Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 1F0K
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 THR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 2.8 5.9 + - - +
15A GLY* 1.3 84.7 - - - +
17A GLY* 1.3 64.8 + - - +
18A GLY* 3.5 6.4 + - - -
19A HIS* 3.1 34.0 + - + +
20A VAL* 3.0 21.1 + - - +
45A ARG* 5.9 0.9 - - - +
46A MET* 4.0 9.0 - - - +
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Residues in contact with GLY 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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16A THR* 1.3 73.7 - - - +
18A GLY* 1.3 63.3 + - - +
20A VAL 4.3 0.9 - - - -
21A PHE* 2.9 60.5 + - - +
22A PRO* 3.5 0.3 - - - +
46A MET* 3.6 17.6 - - - +
265A LEU* 3.9 0.4 - - - +
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.0 9.3 + - - -
17A GLY* 1.3 76.9 - - - +
19A HIS* 1.3 57.2 + - - +
22A PRO* 3.1 20.6 - - - +
127A GLN* 2.9 20.3 - - - +
264A ALA* 6.3 1.8 - - - -
265A LEU* 4.1 14.3 - - - +
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Residues in contact with HIS 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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13A ALA* 3.7 15.7 - - + +
14A GLY* 4.0 12.1 - - - +
16A THR* 3.1 28.9 + - + +
18A GLY* 1.3 77.4 - - - +
20A VAL* 1.3 64.3 + - - +
22A PRO* 3.2 8.4 - - - +
23A GLY 3.4 9.0 + - - -
103A MET* 2.8 39.0 + - - +
104A GLY* 3.7 19.7 - - - +
105A GLY* 3.7 15.2 + - - -
126A GLU* 5.1 5.6 - - - -
127A GLN* 2.8 18.5 + - - -
128A ASN* 4.4 14.6 - - - -
288A GLN* 5.9 1.3 - - - -
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Residues in contact with VAL 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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13A ALA 4.1 6.3 - - - +
14A GLY 2.9 26.9 - - - +
16A THR 3.0 9.5 + - - +
17A GLY* 4.4 1.6 - - - -
19A HIS* 1.3 75.0 - - - +
21A PHE* 1.3 65.8 + - - +
23A GLY* 3.1 2.9 + - - -
24A LEU* 2.9 29.3 + - + +
39A TRP* 3.6 18.8 - - + -
46A MET* 3.6 18.2 - - + -
47A GLU* 4.1 16.8 - - + -
50A LEU* 3.7 28.5 - - + -
51A VAL* 4.8 2.9 - - + -
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Residues in contact with PHE 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 GLY* 2.9 44.6 + - - +
20A VAL* 1.3 72.2 - - - +
22A PRO* 1.3 65.3 - - + +
24A LEU* 3.2 12.1 + - + +
25A ALA* 3.1 20.1 + - - +
46A MET* 4.3 8.5 - - + -
50A LEU* 3.7 30.7 - - + -
265A LEU* 3.9 16.8 - - + -
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Residues in contact with PRO 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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17A GLY 3.5 0.4 - - - +
18A GLY 3.1 28.3 - - - +
19A HIS 3.2 8.1 - - - +
21A PHE* 1.3 94.3 - - + +
23A GLY* 1.3 60.1 + - - +
25A ALA* 3.2 5.7 + - + +
26A VAL* 3.2 26.3 + - - +
103A MET* 3.5 18.8 - - + -
127A GLN* 4.0 7.9 - - + -
162A PRO* 3.9 28.2 - - + +
265A LEU* 3.6 23.6 - - + -
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Residues in contact with GLY 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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11A VAL* 4.3 7.2 - - - +
19A HIS 3.4 5.0 + - - -
20A VAL 3.1 7.2 + - - -
22A PRO* 1.3 81.2 - - - +
24A LEU* 1.3 55.0 + - - +
26A VAL* 3.3 5.7 + - - +
27A ALA* 2.9 28.1 + - - +
39A TRP* 3.7 16.5 - - - -
101A LEU* 5.4 0.2 - - - -
103A MET* 3.7 22.8 - - - +
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Residues in contact with LEU 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 VAL* 2.9 21.7 + - + +
21A PHE* 3.2 13.9 + - + +
23A GLY* 1.3 73.9 - - - +
25A ALA* 1.3 60.9 + - - +
27A ALA* 3.5 3.0 - - - +
28A HIS* 2.9 38.1 + - + -
39A TRP* 3.7 21.5 - - + -
50A LEU* 3.9 25.1 - - + -
51A VAL* 4.5 9.2 - - + -
54A HIS* 3.6 49.6 - - + +
