Contacts of the helix formed by residues 19 - 32 (chain A) in PDB entry 3F2F
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASN* 5.5 0.4 - - - +
17A THR 3.5 0.2 + - - -
18A ASN* 1.3 73.8 - - - +
20A THR* 1.3 54.5 + - - +
21A ALA 3.4 2.4 - - - +
22A ASP* 3.2 17.2 + - - -
23A LEU* 2.7 38.3 + - - +
48A TRP* 3.4 24.3 - - - -
52A ARG* 4.3 4.4 - - - +
56A VAL* 4.5 3.1 - - - -
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Residues in contact with THR 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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14A VAL* 3.3 31.9 - - + +
15A ASN* 3.8 8.9 - - - +
16A ARG* 4.0 3.2 + - + +
17A THR* 2.8 40.6 + - - +
18A ASN 3.3 3.0 + - - -
19A GLY* 1.3 75.6 - - - +
21A ALA* 1.3 52.7 + - - +
23A LEU* 3.1 3.5 + - - +
24A LEU* 2.7 39.6 + - + +
56A VAL* 3.9 14.5 - - + +
74A TYR* 3.7 20.9 - - - +
203A LEU* 6.4 0.2 - - + -
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Residues in contact with ALA 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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15A ASN* 4.6 6.8 - - - +
19A GLY 3.4 0.4 - - - +
20A THR* 1.3 76.4 - - - +
22A ASP* 1.3 64.8 + - - +
23A LEU 3.3 0.3 + - - -
24A LEU* 4.3 7.0 - - - -
25A VAL* 3.5 28.5 + - + +
203A LEU* 4.0 22.9 - - + +
206A THR* 3.6 28.5 - - - +
207A MET* 3.8 17.6 - - + +
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Residues in contact with ASP 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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19A GLY* 3.2 21.0 + - - +
21A ALA* 1.3 75.9 - - - +
23A LEU* 1.3 57.6 + - - +
26A PRO* 2.9 27.4 - - - +
46A LEU* 3.2 11.1 - - + +
48A TRP* 3.9 18.1 - - + -
52A ARG* 5.7 0.3 + - - -
206A THR 5.0 2.6 - - - +
207A MET* 3.5 21.1 - - + +
208A SER* 2.8 47.9 + - - -
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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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19A GLY 2.7 19.6 + - - +
20A THR 3.6 3.4 - - - +
22A ASP* 1.3 75.4 - - - +
24A LEU* 1.3 67.4 + - - +
26A PRO* 3.1 5.0 - - - +
27A LEU* 3.0 48.4 + - + +
42A LEU* 4.4 8.7 - - + +
46A LEU* 4.2 16.4 - - + -
48A TRP* 4.3 6.5 - - + -
53A VAL* 3.9 33.2 - - + +
56A VAL* 3.8 31.4 - - + -
57A LEU* 4.0 14.8 - - + -
74A TYR* 4.4 7.9 - - + -
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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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14A VAL* 4.2 25.1 - - + -
20A THR* 2.7 25.1 + - + +
21A ALA* 3.5 5.4 + - - +
23A LEU* 1.3 76.7 - - - +
25A VAL* 1.3 59.2 + - + +
27A LEU* 3.2 5.9 + - + +
28A LEU* 2.8 61.4 + - + +
74A TYR* 3.5 40.2 - - + +
103A PHE* 5.8 3.1 - - + -
106A LEU* 5.2 1.8 - - + -
199A PHE* 6.2 0.7 - - + -
203A LEU* 4.2 23.1 - - + -
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Residues in contact with VAL 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 ALA* 3.5 7.2 + - + +
24A LEU* 1.3 79.7 - - + +
26A PRO* 1.3 70.3 - - + +
28A LEU* 3.3 8.2 + - - +
29A ARG* 3.1 61.9 + - - +
106A LEU* 3.6 24.7 - - + +
203A LEU* 5.5 4.7 - - + -
204A LEU* 4.1 15.3 - - + -
207A MET* 3.6 32.8 - - + -
