Contacts of the helix formed by residues 12 - 27 (chain B) in PDB entry 2F4W
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 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 1.3 93.2 - - - +
13B ALA* 1.3 66.2 + - - +
14B THR* 3.1 22.0 + - - -
15B GLN* 3.1 37.5 + - - +
16B ARG* 3.2 7.4 + - - +
69B ARG* 6.4 2.0 - - - -
71B PHE 4.0 1.3 - - - +
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Residues in contact with ALA 13 (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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12B THR* 1.3 73.4 - - - +
14B THR* 1.3 59.2 + - + +
16B ARG* 3.3 2.8 + - - +
17B LEU* 3.0 35.4 + - + +
42B LEU* 3.9 22.4 - - + -
68B PRO 3.9 7.6 - - - +
69B ARG* 3.5 25.3 + - - +
71B PHE* 3.1 30.8 + - + +
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.1 15.6 + - - -
13B ALA* 1.3 75.2 - - - +
15B GLN* 1.3 65.3 + - - +
17B LEU* 4.0 1.1 - - - +
18B LYS* 3.0 37.7 + - - +
41B ILE* 3.7 29.9 - - + +
42B LEU* 4.6 4.3 - - + -
69B ARG* 3.7 25.4 - - - +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B THR* 3.8 14.4 + - + +
12B THR* 3.1 52.5 + - - +
14B THR* 1.3 79.6 + - - +
16B ARG* 1.3 61.5 + - - +
18B LYS* 3.7 10.0 + - + +
19B GLN* 3.3 27.6 + - - +
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B THR* 3.5 13.1 - - + +
12B THR 3.2 16.4 + - - +
13B ALA 3.7 3.1 - - - +
15B GLN* 1.3 79.2 - - - +
17B LEU* 1.3 59.6 + - - +
19B GLN* 3.3 20.0 + - - +
20B ASP* 2.8 56.5 + - - +
23B ARG* 5.3 3.3 - - - +
71B PHE* 3.7 19.8 - - + -
72B PRO* 3.7 17.6 - - + +
107B PRO 2.5 32.7 + - - -
108B ALA* 3.6 14.8 + - - +
109B TRP 3.4 13.3 + - - -
110B SER* 4.0 2.2 - - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.0 22.2 + - - +
14B THR 4.1 1.8 - - - +
16B ARG* 1.3 74.4 - - - +
18B LYS* 1.3 60.3 + - - +
20B ASP* 3.3 2.1 + - - +
21B TYR* 2.9 25.5 + - - +
41B ILE* 3.5 37.9 - - + +
42B LEU* 3.6 25.6 - - + -
44B TRP* 3.4 16.8 - - + +
67B PHE* 3.9 35.4 - - + -
71B PHE* 3.3 30.1 - - + -
111B VAL* 4.0 11.2 - - + -
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Residues in contact with LYS 18 (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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14B THR* 3.0 26.8 + - - +
15B GLN* 3.8 11.7 - - + +
17B LEU* 1.3 75.9 - - - +
19B GLN* 1.3 61.9 + - + +
21B TYR* 3.2 7.2 + - - +
22B LEU* 3.2 33.0 + - + +
41B ILE* 3.6 21.0 - - + +
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Residues in contact with GLN 19 (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 THR* 4.9 8.1 + - - +
15B GLN* 3.3 18.0 + - - +
16B ARG* 3.4 25.8 + - - +
17B LEU 3.3 0.4 - - - -
18B LYS* 1.3 74.7 - - + +
20B ASP* 1.3 66.9 + - - +
22B LEU* 3.6 12.9 + - + +
23B ARG* 3.2 29.9 + - - +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.8 53.3 + - - +
17B LEU* 3.3 6.0 + - - +
19B GLN* 1.3 73.4 - - - +
21B TYR* 1.3 61.5 + - - +
23B ARG* 2.9 27.3 + - - +
24B ILE* 3.1 26.0 + - - +
44B TRP* 4.0 3.0 - - + -
71B PHE* 4.0 5.4 - - - -
110B SER* 3.8 5.3 - - - -
111B VAL* 3.0 47.8 + - + +
112B SER* 5.0 0.9 + - - -
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU 2.9 17.6 + - - +
18B LYS* 3.5 8.5 - - - +
19B GLN 3.1 0.2 - - - -
20B ASP* 1.3 74.5 - - - +
22B LEU* 1.3 76.4 + - + +
23B ARG 3.2 0.2 + - - -
24B ILE* 3.3 7.1 - - + +
25B LYS* 3.1 63.0 + - + +
34B ALA 4.2 1.1 - - - -
35B GLU* 2.8 26.2 + - - -
36B PRO* 3.4 30.7 - - + -
41B ILE* 5.8 1.8 - - + -
44B TRP* 3.6 17.9 - + + -
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Residues in contact with LEU 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 LYS* 3.3 20.9 - - + +
19B GLN* 3.8 13.0 - - + +
21B TYR* 1.3 85.4 - - + +
23B ARG* 1.3 56.3 + - - +
25B LYS* 3.8 4.5 - - - +
26B LYS* 2.9 33.1 + - - +
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 5.1 4.4 - - - +
19B GLN* 3.2 26.2 + - - +
20B ASP* 2.9 30.9 + - - +
21B TYR 3.2 0.4 - - - -
22B LEU* 1.3 80.2 - - - +
24B ILE* 1.3 56.5 + - - +
26B LYS* 3.3 7.8 + - - +
27B ASP* 2.9 41.8 + - + +
108B ALA 5.6 3.2 + - - -
110B SER* 3.8 27.8 + - - -
112B SER* 4.3 9.6 - - - +
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Residues in contact with ILE 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 ASP 3.1 13.2 + - - +
21B TYR* 3.3 18.6 - - + +
23B ARG* 1.3 77.2 - - - +
25B LYS* 1.3 79.1 + - + +
27B ASP 4.0 3.4 - - - +
28B PRO* 3.3 29.4 - - + +
29B VAL* 4.7 12.1 - - + +
32B ILE* 4.8 6.3 - - + +
34B ALA* 4.1 26.2 - - + +
44B TRP* 4.4 11.4 - - + -
111B VAL* 4.8 3.1 - - + -
112B SER* 3.6 37.9 - - - +
115B LEU* 4.3 10.1 - - + -
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.1 63.1 + - + +
22B LEU* 3.9 4.9 - - - +
24B ILE* 1.3 85.3 - - + +
26B LYS* 1.3 62.5 + - - +
28B PRO* 4.0 10.4 - - - +
33B CYS* 4.0 14.8 - - - -
34B ALA 3.2 15.7 + - - +
35B GLU* 2.7 25.6 + - - -
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Residues in contact with LYS 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 LEU 2.9 20.2 + - - +
23B ARG* 3.6 7.9 - - - +
25B LYS* 1.3 79.5 - - - +
27B ASP* 1.3 60.9 + - + +
28B PRO* 3.7 5.4 - - - +
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 2.9 21.9 + - + +
24B ILE* 3.5 8.7 - - - +
26B LYS* 1.3 83.6 - - + +
28B PRO* 1.4 73.4 - - - +
29B VAL* 4.1 7.3 - - - +
112B SER* 4.7 2.1 + - - -
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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