Contacts of the helix formed by residues 13 - 26 (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 GLY 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY 3.5 3.8 - - - -
12A GLY* 1.3 79.1 - - - +
14A ILE* 1.3 66.6 + - - -
15A SER 3.2 2.8 + - - -
16A GLY 3.3 1.8 + - - +
17A MET* 2.9 20.8 + - - +
40A GLY 3.9 17.5 - - - -
218A SER* 3.8 4.3 - - - -
1500A FAD 3.4 30.0 - - - -
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Residues in contact with ILE 14 (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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13A GLY* 1.3 71.1 - - - -
15A SER* 1.3 58.7 + - - +
17A MET* 3.9 2.6 - - - +
18A ALA* 2.8 28.4 + - - +
40A GLY 4.4 2.8 + - - +
43A THR* 3.9 17.9 - - + +
68A ILE* 4.4 11.0 - - + -
71A LEU* 4.7 1.7 - - + +
214A SER 4.8 1.6 - - - +
217A VAL* 4.1 22.9 - - + -
218A SER* 3.5 18.3 + - - +
221A ILE* 5.3 0.3 - - - +
436A MET* 3.7 41.5 - - + +
439A ALA* 3.9 14.4 - - + -
440A VAL* 3.6 30.3 - - + -
1500A FAD 3.3 7.5 + - - +
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Residues in contact with SER 15 (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* 1.3 79.1 - - - +
16A GLY* 1.3 57.3 + - - -
18A ALA* 3.8 0.4 - - - -
19A ALA* 2.9 23.9 + - - +
263A ALA* 4.3 3.1 - - - -
424A ALA* 3.5 1.6 - - - +
425A GLY* 2.8 33.3 + - - -
439A ALA* 2.8 29.0 + - - +
443A GLY* 3.3 19.3 + - - -
1500A FAD 2.9 24.6 + - - -
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Residues in contact with GLY 16 (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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9A VAL* 3.5 14.2 - - - +
11A GLY 3.3 23.3 + - - -
13A GLY 3.3 5.1 + - - +
15A SER* 1.3 79.3 - - - +
17A MET* 1.3 58.7 + - - +
19A ALA* 3.4 2.3 + - - +
20A ALA* 2.8 30.8 + - - +
32A VAL* 5.2 0.4 - - - -
263A ALA* 3.5 16.7 - - - +
1500A FAD 4.2 0.6 + - - -
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Residues in contact with MET 17 (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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11A GLY 4.5 0.2 + - - -
12A GLY* 3.6 26.7 - - - +
13A GLY 2.9 22.0 + - - +
14A ILE* 3.9 3.4 - - - +
16A GLY* 1.3 77.0 - - - +
18A ALA* 1.3 55.6 + - - +
20A ALA* 3.9 1.7 - - - +
21A LYS* 2.9 31.2 + - - +
32A VAL* 4.2 19.1 - - - -
39A VAL* 4.3 7.6 - - + -
218A SER* 3.5 19.3 - - - +
221A ILE* 3.5 30.4 - - + +
222A MET* 3.2 43.7 - - + +
225A LEU* 4.0 1.8 - - + -
229A VAL* 3.8 11.0 - - + -
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Residues in contact with ALA 18 (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 2.8 22.5 + - - +
15A SER 3.8 3.6 - - - +
17A MET* 1.3 69.8 - - - +
19A ALA* 1.3 67.4 + - - +
21A LYS* 3.5 5.7 + - - +
22A LEU* 3.1 23.6 + - - +
71A LEU* 4.2 21.3 - - + -
221A ILE* 4.3 5.7 - - - +
440A VAL* 4.2 16.2 - - + +
444A GLU* 4.2 24.5 - - + +
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Residues in contact with ALA 19 (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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9A VAL* 4.7 2.0 - - + -
15A SER 2.9 16.1 + - - +
16A GLY* 3.6 7.6 - - - +
18A ALA* 1.3 75.1 - - - +
20A ALA* 1.3 66.9 + - - +
22A LEU* 3.3 3.3 + - - +
