Contacts of the helix formed by residues 4 - 30 (chain D) in PDB entry 2FBW
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 LYS 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLN* 3.5 12.1 - - - +
242B MET 3.2 19.4 + - - -
243B ALA 4.3 8.5 + - - -
244B THR 4.4 0.6 - - - -
245B TYR* 2.6 52.1 + - + +
247B GLU* 4.0 22.4 - - - +
3D SER* 1.3 82.2 - - - +
5D ALA* 1.3 63.8 + - - +
6D ALA 3.3 2.9 - - - -
7D SER* 3.2 16.3 + - - +
8D LEU* 2.9 37.5 + - + +
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Residues in contact with ALA 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 5.4 0.2 - - - +
3D SER 3.4 11.5 + - - +
4D LYS* 1.3 77.4 - - - +
6D ALA* 1.3 63.4 + - - +
8D LEU* 3.4 8.2 + - - +
9D HIS* 2.9 24.6 + - - +
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Residues in contact with ALA 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 3.3 12.7 + - - +
208B ASP* 3.5 35.2 - - - +
209B PRO* 5.3 1.8 - - + -
213B TYR* 3.7 19.9 - - + -
4D LYS 3.3 0.8 - - - -
5D ALA* 1.3 78.5 - - - +
7D SER* 1.3 62.6 + - - +
9D HIS* 3.2 7.2 + - - +
10D TRP* 3.0 22.2 + - - +
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Residues in contact with SER 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 3.0 28.5 + - - -
213B TYR* 3.3 23.5 + - - -
242B MET* 3.4 28.1 + - - -
243B ALA* 4.4 3.5 - - - -
4D LYS* 3.2 14.7 + - - -
6D ALA* 1.3 75.0 - - - +
8D LEU* 1.3 59.0 + - - +
10D TRP* 3.3 3.3 + - - +
11D THR* 2.9 33.3 + - - -
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LYS* 2.9 33.4 + - + +
5D ALA* 3.7 7.4 - - - +
7D SER* 1.3 78.4 + - - +
9D HIS* 1.3 56.9 + - - +
11D THR* 3.3 10.3 + - + -
12D SER* 2.9 38.7 + - - +
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Residues in contact with HIS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ALA 2.9 17.4 + - - +
6D ALA* 3.2 6.3 + - - +
8D LEU* 1.3 73.9 - - - +
10D TRP* 1.3 65.9 + - - +
12D SER* 3.0 6.4 + - - -
13D GLU* 2.7 67.4 + - + +
49D TRP* 3.2 48.2 + + - +
53D GLN* 4.4 8.4 + - - -
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Residues in contact with TRP 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.6 34.3 - + + -
239B LYS* 4.0 43.9 - - + +
240B LYS* 5.1 2.5 - - + -
243B ALA* 4.0 22.2 - - + -
109C ASP* 3.8 45.1 + - + -
6D ALA 3.0 12.5 + - - +
7D SER 3.5 7.9 - - - +
9D HIS* 1.3 79.1 - - - +
11D THR* 1.3 75.5 + - + +
13D GLU* 3.3 11.7 + - - +
14D ARG* 3.2 66.7 + - + +
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Residues in contact with THR 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ALA* 3.5 28.8 + - + +
7D SER 2.9 18.0 + - - -
8D LEU* 3.5 10.9 - - + -
10D TRP* 1.3 84.1 - - + +
12D SER* 1.3 63.2 + - - +
14D ARG* 3.2 6.6 + - + +
15D ALA* 3.0 22.9 + - + +
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Residues in contact with SER 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 2.9 24.5 + - - +
9D HIS* 3.0 10.6 + - - -
11D THR* 1.3 76.4 - - - +
13D GLU* 1.3 57.4 + - - +
15D ALA* 3.1 9.2 + - - +
16D VAL* 2.9 33.3 + - - +
49D TRP* 3.9 22.4 - - - -
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D HIS* 2.7 47.1 + - - +
10D TRP* 3.5 15.4 - - - +
12D SER* 1.3 76.3 - - - +
14D ARG* 1.3 82.2 + - - +
16D VAL* 3.4 2.6 + - - +
17D SER* 3.0 31.4 + - - -
46D HIS* 4.8 1.7 + - - -
49D TRP* 3.8 31.9 - - + +
53D GLN* 2.9 30.5 + - - +
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Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS* 5.8 1.2 - - - +
105C HIS* 5.9 3.0 + - - +
106C LEU* 3.9 17.1 - - + +
109C ASP* 2.9 36.6 + - + +
10D TRP* 3.2 58.6 + - + +
11D THR* 3.2 9.2 + - + +
13D GLU* 1.3 114.4 + - - +
15D ALA* 1.3 62.5 + - - +
17D SER* 3.2 7.4 + - - -
18D ALA* 2.9 23.9 + - - +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D THR* 3.0 16.2 + - + +
12D SER* 3.5 11.7 - - - +
14D ARG* 1.3 75.5 - - - +
16D VAL* 1.3 59.6 + - + +
18D ALA* 3.2 8.1 + - - +
19D LEU* 2.9 27.1 + - - +
