Contacts of the helix formed by residues 24 - 38 (chain B) in PDB entry 4DWN
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 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 5.8 2.5 - - - -
21B GLY 5.0 0.6 + - - -
23B LEU* 1.3 76.9 - - - +
25B GLU* 1.3 65.5 + - - +
26B GLN* 3.5 9.6 + - - +
27B GLN* 2.9 38.0 + - - +
28B VAL* 2.9 22.0 + - - +
58B LEU* 3.6 2.9 - - - -
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Residues in contact with GLU 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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11A VAL* 5.4 2.5 - - + +
15A PRO* 6.0 6.1 - - + -
24B SER* 1.3 73.6 - - - +
26B GLN* 1.3 65.9 + - - +
28B VAL 3.2 0.7 + - - -
29B ASP* 2.5 61.4 + - - +
52B ARG 4.5 2.9 - - - +
54B PRO* 6.1 1.6 - - - -
58B LEU* 3.3 26.4 - - + +
61B ARG* 2.8 41.6 + - - -
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Residues in contact with GLN 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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24B SER* 3.3 9.1 + - - +
25B GLU* 1.3 80.1 - - - +
27B GLN* 1.3 62.5 + - - +
29B ASP* 3.4 18.4 + - - +
30B ARG* 3.0 65.1 + - - +
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Residues in contact with GLN 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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22B ARG 3.9 4.5 + - - +
23B LEU* 3.5 18.6 - - + +
24B SER* 2.9 40.7 + - - +
26B GLN* 1.3 79.1 - - - +
28B VAL* 1.3 58.0 + - - +
30B ARG* 3.4 12.2 + - - +
31B ILE* 3.0 35.7 + - + +
87B HIS* 3.3 22.0 + - - +
88B ALA* 3.5 27.0 - - + +
90B PRO* 5.2 5.9 - - - +
91B LEU* 6.0 0.8 - - - +
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Residues in contact with VAL 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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23B LEU* 3.9 24.5 - - + -
24B SER 2.9 17.4 + - - +
25B GLU 3.9 1.1 - - - +
27B GLN* 1.3 75.6 - - - +
29B ASP* 1.3 64.8 + - - +
31B ILE* 3.3 9.2 + - + +
32B ILE* 3.0 40.6 + - + +
51B PHE 4.8 4.7 - - - +
58B LEU* 3.7 33.0 - - + -
61B ARG* 4.9 0.9 - - - +
62B LEU* 4.2 31.4 - - + +
65B LEU* 4.7 6.3 - - + -
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Residues in contact with ASP 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 GLU* 2.5 56.3 + - - +
26B GLN* 3.7 21.0 + - - +
28B VAL* 1.3 78.9 - - - +
30B ARG* 1.3 57.2 + - + +
32B ILE* 3.3 4.6 + - - +
33B LEU* 3.0 19.2 + - + +
52B ARG* 2.9 56.6 + - - +
61B ARG* 4.3 1.4 + - - -
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Residues in contact with ARG 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 GLN* 3.0 54.3 + - - +
27B GLN* 3.9 9.7 - - - +
29B ASP* 1.3 72.9 - - - +
31B ILE* 1.3 61.1 + - - +
33B LEU* 3.4 12.5 + - + +
34B GLN* 2.9 29.8 + - - +
87B HIS* 3.5 44.5 + - + +
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Residues in contact with ILE 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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23B LEU* 4.3 14.8 - - + -
27B GLN 3.0 25.5 + - - +
28B VAL* 3.5 8.1 - - + +
30B ARG* 1.3 73.4 - - - +
32B ILE* 1.3 65.5 + - - +
34B GLN* 3.3 3.6 + - - +
35B LEU* 3.1 33.5 + - + +
62B LEU* 6.4 0.7 - - + -
65B LEU* 4.7 7.4 - - + -
80B PHE* 4.0 25.1 - - + -
