Contacts of the helix formed by residues 13 - 26 (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 GLY 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLY 3.5 3.8 - - - -
12B GLY* 1.3 78.8 - - - +
14B ILE* 1.3 66.5 + - - -
15B SER 3.2 3.1 + - - -
16B GLY 3.3 1.4 + - - +
17B MET* 2.9 21.5 + - - +
40B GLY 3.9 16.6 - - - -
218B SER* 3.7 3.8 - - - -
1500B FAD 3.4 29.5 + - - -
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Residues in contact with ILE 14 (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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13B GLY* 1.3 71.7 - - - -
15B SER* 1.3 58.1 + - - +
17B MET* 3.9 3.0 - - - +
18B ALA* 2.8 27.9 + - - +
40B GLY 4.5 2.0 + - - +
43B THR* 3.9 17.7 - - + +
68B ILE* 4.3 10.1 - - + -
71B LEU* 4.8 2.0 - - + -
214B SER 4.9 1.8 - - - +
217B VAL* 4.1 22.9 - - + -
218B SER* 3.5 18.1 + - - +
221B ILE* 5.3 0.3 - - - +
436B MET* 3.7 41.3 - - + +
439B ALA* 3.8 14.4 - - + -
440B VAL* 3.6 29.4 - - + -
1500B FAD 3.2 8.1 + - - +
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Residues in contact with SER 15 (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* 1.3 76.5 - - - +
16B GLY* 1.3 56.1 + - - +
18B ALA* 3.8 0.2 - - - +
19B ALA* 2.9 25.5 + - - +
263B ALA* 4.3 4.0 - - - -
424B ALA* 3.5 1.6 - - - +
425B GLY* 2.9 28.7 + - - -
439B ALA* 2.8 30.2 + - - +
443B GLY* 3.3 19.1 + - - -
1500B FAD 2.8 32.4 + - - -
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Residues in contact with GLY 16 (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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9B VAL* 3.5 11.8 - - - +
11B GLY 3.3 23.1 + - - -
13B GLY 3.3 4.6 + - - +
15B SER* 1.3 78.6 - - - +
17B MET* 1.3 57.4 + - - +
19B ALA* 3.4 4.5 + - - +
20B ALA* 2.8 31.6 + - - +
32B VAL* 5.2 0.7 - - - -
263B ALA* 3.5 17.8 - - - +
1500B FAD 4.2 0.6 + - - -
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Residues in contact with MET 17 (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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11B GLY 4.4 0.2 + - - -
12B GLY* 3.6 18.6 - - - +
13B GLY 2.9 22.6 + - - +
14B ILE* 3.9 4.0 - - - +
16B GLY* 1.3 77.3 - - - +
18B ALA* 1.3 55.3 + - - +
20B ALA* 3.3 2.0 + - - +
21B LYS* 2.9 31.7 + - - +
32B VAL* 4.4 10.5 - - + -
39B VAL* 3.1 38.8 - - + -
218B SER* 3.9 21.1 - - - +
221B ILE* 3.5 36.7 - - + +
222B MET* 3.9 11.2 - - + -
225B LEU* 4.5 1.3 - - - -
229B VAL* 4.0 20.6 - - + -
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Residues in contact with ALA 18 (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 2.8 22.1 + - - +
15B SER 3.8 3.1 - - - +
17B MET* 1.3 71.8 - - - +
19B ALA* 1.3 62.0 + - - +
21B LYS* 3.5 4.0 + - - +
22B LEU* 3.1 24.1 + - - +
71B LEU* 4.2 21.1 - - + -
221B ILE* 4.2 7.5 - - - +
439B ALA 4.8 0.2 - - - +
440B VAL* 4.2 20.0 - - + +
444B GLU* 4.1 19.3 - - + +
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Residues in contact with ALA 19 (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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9B VAL* 4.7 2.5 - - + -
15B SER 2.9 16.5 + - - +