23A LEU* 3.0 28.8 + - - +
261A ILE* 3.7 27.8 - - + -
443A GLY* 3.2 29.2 - - - +
447A ALA* 3.8 3.3 - - + +
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Residues in contact with ALA 20 (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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9A VAL* 4.2 10.0 - - + +
16A GLY 2.8 21.2 + - - +
17A MET 3.9 2.2 - - - +
19A ALA* 1.3 73.2 - - - +
21A LYS* 1.3 58.2 + - - +
23A LEU* 3.3 3.4 + - - +
24A HIS* 2.8 32.7 + - - +
30A VAL* 3.7 15.5 - - + +
32A VAL* 3.5 28.0 - - + -
225A LEU* 3.8 13.9 - - + -
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Residues in contact with LYS 21 (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 2.9 19.8 + - - +
18A ALA* 3.9 5.2 - - - +
20A ALA* 1.3 78.0 - - - +
22A LEU* 1.3 52.5 + - - +
24A HIS* 3.3 7.0 + - + +
25A ASP* 2.8 70.9 + - - +
71A LEU* 4.1 24.9 - - + +
74A GLU* 2.8 35.1 + - - -
75A LEU* 4.4 4.3 - - - -
221A ILE* 3.9 22.0 - - + -
224A LEU* 3.9 23.8 - - + -
225A LEU* 4.6 6.6 - - + +
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Residues in contact with LEU 22 (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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18A ALA 3.1 17.2 + - - +
19A ALA 3.7 3.6 - - - +
21A LYS* 1.3 77.0 - - - +
23A LEU* 1.3 65.3 + - - +
25A ASP* 3.3 9.1 + - - +
26A SER* 3.0 21.4 + - - -
444A GLU* 3.7 45.1 - - + +
447A ALA* 3.9 13.7 - - + -
448A ARG* 4.0 19.3 - - + +
451A LEU* 3.6 30.1 - - + -
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Residues in contact with LEU 23 (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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7A VAL* 3.9 30.1 - - + -
9A VAL* 4.6 3.4 - - + -
19A ALA 3.0 22.5 + - - +
20A ALA 3.8 0.7 - - - +
22A LEU* 1.3 76.1 - - - +
24A HIS* 1.3 61.9 + - - +
26A SER* 2.7 20.6 + - - -
28A LEU* 3.0 38.7 + - + +
30A VAL* 3.4 22.9 - - + -
261A ILE* 3.9 15.7 - - + -
447A ALA* 3.6 30.5 - - + +
450A ILE* 4.6 6.5 - - + -
451A LEU* 4.1 10.8 - - + -
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Residues in contact with HIS 24 (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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20A ALA 2.8 21.4 + - - +
21A LYS* 3.6 3.8 - - + +
23A LEU* 1.3 72.3 - - - +
25A ASP* 1.3 71.5 + - - +
27A GLY* 3.0 20.8 + - - -
28A LEU 3.7 14.1 + - - +
30A VAL* 4.2 5.1 - - + +
224A LEU* 4.4 14.1 + - + -
225A LEU* 3.7 22.3 - - + +
228A ARG* 3.6 44.6 + - - -
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 2.8 57.7 + - - +
22A LEU* 3.7 7.3 - - - +
24A HIS* 1.3 86.6 - - - +
26A SER* 1.3 59.9 + - - +
27A GLY* 3.2 1.1 + - - -
224A LEU* 6.0 1.0 - - - +
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Residues in contact with SER 26 (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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22A LEU* 3.0 16.2 + - - -
23A LEU 2.7 14.6 + - - -
24A HIS 3.2 0.4 - - - -
25A ASP* 1.3 74.9 - - - +
27A GLY* 1.3 57.1 + - - +
28A LEU* 3.7 8.8 + - - +
451A LEU* 3.6 36.7 - - - +
456A LYS* 5.6 4.0 - - - +
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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