - - + +
30B VAL* 4.3 10.5 - - + -
32B VAL* 4.2 5.2 - - + -
221B ILE* 2.9 34.7 + - + +
222B MET 3.2 0.2 + - - -
224B LEU* 1.3 79.4 - - + +
226B GLY* 1.4 63.0 + - - +
227B ASP 3.4 0.7 + - - -
228B ARG* 2.9 41.4 + - + +
229B VAL* 4.0 26.9 - - + -
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Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B MET* 2.9 16.8 + - - +
223B ASP 3.6 6.2 + - - -
224B LEU 3.3 3.4 + - - -
225B LEU* 1.4 73.8 - - - +
227B ASP* 1.3 59.8 + - - -
228B ARG* 3.0 5.2 + - - -
229B VAL* 3.3 19.2 + - - +
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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