Contacts of the helix formed by residues 214 - 226 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.8 1.9 - - - +
43A THR* 3.5 14.6 + - - -
44A TYR 4.8 0.3 + - - -
55A ASP* 3.0 15.6 + - - -
58A GLY 2.7 27.8 + - - -
59A SER* 4.6 1.3 - - - -
210A PHE* 4.0 21.6 - - - +
213A GLY* 1.3 67.9 - - - -
215A GLY* 1.3 64.0 + - - +
216A GLN 3.0 5.8 - - - -
217A VAL* 3.0 22.2 + - - +
218A SER 4.3 0.7 + - - -
436A MET* 3.8 23.1 - - - -
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Residues in contact with GLY 215 (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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39A VAL 5.5 0.6 - - - +
40A GLY* 5.4 2.1 - - - -
43A THR* 4.2 15.0 - - - -
44A TYR* 5.0 0.9 - - - -
45A THR* 2.9 26.8 + - - -
214A SER* 1.3 79.2 + - - +
216A GLN* 1.3 61.6 + - - +
217A VAL 3.1 0.9 + - - -
218A SER* 3.3 7.4 + - - -
219A GLU* 3.1 34.6 + - - +
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Residues in contact with GLN 216 (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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47A ARG* 3.6 21.0 + - - +
77A LEU* 3.7 31.2 - - + +
210A PHE* 4.9 1.0 - - - +
211A VAL 2.8 28.2 + - - +
212A GLY* 3.1 15.2 - - - +
213A GLY 2.9 20.4 + - - +
214A SER 3.0 0.2 - - - -
215A GLY* 1.3 75.2 - - - +
217A VAL* 1.3 59.9 + - - +
219A GLU* 3.4 10.3 - - - +
220A ARG* 2.8 52.6 + - + +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.1 21.8 - - + -
68A ILE* 4.3 14.8 - - + -
71A LEU* 4.0 27.6 - - + -
72A ALA* 4.3 14.4 - - + -
75A LEU* 3.6 13.3 - - + +
77A LEU* 3.6 19.7 - - + -
210A PHE* 4.5 9.9 - - + -
214A SER* 3.0 16.0 + - - +
216A GLN* 1.3 79.9 - - - +
218A SER* 1.3 62.9 + - - +
221A ILE* 3.2 26.8 + - + +
436A MET* 5.9 0.2 - - - -
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 3.8 1.0 - - - -
14A ILE* 3.5 28.9 + - - +
17A MET* 3.5 22.3 - - - +
39A VAL* 3.6 8.7 - - - +
40A GLY* 3.5 38.0 - - - -
43A THR* 4.4 0.9 + - - -
214A SER 4.3 0.2 + - - -
215A GLY 3.3 6.2 + - - -
217A VAL* 1.3 78.7 - - - +
219A GLU* 1.3 58.4 + - - +
221A ILE 3.4 0.9 + - - -
222A MET* 2.9 25.3 + - - +
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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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39A VAL* 3.9 20.3 - - + +
45A THR* 5.0 1.6 + - - +
47A ARG* 2.9 44.6 + - - -
215A GLY* 3.1 20.1 + - - +
216A GLN* 3.4 12.2 - - - +
218A SER* 1.3 75.6 - - - +
220A ARG* 1.3 59.9 + - + +
222A MET* 3.2 12.9 + - + +
223A ASP* 3.0 34.6 + - - +
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Residues in contact with ARG 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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75A LEU* 2.8 54.9 + - + +
76A GLY* 3.6 21.6 + - - -
77A LEU* 3.7 17.3 - - - +
216A GLN* 2.8 41.2 + - + +
217A VAL 4.3 0.2 - - - +
219A GLU* 1.3 74.0 - - + +
221A ILE* 1.3 66.0 + - - +
223A ASP* 3.2 16.9 + - + +
224A LEU* 3.1 25.3 + - - +
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Residues in contact with ILE 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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14A ILE 5.3 0.7 - - - +
17A MET* 3.5 52.9 - - + +
18A ALA* 4.3 0.9 - - - +
21A LYS* 3.9 19.5 - - + -
71A LEU* 4.1 23.1 - - + -
75A LEU* 3.8 24.9 - - + -
217A VAL* 3.2 22.3 + - + +
218A SER 3.8 3.8 - - - +
220A ARG* 1.3 76.5 - - - +
222A MET* 1.3 65.7 + - - +
224A LEU* 3.1 9.1 + - + +
225A LEU* 3.0 32.4 + - + +
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Residues in contact with MET 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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17A MET* 3.2 15.6 - - + +
38A ARG* 6.0 0.4 - - - -
39A VAL* 3.9 34.5 - - + +
218A SER 2.9 14.1 + - - +
219A GLU* 3.2 17.0 + - + +
221A ILE* 1.3 76.0 - - - +
223A ASP* 1.3 66.4 + - - +
225A LEU* 3.2 1.6 + - - +
226A GLY* 3.0 26.8 + - - +
229A VAL* 4.0 24.2 - - + +
231A LEU* 4.5 18.4 - - + -
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Residues in contact with ASP 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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219A GLU* 3.0 22.1 + - - +
220A ARG* 3.4 20.6 - - - +
221A ILE 3.1 0.2 - - - -
222A MET* 1.3 83.8 - - - +
224A LEU* 1.3 62.5 + - + +
226A GLY* 3.6 8.2 + - - -
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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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21A LYS* 3.9 26.5 - - + -
24A HIS* 4.4 15.9 + - + -
25A ASP* 6.0 0.7 - - - +
75A LEU* 3.8 26.7 - - + -
220A ARG 3.1 14.1 + - - +
221A ILE* 3.1 9.1 + - + +
223A ASP* 1.3 77.8 - - + +
225A LEU* 1.3 64.8 + - + +
226A GLY 3.7 0.3 + - - -
228A ARG* 4.6 2.6 + - - -
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Residues in contact with LEU 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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17A MET* 4.0 5.2 - - + -
20A ALA* 3.8 28.9 - - + +
21A LYS* 4.6 2.9 - - - -
24A HIS* 3.7 40.2 - - + +
30A VAL* 4.3 8.7 - - + -
32A VAL* 4.2 4.3 - - + -
221A ILE* 3.0 35.1 + - + +
222A MET 3.2 3.6 + - - +
224A LEU* 1.3 80.3 - - + +
226A GLY* 1.3 64.4 + - - +
228A ARG* 2.9 40.1 + - + +
229A VAL* 4.0 24.7 - - + -
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Residues in contact with GLY 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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222A MET* 3.0 18.3 + - - +
223A ASP 3.6 6.1 + - - -
224A LEU 3.4 3.6 + - - -
225A LEU* 1.3 76.1 - - - +
227A ASP* 1.3 57.4 + - - -
228A ARG* 2.9 7.9 + - - -
229A VAL* 3.4 14.7 + - - +
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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