Contacts of the helix formed by residues 19 - 32 (chain B) 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 HIS 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ALA* 3.6 13.4 - - + +
14B GLY 3.4 9.8 + - - +
16B THR 3.2 22.2 + - - -
17B GLY* 3.8 18.1 + - - -
18B GLY* 1.3 77.1 - - - +
20B VAL* 1.3 64.9 + - - +
21B PHE 3.3 0.9 - - - -
22B PRO* 3.2 10.4 - - - +
23B GLY 3.2 10.2 + - - -
103B MET* 3.1 33.1 + - + +
104B GLY* 3.6 12.3 + - - +
105B GLY* 3.6 22.7 + - - -
126B GLU* 5.3 3.2 + - - -
127B GLN* 2.8 28.9 - - - -
128B ASN* 4.4 12.8 + - - -
288B GLN* 5.8 1.4 + - - -
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Residues in contact with VAL 20 (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 ALA* 3.6 18.2 - - - +
14B GLY 3.3 3.0 + - - -
15B GLY* 3.7 12.8 - - - +
19B HIS* 1.3 79.0 - - - +
21B PHE* 1.3 70.7 + - + +
23B GLY* 3.3 0.9 + - - -
24B LEU* 2.8 43.4 + - + +
39B TRP* 3.6 18.3 - - + -
46B MET* 3.7 32.3 - - + -
47B GLU* 4.4 6.3 - - + -
50B LEU* 4.1 9.0 - - + -
51B VAL* 4.1 13.9 - - + -
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Residues in contact with PHE 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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18B GLY* 4.3 19.5 - - - -
20B VAL* 1.3 79.9 - - + +
22B PRO* 1.3 67.9 - - + +
24B LEU* 3.2 11.2 + - + +
25B ALA* 3.0 21.3 + - - +
46B MET* 3.6 28.3 - - + -
50B LEU* 3.7 24.7 - - + -
265B LEU* 4.2 15.7 - - + -
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Residues in contact with PRO 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 GLY 3.4 13.2 - - - +
19B HIS 3.2 11.7 - - - +
21B PHE* 1.3 96.0 - - + +
23B GLY* 1.3 59.4 + - - +
25B ALA* 3.2 5.5 + - + +
26B VAL* 3.2 26.7 + - - +
103B MET* 3.7 19.3 - - + -
127B GLN* 4.1 12.1 - - + -
162B PRO* 3.9 27.5 - - + +
265B LEU* 3.5 31.2 - - + -
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Residues in contact with GLY 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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11B VAL* 4.4 6.7 - - - +
19B HIS 3.2 9.5 + - - -
20B VAL 3.7 2.9 - - - -
21B PHE 3.2 0.6 - - - -
22B PRO* 1.3 78.6 - - - +
24B LEU* 1.3 57.4 + - - +
26B VAL* 3.3 5.5 + - - +
27B ALA* 2.9 27.9 + - - +
39B TRP* 3.7 15.4 - - - -
103B MET* 3.8 25.5 - - - +
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Residues in contact with LEU 24 (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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20B VAL* 2.8 29.3 + - + +
21B PHE* 3.2 12.1 + - + +
23B GLY* 1.3 75.2 - - - +
25B ALA* 1.3 64.7 + - - +
27B ALA* 3.7 2.3 - - - +
28B HIS* 2.9 36.2 + - + +
39B TRP* 3.9 15.5 - - + -
50B LEU* 3.8 30.1 - - + -
51B VAL* 4.7 7.4 - - + -
54B HIS* 3.8 37.5 - - + +
56B ILE* 3.8 27.4 - - + -
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Residues in contact with ALA 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 PHE 3.0 12.1 + - - +
22B PRO* 3.4 9.9 - - + +
24B LEU* 1.3 77.5 - - - +
26B VAL* 1.3 57.4 + - - +
28B HIS* 3.6 5.4 + - - +
29B HIS* 3.1 27.4 + - - +
162B PRO* 3.9 24.5 - - + -
343B THR* 3.6 12.7 - - + +