83B ALA* 3.8 34.5 - - + +
84B LEU* 3.8 31.2 - - + -
87B HIS* 4.2 7.2 - - + -
88B ALA* 5.0 1.6 - - + -
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Residues in contact with ILE 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 VAL* 3.0 34.1 + - + +
29B ASP* 3.5 6.3 - - - +
31B ILE* 1.3 74.8 - - - +
33B LEU* 1.3 64.4 + - + +
35B LEU* 3.1 5.5 + - - +
36B ASN* 3.0 21.0 + - - +
43B LEU* 3.9 13.7 - - + +
48B ALA* 3.5 38.4 - - + +
51B PHE* 3.3 40.6 - - + +
52B ARG* 3.9 18.6 - - + +
65B LEU* 4.1 19.3 - - + -
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Residues in contact with LEU 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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29B ASP 3.0 9.6 + - - +
30B ARG* 3.6 15.5 - - + +
31B ILE 3.3 0.2 - - - -
32B ILE* 1.3 74.5 - - + +
34B GLN* 1.3 65.7 + - - +
36B ASN* 3.1 8.9 + - + +
37B ARG* 2.9 53.0 + - + +
38B TYR* 5.1 0.7 - - - -
48B ALA* 5.9 1.8 - - + -
52B ARG* 3.4 39.5 - - - +
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Residues in contact with GLN 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 ARG 2.9 17.2 + - - +
31B ILE 3.5 6.1 - - - +
33B LEU* 1.3 77.3 - - - +
35B LEU* 1.3 60.4 + - + +
36B ASN 3.4 0.2 + - - -
37B ARG 3.9 0.9 + - - -
38B TYR* 3.5 51.6 + - - +
40B PRO 5.3 1.6 - - - +
79B GLU 5.8 0.2 - - - +
82B ARG* 4.1 18.9 - - + +
83B ALA* 3.9 26.2 - - + +
86B ILE* 3.9 21.6 - - + +
87B HIS* 3.0 23.1 + - - +
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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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31B ILE* 3.1 30.0 + - + +
32B ILE* 3.1 8.5 + - - +
34B GLN* 1.3 76.9 - - + +
36B ASN* 1.3 59.0 + - - +
38B TYR 5.2 0.4 - - - -
40B PRO 5.2 1.6 - - - -
41B GLN* 3.8 0.8 - - - -
42B ILE* 2.8 42.5 + - + -
43B LEU* 3.0 29.2 + - + -
65B LEU* 4.6 3.6 - - + -
69B LEU* 4.4 26.9 - - + -
76B ASP 5.1 0.2 - - - +
79B GLU* 3.8 42.2 - - + +
80B PHE* 4.0 4.9 - - + +
83B ALA* 4.4 6.5 - - + -
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Residues in contact with ASN 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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32B ILE 3.0 14.4 + - - +
33B LEU* 3.9 9.3 - - + +
35B LEU* 1.3 80.5 - - - +
37B ARG* 1.3 77.0 + - - +
38B TYR 3.5 1.8 - - - -
41B GLN* 3.1 27.4 + - - +
43B LEU* 2.9 26.4 + - + +
44B THR 3.2 2.4 + - - -
45B ASN* 2.9 41.0 + - - +
48B ALA* 4.1 17.6 - - + +
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Residues in contact with ARG 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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33B LEU* 2.9 39.0 + - + +
34B GLN 3.9 0.6 + - - -
35B LEU 3.7 0.2 - - - -
36B ASN* 1.3 94.2 - - - +
38B TYR* 1.3 84.3 + - + +
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Residues in contact with TYR 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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33B LEU 4.5 0.7 - - - -
34B GLN* 3.5 55.0 + - - +
36B ASN 3.5 0.4 - - - -
37B ARG* 1.3 103.7 + - + +
39B TYR* 1.3 65.8 + - - +
40B PRO 3.6 4.5 + - - +
41B GLN* 3.2 26.5 + - - +
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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