56A ILE* 4.0 18.8 - - + -
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Residues in contact with ALA 25 (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 PHE 3.1 11.6 + - - +
22A PRO 3.2 9.6 + - - +
24A LEU* 1.3 78.1 - - - +
26A VAL* 1.3 61.8 + - - +
28A HIS* 4.0 4.8 - - - +
29A HIS* 3.0 24.6 + - - +
162A PRO* 4.0 11.9 - - + -
343A THR* 3.7 25.0 - - + +
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Residues in contact with VAL 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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9A LEU* 4.9 2.9 - - + -
11A VAL* 5.9 0.2 - - + -
22A PRO 3.2 14.5 + - - +
23A GLY 3.8 6.1 - - - +
24A LEU 3.3 0.2 - - - -
25A ALA* 1.3 74.3 - - + +
27A ALA* 1.3 65.5 + - - +
29A HIS* 3.5 5.3 + - - +
30A LEU* 3.1 41.0 + - + +
101A LEU* 3.9 25.4 - - + -
103A MET* 5.1 3.6 - - + -
162A PRO* 5.0 4.0 - - + -
343A THR* 4.2 15.9 - - + +
346A VAL* 4.0 24.2 - - + -
347A ALA* 4.2 16.8 - - - +
350A VAL* 4.8 2.0 - - + -
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Residues in contact with ALA 27 (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 LEU* 5.0 3.6 - - - -
11A VAL* 4.7 2.0 - - + +
23A GLY 2.9 17.9 + - - +
24A LEU* 3.5 7.0 - - - +
25A ALA 3.3 0.2 - - - -
26A VAL* 1.3 77.1 - - - +
28A HIS* 1.3 58.0 + - - +
30A LEU* 3.1 4.4 + - - +
31A MET* 2.9 35.0 + - + +
37A VAL* 3.9 29.5 - - + +
39A TRP* 4.6 4.9 - - + -
56A ILE* 4.0 19.1 - - + -
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Residues in contact with HIS 28 (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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24A LEU* 2.9 30.0 + - + +
25A ALA* 4.0 4.7 - - - +
27A ALA* 1.3 74.4 - - - +
29A HIS* 1.3 63.8 + - - +
31A MET* 3.3 21.1 - - + +
32A ALA* 3.1 25.8 + - - +
54A HIS* 2.7 57.8 + + + +
56A ILE* 4.6 0.9 - - + -
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Residues in contact with HIS 29 (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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25A ALA 3.0 20.4 + - - +
26A VAL* 3.6 6.1 - - - +
27A ALA 3.2 0.2 - - - -
28A HIS* 1.3 79.1 - - - +
30A LEU* 1.3 59.4 + - + +
32A ALA* 3.7 7.2 + - - +
33A GLN* 2.8 53.4 + - - +
343A THR* 3.8 16.3 - - + +
344A GLU* 3.5 40.5 + - + +
347A ALA* 3.5 24.2 - - + +
348A ASN* 5.7 1.8 + - - -
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Residues in contact with LEU 30 (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 LEU* 3.7 27.6 - - + -
26A VAL* 3.1 22.8 + - + +
27A ALA 3.1 4.8 + - - +
29A HIS* 1.3 76.9 - - + +
31A MET* 1.3 61.8 + - - +
32A ALA 3.1 1.8 - - - -
33A GLN* 2.9 27.7 + - - +
35A TRP* 3.0 54.0 + - + +
37A VAL* 4.9 3.1 - - + -
347A ALA* 3.8 29.6 - - + +
350A VAL* 4.0 20.6 - - + -
351A SER* 5.3 2.2 - - - -
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Residues in contact with MET 31 (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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27A ALA 2.9 13.1 + - - +
28A HIS* 3.3 49.6 - - + +
30A LEU* 1.3 70.7 - - - +
32A ALA* 1.3 58.0 + - - +
33A GLN 2.9 10.3 + - - -
34A GLY* 3.2 12.5 + - - -
35A TRP 3.3 15.9 + - - +
36A GLN* 5.3 0.2 - - - -
37A VAL* 3.4 26.9 - - + +
54A HIS 5.1 0.9 - - - +
55A GLY 5.8 1.1 - - - +
56A ILE* 3.5 34.1 - - + -
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Residues in contact with ALA 32 (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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28A HIS 3.1 16.5 + - - +
29A HIS* 3.9 8.1 - - - +
30A LEU 3.1 0.4 - - - -
31A MET* 1.3 75.9 - - - +
33A GLN* 1.3 63.1 + - + +
34A GLY 3.6 0.9 - - - -
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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