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Residues in contact with VAL 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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9B LEU* 5.0 1.1 - - + -
22B PRO 3.2 14.6 + - - +
23B GLY 3.7 6.5 - - - +
24B LEU 3.2 0.2 - - - -
25B ALA* 1.3 74.8 - - + +
27B ALA* 1.3 64.3 + - - +
29B HIS* 3.3 2.9 + - - +
30B LEU* 3.0 40.1 + - + +
101B LEU* 3.9 25.6 - - + -
103B MET* 4.8 5.6 - - + -
162B PRO* 5.1 3.8 - - + -
343B THR* 4.2 16.2 - - + +
346B VAL* 3.9 28.3 - - + -
347B ALA* 4.3 15.0 - - - -
350B VAL* 4.9 1.6 - - + -
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Residues in contact with ALA 27 (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 LEU* 4.9 3.4 - - - -
11B VAL* 4.6 2.4 - - + +
23B GLY 2.9 18.3 + - - +
24B LEU* 3.7 6.5 - - - +
26B VAL* 1.3 77.8 - - - +
28B HIS* 1.3 57.9 + - - +
30B LEU* 3.2 4.0 + - - +
31B MET* 2.8 46.9 + - + +
37B VAL* 3.9 28.0 - - + +
39B TRP* 4.4 5.4 - - + -
56B ILE* 4.2 9.4 - - + -
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Residues in contact with HIS 28 (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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24B LEU* 2.9 30.3 + - + +
25B ALA* 4.0 4.9 - - - +
27B ALA* 1.3 76.5 - - - +
29B HIS* 1.3 63.5 + - - +
31B MET* 3.3 25.4 + - + +
32B ALA* 3.2 23.4 + - - +
54B HIS* 2.8 53.4 + + + +
56B ILE* 4.5 1.4 - - + +
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Residues in contact with HIS 29 (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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25B ALA 3.1 19.2 + - - +
26B VAL* 3.5 6.3 - - - +
27B ALA 3.2 0.2 - - - -
28B HIS* 1.3 78.1 - - - +
30B LEU* 1.3 58.6 + - - +
32B ALA* 3.5 6.4 + - - +
33B GLN* 3.0 48.5 + - + +
343B THR* 3.9 17.3 - - + +
344B GLU* 3.4 36.3 - - + +
347B ALA* 3.5 24.9 - - + +
348B ASN* 5.3 4.0 + - - -
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Residues in contact with LEU 30 (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 LEU* 3.5 28.7 - - + -
26B VAL* 3.0 24.3 + - + +
27B ALA 3.9 3.4 - - - +
29B HIS* 1.3 73.0 - - + +
31B MET* 1.3 61.4 + - - +
32B ALA 3.1 2.0 - - - -
33B GLN* 2.8 27.2 + - + +
35B TRP* 3.0 57.6 + - + +
37B VAL* 4.8 3.4 - - + -
347B ALA* 3.8 30.1 - - + +
350B VAL* 4.0 20.6 - - + -
351B SER* 5.0 2.9 - - - -
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Residues in contact with MET 31 (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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27B ALA* 2.8 37.8 + - + +
28B HIS* 3.4 32.1 - - + +
30B LEU* 1.3 76.5 - - - +
32B ALA* 1.3 56.6 + - - +
33B GLN 3.0 0.4 - - - -
34B GLY* 3.2 16.3 + - - -
35B TRP 3.5 16.9 + - - +
37B VAL* 3.7 24.2 - - + +
54B HIS 5.7 0.2 - - - +
55B GLY 5.8 1.3 - - - +
56B ILE* 3.4 35.7 - - + -
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Residues in contact with ALA 32 (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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28B HIS 3.2 11.7 + - - +
29B HIS* 3.6 13.2 - - - +
30B LEU 3.1 0.6 - - - -
31B MET* 1.3 76.4 - - - +
33B GLN* 1.3 67.6 + - - +
34B GLY 3.3 1.7 + - - -
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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