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Residues in contact with PRO 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 ASP 2.9 29.6 - - - +
23A LEU 3.1 6.7 - - - +
25A VAL* 1.3 93.9 - - + +
27A LEU* 1.3 60.3 + - - +
29A ARG* 3.3 12.7 + - + +
30A GLU* 3.0 28.9 + - - +
42A LEU* 4.5 6.7 - - + -
45A ILE* 4.1 27.5 - - + +
46A LEU* 3.8 15.9 - - + -
207A MET* 4.9 3.6 - - + -
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Residues in contact with LEU 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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23A LEU* 3.0 34.3 + - + +
24A LEU* 3.5 6.5 - - + +
26A PRO* 1.3 77.2 - - - +
28A LEU* 1.3 57.3 + - + +
30A GLU* 3.2 1.8 + - - +
31A LEU* 2.8 45.2 + - + +
37A VAL* 3.9 29.8 - - + -
42A LEU* 3.9 19.0 - - + +
57A LEU* 4.3 5.6 - - + -
71A ILE* 4.2 14.6 - - + -
74A TYR* 3.4 38.6 - - + -
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Residues in contact with LEU 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* 2.8 39.8 + - + +
25A VAL* 3.6 6.3 - - - +
27A LEU* 1.3 75.5 - - + +
29A ARG* 1.3 57.2 - - - +
31A LEU* 3.4 5.1 + - + -
32A ALA* 2.9 30.1 + - - +
74A TYR* 3.7 24.0 - - + +
76A LEU* 3.8 27.5 - - + +
103A PHE* 4.0 22.9 - - + -
106A LEU* 3.7 36.6 - - + -
107A ILE* 4.0 13.9 - - + +
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Residues in contact with ARG 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 VAL* 3.1 32.7 + - - +
26A PRO* 3.7 10.3 - - + +
27A LEU 3.2 0.4 - - - -
28A LEU* 1.3 73.8 - - - +
30A GLU* 1.3 71.3 + - - +
32A ALA* 3.6 16.0 + - - +
33A LYS* 3.9 14.3 - - - +
105A ALA 5.1 2.6 + - - -
106A LEU 3.0 23.4 + - - +
107A ILE* 3.8 32.2 + - + +
108A GLY* 5.0 2.2 - - - +
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Residues in contact with GLU 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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26A PRO 3.0 20.1 + - - +
27A LEU* 3.6 3.6 - - - +
29A ARG* 1.3 76.7 - - - +
31A LEU* 1.3 65.4 + - - +
32A ALA 3.0 1.6 - - - -
33A LYS* 2.9 55.3 + - - +
34A GLY 4.3 0.5 + - - -
35A ARG 4.5 2.3 - - - +
37A VAL* 3.7 26.4 - - + +
41A THR* 4.0 16.9 - - + +
42A LEU* 4.8 1.3 - - + -
45A ILE* 3.5 30.7 - - + +
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Residues in contact with LEU 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 LEU* 2.8 41.3 + - + +
28A LEU* 3.8 5.4 - - - +
30A GLU* 1.3 71.6 - - - +
32A ALA* 1.3 56.7 + - - +
34A GLY* 2.8 24.3 + - - -
35A ARG 4.2 8.0 + - - +
37A VAL* 3.7 13.9 - - + +
71A ILE* 3.8 24.9 - - + +
72A ILE* 3.8 19.7 - - - +
73A GLY 4.6 1.6 - - - +
74A TYR* 4.1 17.7 - - + +
76A LEU* 3.6 34.5 - - + +
77A THR* 5.6 0.2 - - - -
78A LEU* 4.1 10.8 - - + +
92A LEU* 3.7 6.9 - - - +
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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 LEU 2.9 19.1 + - - +
29A ARG 3.6 8.3 - - - +
30A GLU 3.0 0.6 - - - -
31A LEU* 1.3 75.8 - - - +
33A LYS* 1.3 59.4 + - - +
34A GLY 3.1 2.5 + - - -
76A LEU* 4.1 2.5 - - + -
87A ILE* 4.3 19.5 - - + +
90A ARG* 4.5 5.9 - - - +
92A LEU* 3.6 24.0 - - + +
107A ILE* 4.0 30.5 - - + -
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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