Contacts of the helix formed by residues 19 - 32 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B THR* 1.3 68.2 + - - +
21B ALA 3.3 2.5 - - - -
22B ASP* 3.3 14.0 + - - +
23B LEU* 3.2 18.2 + - - +
48B TRP* 3.5 13.1 - - - -
52B ARG* 3.5 32.7 - - - +
56B VAL* 4.1 13.2 - - - -
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Residues in contact with THR 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 SER 6.0 1.8 - - - +
19B GLY* 1.3 76.6 - - - +
21B ALA* 1.3 58.3 + - - +
23B LEU* 3.3 4.3 + - - +
24B LEU* 3.0 29.4 + - + +
56B VAL* 3.9 22.9 + - + +
59B GLN* 6.1 0.9 - - - +
74B TYR* 3.8 22.2 + - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.3 0.4 - - - +
20B THR* 1.3 76.2 - - - +
22B ASP* 1.3 69.1 + - - +
23B LEU 3.3 0.3 + - - -
24B LEU* 3.4 13.4 + - - +
25B VAL* 3.7 18.7 + - - +
203B LEU* 3.5 34.6 - - + +
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Residues in contact with ASP 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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19B GLY* 3.3 23.2 + - - +
21B ALA* 1.3 80.8 + - - +
23B LEU* 1.3 57.9 + - - +
26B PRO* 3.1 24.9 - - - +
46B LEU* 3.2 11.4 - - + +
48B TRP* 4.0 14.8 - - + -
52B ARG* 4.3 6.9 + - - -
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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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19B GLY 3.2 11.2 + - - +
20B THR 3.8 6.3 - - - +
21B ALA 3.2 0.4 - - - -
22B ASP* 1.3 79.2 - - - +
24B LEU* 1.3 68.0 + - - +
26B PRO* 3.1 4.9 - - - +
27B LEU* 3.1 44.7 + - + +
42B LEU* 4.3 13.4 - - + +
46B LEU* 4.2 17.3 - - + -
48B TRP* 4.2 13.9 - - + -
53B VAL* 4.2 24.0 - - + +
56B VAL* 4.0 27.8 - - + -
57B LEU* 4.3 13.2 - - + -
74B TYR* 4.5 7.4 - - + -
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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 THR* 3.0 20.8 + - + +
21B ALA* 3.4 8.5 + - - +
23B LEU* 1.3 81.6 - - - +
25B VAL* 1.3 65.4 + - + +
27B LEU* 3.1 5.1 + - + +
28B LEU* 2.9 48.4 + - + +
74B TYR* 3.4 39.9 - - + +
103B PHE* 6.2 1.3 - - + -
106B LEU* 4.7 2.0 - - + -
199B PHE* 5.4 6.7 - - + -
203B LEU* 3.9 29.8 - - + -
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Residues in contact with VAL 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 ALA 3.7 12.5 + - - +
24B LEU* 1.3 74.8 - - + +
26B PRO* 1.3 72.1 - - + +
28B LEU* 3.3 8.0 + - - +
29B ARG* 3.0 61.3 + - - +
106B LEU* 3.7 24.0 - - + +
203B LEU* 4.4 11.2 - - + -
204B LEU* 3.9 28.0 - - + -
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Residues in contact with PRO 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 ASP 3.1 26.2 - - - +
23B LEU 3.1 7.0 - - - +
25B VAL* 1.3 96.6 - - + +
27B LEU* 1.3 55.6 + - - +
29B ARG* 3.4 11.0 + - + +
30B GLU* 3.0 35.1 + - - +
42B LEU* 4.4 8.1 - - + -
45B ILE* 4.1 24.2 - - + +
46B LEU* 3.6 16.8 - - + -
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Residues in contact with LEU 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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23B LEU* 3.1 33.1 + - + +
24B LEU* 3.5 4.5 - - + +
26B PRO* 1.3 77.6 - - - +
28B LEU* 1.3 53.1 + - + +
30B GLU* 3.2 2.4 + - - +
31B LEU* 2.8 47.9 + - + +
37B VAL* 3.9 31.9 - - + -
42B LEU* 3.9 17.4 - - + +
71B ILE* 4.2 20.0 - - + -
74B TYR* 3.3 41.5 - - + -
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Residues in contact with LEU 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 34.4 + - + +
25B VAL* 3.6 7.2 - - - +
27B LEU* 1.3 75.6 - - + +
29B ARG* 1.3 58.2 - - - +
31B LEU* 4.3 5.2 - - + -
32B ALA* 2.9 30.3 + - - +
74B TYR* 3.4 26.2 - - + +
76B LEU* 3.6 27.3 - - + +
103B PHE* 3.8 24.7 - - + -
106B LEU* 3.7 35.9 - - + -
107B ILE* 3.9 12.5 - - + +
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Residues in contact with ARG 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 VAL* 3.0 36.4 + - - +
26B PRO* 3.7 8.9 - - + +
28B LEU* 1.3 75.4 - - - +
30B GLU* 1.3 62.6 + - + +
32B ALA* 3.5 17.1 + - - +
33B LYS* 3.8 14.5 - - - +
105B ALA 4.9 3.4 + - - -
106B LEU* 3.0 29.4 + - - +
107B ILE* 4.1 21.4 + - + +
108B GLY* 5.0 2.2 - - - +
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Residues in contact with GLU 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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26B PRO 3.0 20.9 + - - +
27B LEU* 3.6 2.7 - - - +
29B ARG* 1.3 74.8 - - - +
31B LEU* 1.3 65.0 + - - +
32B ALA 3.1 1.8 - - - -
33B LYS* 2.9 58.2 + - - +
34B GLY 4.2 0.7 + - - -
35B ARG 4.3 2.9 - - - +
37B VAL* 3.5 33.0 - - + +
41B THR* 4.3 10.3 - - + +
42B LEU* 4.9 1.1 - - + -
45B ILE* 3.5 32.0 - - + +
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Residues in contact with LEU 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 LEU* 2.8 45.0 + - + +
28B LEU* 3.7 6.1 - - - +
30B GLU* 1.3 73.7 - - - +
32B ALA* 1.3 58.8 + - - +
33B LYS 3.0 0.2 - - - -
34B GLY* 2.9 22.2 + - - -
35B ARG 4.3 7.6 - - - +
37B VAL* 3.8 9.2 - - + +
71B ILE* 3.8 16.6 - - + +
72B ILE* 3.8 27.1 - - - +
73B GLY 4.2 1.3 - - - +
74B TYR* 3.9 18.6 - - + +
76B LEU* 3.5 37.0 - - + +
78B LEU* 4.1 11.9 - - + +
92B LEU* 3.9 5.7 - - - +
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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 LEU 2.9 17.5 + - - +
29B ARG* 3.6 11.7 - - - +
30B GLU 3.1 0.8 - - - -
31B LEU* 1.3 76.1 - - - +
33B LYS* 1.3 58.6 + - - +
34B GLY* 3.1 2.0 + - - -
76B LEU* 3.9 2.7 - - + +
87B ILE* 3.6 25.7 - - + +
88B ASP* 5.5 2.1 - - - +
90B ARG* 4.3 9.5 + - - -
92B LEU* 3.8 19.5 - - - +
107B ILE* 4.1 14.6 - - + -
109B ARG* 6.1 2.0 - - + -
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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