16B GLY* 3.6 8.1 - - - +
18B ALA* 1.3 75.9 - - - +
20B ALA* 1.3 61.9 + - - +
22B LEU* 3.2 3.8 + - - +
23B LEU* 3.0 30.0 + - - +
261B ILE* 3.7 28.7 - - + -
443B GLY* 3.2 29.2 - - - +
447B ALA* 3.8 3.1 - - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.2 10.7 - - + +
16B GLY 2.8 20.5 + - - +
17B MET* 3.9 2.5 - - - +
19B ALA* 1.3 73.3 - - - +
21B LYS* 1.3 57.3 + - - +
23B LEU* 3.4 3.4 + - - +
24B HIS* 2.8 32.9 + - - +
30B VAL* 3.7 14.8 - - + +
32B VAL* 3.5 28.7 - - + -
225B LEU* 3.8 14.4 - - + -
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Residues in contact with LYS 21 (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 2.9 19.1 + - - +
18B ALA* 3.8 5.2 - - - +
20B ALA* 1.3 77.0 - - - +
22B LEU* 1.3 57.6 + - - +
24B HIS* 3.4 6.6 + - + +
25B ASP* 2.8 67.2 + - - +
71B LEU* 4.0 25.3 - - + +
74B GLU* 2.7 35.0 + - - -
75B LEU* 4.4 5.6 - - - -
221B ILE* 4.0 17.6 - - + +
224B LEU* 4.0 29.4 - - + -
225B LEU* 4.8 4.0 - - + -
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Residues in contact with LEU 22 (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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18B ALA 3.1 18.1 + - - +
19B ALA 3.2 3.8 + - - +
21B LYS* 1.3 77.5 - - - +
23B LEU* 1.3 64.6 + - - +
25B ASP* 3.4 7.5 + - - +
26B SER* 3.1 20.4 + - - -
444B GLU* 3.7 44.0 - - + +
447B ALA* 4.0 12.8 - - + -
448B ARG* 4.0 19.1 - - + +
451B LEU* 3.7 29.8 - - + -
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Residues in contact with LEU 23 (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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7B VAL* 3.8 33.4 - - + -
9B VAL* 4.7 3.6 - - + -
19B ALA 3.0 21.9 + - - +
22B LEU* 1.3 76.3 - - - +
24B HIS* 1.3 62.0 + - - +
26B SER* 2.7 23.0 + - - -
28B LEU* 3.1 34.9 + - + +
30B VAL* 3.4 17.9 - - + -
261B ILE* 3.9 16.6 - - + -
447B ALA* 3.6 31.0 - - + +
450B ILE* 4.6 6.7 - - + -
451B LEU* 4.0 11.2 - - + -
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Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 2.8 19.3 + - - +
21B LYS* 3.6 5.4 - - + +
23B LEU* 1.3 75.9 - - - +
25B ASP* 1.3 72.4 + - - +
27B GLY* 2.9 21.7 + - - -
28B LEU 3.6 14.8 + - - +
30B VAL* 4.0 6.3 - - + +
224B LEU* 5.0 11.6 + - + +
225B LEU* 3.7 25.4 - - + +
228B ARG* 3.6 41.9 + - - -
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Residues in contact with ASP 25 (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* 2.8 58.6 + - - +
22B LEU* 3.7 7.2 - - - +
23B LEU 3.3 0.2 - - - -
24B HIS* 1.3 85.5 - - - +
26B SER* 1.3 60.2 + - - +
27B GLY 3.2 1.8 + - - -
224B LEU* 5.9 1.4 - - - +
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Residues in contact with SER 26 (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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22B LEU* 3.1 12.6 + - - -
23B LEU 2.7 17.2 + - - -
25B ASP* 1.3 76.2 - - - +
27B GLY* 1.3 57.1 + - - +
28B LEU* 3.7 8.3 + - - +
451B LEU* 3.7 34.4 - - - +
456B LYS* 5.4 5.1 - - - +
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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