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 2.9 19.0 + - - +
13D GLU 3.9 3.6 - - - +
15D ALA* 1.3 76.7 - - + +
17D SER* 1.3 65.0 + - - +
19D LEU* 3.3 12.8 + - + +
20D LEU* 2.9 22.5 + - - +
42D ALA* 4.0 15.3 - - + +
45D LEU* 3.8 17.5 - - + -
46D HIS* 3.7 37.7 - - + +
49D TRP* 3.6 19.5 - - + -
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.4 18.5 - - - +
13D GLU 3.0 16.0 + - - -
14D ARG* 3.2 11.8 + - - -
16D VAL* 1.3 78.0 - - - +
18D ALA* 1.3 62.0 + - - +
20D LEU* 3.4 6.1 + - - +
21D LEU* 3.1 20.3 + - - +
46D HIS* 3.0 32.4 + - - -
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.3 13.8 - - + +
14D ARG 2.9 13.1 + - - +
15D ALA* 3.6 9.4 - - - +
17D SER* 1.3 76.4 - - - +
19D LEU* 1.3 64.1 + - - +
21D LEU* 3.0 13.2 + - + +
22D GLY* 2.9 18.7 + - - -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA 2.9 13.6 + - - +
16D VAL* 3.3 17.2 + - + +
18D ALA* 1.3 75.8 - - - +
20D LEU* 1.3 64.8 + - - +
22D GLY* 2.8 14.6 + - - +
23D LEU* 2.9 34.0 + - + +
38D SER* 5.4 3.4 - - - +
42D ALA* 3.9 21.5 - - + -
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL 2.9 12.1 + - - +
17D SER* 3.5 9.4 - - - +
19D LEU* 1.3 75.9 - - - +
21D LEU* 1.3 62.6 + - - +
23D LEU* 3.2 13.6 + - + +
24D LEU* 3.3 21.5 + - + +
39D LEU* 3.9 25.6 - - + -
42D ALA* 3.8 27.1 - - + +
43D LEU* 4.0 26.0 - - + +
46D HIS* 3.6 38.1 - - + +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C THR* 4.1 20.9 - - + +
103C ILE* 3.7 39.9 - - + -
106C LEU* 4.5 16.8 - - + -
17D SER 3.1 11.5 + - - +
18D ALA* 3.0 16.2 + - + +
20D LEU* 1.3 78.8 - - - +
22D GLY* 1.3 53.9 + - - +
24D LEU* 3.3 10.6 + - + +
25D PRO* 2.9 25.0 - - + +
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ALA 2.9 9.1 + - - -
19D LEU* 2.8 12.6 + - - -
21D LEU* 1.3 73.7 - - - +
23D LEU* 1.3 58.9 + - - +
25D PRO* 3.0 24.0 - - - +
26D ALA* 3.3 11.0 + - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 2.9 29.2 + - + +
20D LEU* 3.2 9.1 + - - +
22D GLY* 1.3 77.7 - - - +
24D LEU* 1.3 61.0 + - - +
26D ALA* 3.5 12.3 - - + +
27D ALA* 2.8 31.7 + - - +
35D VAL* 4.5 15.1 - - + +
38D SER* 3.7 47.1 - - - +
39D LEU* 3.8 22.1 - - + +
42D ALA* 4.0 16.4 - - + -
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 5.3 16.6 - - + -
99C THR* 4.0 33.9 - - + +
20D LEU* 3.3 18.8 + - + +
21D LEU* 3.6 10.3 - - + +
23D LEU* 1.3 76.9 - - - +
25D PRO* 1.3 71.4 - - + +
27D ALA* 3.1 13.4 + - + +
28D TYR* 3.4 9.7 + - - +
39D LEU* 5.1 11.7 - - + -
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Residues in contact with PRO 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU 2.9 26.5 - - - +
22D GLY* 3.0 20.2 - - - +
24D LEU* 1.3 83.5 - - + +
26D ALA* 1.3 61.2 + - - +
28D TYR* 3.0 8.9 + - + +
29D LEU* 3.0 35.3 + - + +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLY 3.3 14.2 + - - +
23D LEU* 3.2 17.2 + - + +
24D LEU 3.2 0.8 - - - -
25D PRO* 1.3 78.2 - - - +
27D ALA* 1.3 55.5 + - - +
29D LEU* 4.5 0.9 - - - +
30D TYR* 2.7 49.5 + - + +
35D VAL* 4.1 17.3 - - + -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU 2.8 16.9 + - - +
24D LEU* 3.1 8.0 + - + +
26D ALA* 1.3 75.9 - - - +
28D TYR* 1.3 56.9 - - - +
31D PRO* 3.2 26.3 - - - +
35D VAL* 3.8 21.0 - - + +
39D LEU* 4.2 10.8 - - + -
94D CYS* 3.9 15.5 - - - +
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C MET* 4.7 21.8 - - + +
24D LEU 3.4 6.5 + - - +
25D PRO* 3.0 11.3 + - + +
27D ALA* 1.3 81.7 - - - +
29D LEU* 1.3 79.7 + - + +
31D PRO* 4.0 7.1 - - - +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PRO* 3.0 21.8 + - + +
26D ALA* 5.6 0.4 - - - -
28D TYR* 1.3 106.0 - - + +
30D TYR* 1.3 96.5 + - + +
31D PRO* 3.5 5.7 - - - +
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Residues in contact with TYR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ALA* 2.7 27.3 + - + +
29D LEU* 1.3 109.1 - - + +
31D PRO* 1.3 71.0 - - - +
32D GLY 5.2 0.2 - - - -
35D VAL* 3.2 22.9 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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