Contacts of the helix formed by residues 31 - 45 (chain B) in PDB entry 4DBW
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 ARG 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 5.9 0.2 - - - -
25B ALA* 3.5 17.0 + - - +
26B PRO 3.2 20.8 + - - -
27B PRO* 4.2 8.3 + - - +
29B VAL* 2.8 26.6 + - - +
30B PRO* 1.3 72.0 + - - +
32B SER* 1.3 63.4 + - - +
33B LYS 3.1 0.9 + - - -
34B ALA* 3.3 14.1 + - - +
55B TYR 3.4 23.8 + - - -
56B ASN* 3.5 35.4 + - - +
57B ASN* 4.6 6.6 - - - +
60B GLN* 3.2 37.2 - - - +
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Residues in contact with SER 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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30B PRO* 4.0 14.8 - - - +
31B ARG* 1.3 78.2 - - - +
33B LYS* 1.3 66.8 + - - +
34B ALA 3.3 0.2 - - - -
35B LEU* 3.2 19.4 + - - +
36B GLU* 3.3 11.7 + - - +
60B GLN* 4.6 6.5 - - - +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.6 19.1 - - + -
30B PRO* 2.9 38.7 + - + +
32B SER* 1.3 82.8 + - - +
34B ALA* 1.3 62.9 + - - +
36B GLU* 3.0 38.2 + - - +
37B VAL* 2.9 37.3 + - - +
272B TYR* 3.8 19.1 + - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 5.6 0.7 - - - -
30B PRO 4.4 0.4 + - - -
31B ARG* 3.3 14.0 + - - +
33B LYS* 1.3 77.9 - - - +
35B LEU* 1.3 62.7 + - - +
37B VAL* 3.9 3.4 - - - -
38B THR* 2.9 31.9 + - - +
57B ASN* 4.0 21.5 - - + +
60B GLN* 3.9 13.9 - - + +
61B VAL* 4.4 5.8 - - + -
272B TYR* 3.4 24.7 - - - +
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Residues in contact with LEU 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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32B SER* 3.2 13.1 + - - +
33B LYS 3.2 0.6 - - - -
34B ALA* 1.3 79.0 - - - +
36B GLU* 1.3 63.5 + - - +
39B LYS* 3.2 52.7 + - + +
60B GLN* 3.7 23.8 - - + +
63B LEU* 3.6 24.7 - - + +
64B ALA* 3.4 34.2 - - - +
67B SER* 5.2 1.1 - - - -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER 3.3 8.7 + - - +
33B LYS* 3.0 41.4 + - - +
35B LEU* 1.3 82.0 - - - +
37B VAL* 1.3 63.7 + - - +
39B LYS* 3.5 14.5 + - - +
40B LEU* 3.2 38.4 + - + +
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Residues in contact with VAL 37 (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 PHE* 3.9 8.7 - - + -
33B LYS* 2.9 35.0 + - - +
34B ALA* 3.7 5.2 - - - +
36B GLU* 1.3 77.7 - - + +
38B THR* 1.3 64.4 + - - +
40B LEU* 3.3 13.0 + - + +
41B ALA* 2.9 28.2 + - - +
272B TYR* 3.7 66.0 - - + +
274B GLU 5.8 0.2 - - - +
277B ILE* 3.8 15.6 - - + +
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Residues in contact with THR 38 (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 PHE* 3.7 19.7 - - + -
23B THR* 4.0 10.7 - - - +
34B ALA* 2.9 23.8 + - - -
37B VAL* 1.3 73.3 - - - +
39B LYS* 1.3 66.8 + - - +
41B ALA* 3.2 2.4 + - + +
42B ILE* 3.0 25.0 + - + +
49B ILE* 4.0 30.1 - - + -
61B VAL* 4.0 18.1 - - + +
64B ALA* 3.5 22.2 - - + -
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Residues in contact with LYS 39 (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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35B LEU* 3.2 44.8 + - + +
36B GLU* 3.6 11.2 - - - +
38B THR* 1.3 76.5 - - - +
40B LEU* 1.3 56.5 + - + +
42B ILE* 3.3 2.3 + - - +
43B GLU* 2.9 46.5 + - - +
64B ALA* 3.7 21.1 - - + +
67B SER* 3.5 26.4 + - - +
68B LYS* 4.3 12.1 - - + +
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Residues in contact with LEU 40 (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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36B GLU* 3.2 34.1 + - + +
37B VAL* 3.3 17.5 + - + +
39B LYS* 1.3 77.9 - - + +
41B ALA* 1.3 59.2 + - - +
43B GLU* 3.3 22.5 + - - +
44B ALA* 2.9 29.5 + - - +
274B GLU* 3.9 49.8 - - + +
277B ILE* 4.1 12.0 - - + +
278B ARG* 5.9 2.3 - - + +
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Residues in contact with ALA 41 (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 PHE* 3.7 36.1 - - + -
37B VAL 2.9 16.8 + - - +
38B THR* 3.6 6.1 - - + +
39B LYS 3.2 0.2 - - - -
40B LEU* 1.3 77.2 - - - +
42B ILE* 1.3 61.4 + - + +
44B ALA* 3.1 1.9 + - - +
45B GLY 3.1 6.6 + - - -
46B PHE* 3.0 39.5 + - + +
49B ILE* 6.2 0.7 - - + -
277B ILE* 3.7 12.1 - - + +
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Residues in contact with ILE 42 (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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38B THR* 3.0 18.8 + - + +
39B LYS 3.8 3.6 - - - +
41B ALA* 1.3 75.3 - - + +
43B GLU* 1.3 64.2 + - - +
45B GLY* 3.1 3.6 + - - -
46B PHE 3.5 12.1 - - - +
47B ARG* 2.9 36.3 + - - +
49B ILE* 3.7 31.2 - - + -
64B ALA 4.2 9.2 - - - +
65B ILE* 4.2 11.0 - - + -
68B LYS* 3.8 37.9 - - + -
73B SER* 5.5 0.4 - - - -
74B VAL* 4.3 14.1 - - + -
79B ILE* 4.0 13.7 - - + -
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Residues in contact with GLU 43 (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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39B LYS* 2.9 31.9 + - - +
40B LEU* 3.5 23.5 - - - +
41B ALA 3.2 0.2 - - - -
42B ILE* 1.3 77.4 - - - +
44B ALA* 1.3 60.9 + - - +
45B GLY 3.5 0.5 + - - -
68B LYS* 3.1 36.8 + - - +
278B ARG* 6.3 1.6 - - - +
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Residues in contact with ALA 44 (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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40B LEU 2.9 16.8 + - - +
41B ALA 3.1 5.6 + - - +
43B GLU* 1.3 76.7 - - - +
45B GLY* 1.3 58.0 + - - +
46B PHE 3.8 0.2 - - - -
277B ILE* 4.2 20.4 - - + +
278B ARG* 4.4 20.2 - - + +
281B VAL* 3.6 30.6 - - + +
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Residues in contact with GLY 45 (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 LEU* 6.0 0.6 - - - +
41B ALA 3.1 1.4 + - - -
42B ILE 3.1 4.8 + - - -
43B GLU 3.2 0.8 - - - -
44B ALA* 1.3 80.5 - - - +
46B PHE* 1.3 67.3 + - - +
47B ARG* 3.4 27.6 + - - +
281B VAL* 4.5 5.8 - - - -
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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