Contacts of the helix formed by residues 22 - 36 (chain B) in PDB entry 3D9O
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 SER 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B MSE 3.9 10.9 - - - +
20B PRO 3.7 2.6 + - - -
21B ILE* 1.3 80.2 - - - +
23B LYS* 1.3 59.3 + - - +
24B ALA* 3.6 10.0 + - - +
25B LYS* 3.1 24.3 + - - +
26B MSE 3.0 26.5 + - - +
-1Z PRO* 3.5 16.8 - - - -
0Z SER* 3.9 2.7 - - - +
1Z TYR* 3.9 1.3 - - - -
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Residues in contact with LYS 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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22B SER* 1.3 70.8 - - - +
24B ALA* 1.3 54.4 + - - +
26B MSE 3.2 3.4 + - - +
27B THR* 2.8 41.4 + - - +
-1Z PRO* 2.9 37.4 + - + +
0Z SER 3.6 23.3 - - - +
1Z TYR* 3.6 21.7 - - + +
2Z SER* 4.7 4.0 - - - +
5Z SER* 3.4 30.3 + - - -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.2 9.9 + - - +
23B LYS* 1.3 78.8 - - - +
25B LYS* 1.3 56.8 + - - +
27B THR* 3.5 7.6 + - - +
28B GLN* 3.1 31.9 + - - +
-1Z PRO 4.7 0.2 + - - -
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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
----------------------------------------------------------
10B GLU* 3.3 9.5 + - - +
13B SER* 2.9 32.2 + - - +
14B LEU* 4.0 4.0 - - + -
17B MSE 3.7 31.0 - - + -
21B ILE* 3.6 19.1 - - + -
22B SER* 3.1 20.8 + - - +
24B ALA* 1.3 74.5 - - - +
26B MSE 1.3 65.4 + - - +
28B GLN* 2.9 27.4 + - - +
29B ILE* 3.0 38.3 + - + +
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Residues in contact with MSE 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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14B LEU* 5.2 0.7 - - + -
21B ILE* 3.7 33.4 - - + +
22B SER 3.0 12.9 + - - +
23B LYS 3.2 4.0 + - - +
25B LYS* 1.3 76.6 - - - +
27B THR* 1.3 54.7 + - - +
29B ILE* 3.4 8.9 + - - +
30B THR* 2.7 37.4 + - - -
61B PRO* 4.3 4.9 - - + +
64B TYR* 3.6 24.5 - - + -
65B VAL* 3.8 39.3 - - + -
68B SER* 3.7 17.7 - - - +
1Z TYR* 3.5 37.5 - - + -
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 2.8 25.7 + - - +
24B ALA* 3.5 8.0 - - - +
26B MSE 1.3 73.8 - - - +
28B GLN* 1.3 56.7 + - + +
30B THR* 3.2 6.7 + - - -
31B LYS* 2.7 66.2 + - + +
68B SER* 5.4 0.7 - - - -
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 3.6 22.9 + - - +
24B ALA 3.1 15.8 + - - +
25B LYS* 2.9 39.5 + - - +
27B THR* 1.3 77.4 - - + +
29B ILE* 1.3 61.8 + - - +
31B LYS* 3.8 8.8 - - + +
32B ALA* 3.1 23.4 + - - +
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Residues in contact with ILE 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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7B PHE* 3.8 22.0 - - + -
10B GLU* 3.6 30.7 - - + +
11B LEU* 4.5 6.7 - - - -
14B LEU* 3.5 40.8 - - + -
25B LYS* 3.0 29.0 + - + +
26B MSE 3.7 10.8 - - - +
28B GLN* 1.3 72.3 - - - +
30B THR* 1.3 63.5 + - - +
32B ALA* 3.3 3.8 + - - +
33B ALA* 2.9 26.9 + - - +
65B VAL* 4.1 29.4 - - + -
69B ILE* 5.0 0.4 - - + -
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MSE 2.7 18.3 + - - +
27B THR* 3.6 6.7 - - - -
29B ILE* 1.3 78.6 - - - +
31B LYS* 1.3 64.0 + - + +
33B ALA* 3.2 7.4 + - - +
34B ILE* 3.0 24.6 + - + +
65B VAL* 5.8 0.2 - - - -
68B SER* 2.7 38.6 + - - +
69B ILE* 4.0 11.0 + - - +
72B GLN* 3.4 39.3 - - + +
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Residues in contact with LYS 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 THR* 2.7 45.2 + - + +
28B GLN* 3.8 7.6 - - + +
30B THR* 1.3 74.7 - - + +
32B ALA* 1.3 62.2 + - - +
34B ILE* 3.5 6.4 + - - +
35B LYS* 3.1 49.4 + - - +
72B GLN* 6.2 0.4 - - - -
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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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3B ALA 4.4 2.3 - - - +
6B THR* 4.3 9.2 - - + +
7B PHE* 3.8 29.2 - - + +
10B GLU* 3.9 14.8 - - + -
28B GLN 3.1 16.6 + - - +
29B ILE 3.5 5.2 - - - +
30B THR 3.2 0.2 - - - -
31B LYS* 1.3 74.4 - - - +
33B ALA* 1.3 64.4 + - - +
35B LYS* 3.4 9.3 + - - +
36B ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 33 (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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7B PHE* 3.5 30.7 - - + -
29B ILE 2.9 9.1 + - - +
30B THR 3.2 7.8 + - - +
32B ALA* 1.3 76.4 - - - +
34B ILE* 1.3 60.4 + - - +
36B ALA* 3.1 22.0 + - - +
37B ILE 3.4 1.4 + - - -
43B VAL* 3.9 10.0 - - + +
69B ILE* 3.7 28.5 - - + -
84B PHE* 3.9 12.0 - - + -
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Residues in contact with ILE 34 (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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30B THR* 3.0 20.2 + - + +
31B LYS* 3.9 6.7 - - - +
33B ALA* 1.3 69.8 - - - +
35B LYS* 1.3 66.7 + - + +
36B ALA 3.1 1.8 - - - -
37B ILE* 3.1 25.9 + - - +
69B ILE* 4.4 7.6 - - + +
72B GLN* 3.9 19.3 - - + -
73B SER* 3.9 38.8 - - - +
76B GLN* 3.5 33.4 - - - +
77B PHE* 3.8 15.2 - - + -
84B PHE* 4.2 11.0 - - + -
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Residues in contact with LYS 35 (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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3B ALA* 4.2 11.4 - - + +
31B LYS* 3.1 42.1 + - - +
32B ALA* 3.8 8.5 - - - +
33B ALA 3.4 0.2 - - - -
34B ILE* 1.3 77.6 - - + +
36B ALA* 1.3 57.3 + - - +
37B ILE* 3.3 5.7 + - - +
38B LYS* 5.0 1.2 + - - +
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Residues in contact with ALA 36 (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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3B ALA* 3.7 33.9 - - + +
4B VAL* 4.2 6.3 - - + +
7B PHE* 4.6 0.9 - - + -
32B ALA 3.1 16.0 + - - +
33B ALA* 3.4 9.0 - - - +
34B ILE 3.1 0.8 - - - -
35B LYS* 1.3 76.4 - - - +
37B ILE* 1.3 56.2 + - - +
38B LYS* 3.2 4.5 - - - -
39B PHE* 2.8 31.9 + - - +
40B TYR 3.6 0.2 + - - -
43B VAL* 4.0 16.7 - - + +
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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