Contacts of the helix formed by residues 38 - 51 (chain B) in PDB entry 4EEW
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 ASN 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLN 3.5 2.7 + - - +
37B MET* 1.3 77.9 - - - +
39B VAL* 1.3 60.0 + - - +
40B LYS* 3.3 7.0 + - - +
41B GLU* 2.8 53.0 + - - +
42B PHE* 3.0 25.5 + - - +
68B ASP 3.7 12.2 + - - +
69B ASP* 4.4 10.0 + - - +
70B LYS 3.3 19.7 - - - +
71B LYS* 3.9 4.9 - - + +
72B LEU* 4.5 2.5 - - - -
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Residues in contact with VAL 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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38B ASN* 1.3 74.0 - - - +
40B LYS* 1.3 63.5 + - - +
42B PHE* 3.2 7.6 + - - +
43B LYS* 2.9 37.3 + - - +
59B LEU* 4.3 6.7 - - + +
66B LEU* 3.9 28.3 - - + +
67B GLN 3.2 29.8 - - - +
68B ASP* 3.6 14.6 + - - +
70B LYS 2.9 15.2 + - - +
72B LEU* 4.1 17.7 - - + +
75B TYR* 4.0 11.9 - - + -
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Residues in contact with LYS 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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38B ASN* 3.3 7.8 + - - +
39B VAL* 1.3 74.9 - - - +
41B GLU* 1.3 63.3 + - + +
43B LYS* 3.3 8.4 + - + +
44B GLU* 2.9 57.2 + - + +
54B SER* 5.0 0.4 - - - -
68B ASP* 3.1 43.2 + - + +
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Residues in contact with GLU 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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36B GLN 4.8 0.7 - - - +
37B MET* 3.6 23.6 - - + +
38B ASN* 2.8 45.8 + - - +
40B LYS* 1.3 78.6 - - + +
42B PHE* 1.3 57.6 + - - +
44B GLU* 3.2 18.2 + - - +
45B HIS* 2.8 27.0 + - - +
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Residues in contact with PHE 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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19B VAL* 3.6 36.8 - - + -
21B VAL* 3.7 24.0 - - + -
31B PHE* 4.1 7.4 - + + -
33B VAL* 3.9 27.6 - - + -
37B MET* 3.6 6.0 - - - -
38B ASN 3.0 16.7 + - - +
39B VAL 3.2 4.9 + - - +
41B GLU* 1.3 74.1 - - - +
43B LYS* 1.3 64.9 + - - +
45B HIS* 3.1 3.8 + - + +
46B ILE* 3.0 51.4 + - + +
59B LEU* 3.9 22.7 - - + -
72B LEU* 3.7 30.5 - - + -
82B ILE* 4.6 4.3 - - + -
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Residues in contact with LYS 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 VAL* 2.9 27.9 + - - +
40B LYS* 3.5 9.6 - - + +
42B PHE* 1.3 75.3 - - - +
44B GLU* 1.3 61.9 + - - +
46B ILE* 3.4 1.7 + - - -
47B ALA* 3.1 12.6 + - - +
54B SER* 3.8 25.3 + - - +
57B GLN* 3.0 69.6 + - + +
58B ARG* 4.8 2.0 - - - +
59B LEU* 3.8 21.3 - - + +
66B LEU 4.4 7.7 + - - -
68B ASP* 2.7 32.7 + - - +
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Residues in contact with GLU 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 LYS* 2.9 44.5 + - + +
41B GLU* 3.5 24.5 - - - +
42B PHE 3.2 0.2 - - - -
43B LYS* 1.3 75.8 - - - +
45B HIS* 1.3 63.0 + - - +
46B ILE 3.5 0.3 + - - -
47B ALA* 3.6 11.6 + - - +
48B ALA 4.9 1.0 + - - -
54B SER* 3.8 24.0 + - - +
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Residues in contact with HIS 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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31B PHE* 3.8 27.7 - + + +
32B ILE 4.3 10.0 + - - -
33B VAL* 3.6 30.9 - - + +
37B MET* 4.4 12.2 - - + +
41B GLU 2.8 14.1 + - - +
42B PHE* 3.1 13.0 + - - +
44B GLU* 1.3 78.9 - - - +
46B ILE* 1.3 62.9 + - + +
47B ALA 3.7 0.3 + - - -
48B ALA* 4.8 3.5 + - - +
49B SER* 4.9 4.7 + - - -
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Residues in contact with ILE 46 (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 VAL* 4.2 13.2 - - + -
31B PHE* 3.6 41.3 - - + -
42B PHE* 3.0 52.6 + - + +
43B LYS 3.6 6.1 - - - +
45B HIS* 1.3 77.0 - - + +
47B ALA* 1.3 66.7 + - - +
48B ALA 3.3 2.0 - - - -
49B SER* 3.1 6.5 + - - -
50B VAL* 3.0 24.6 + - + +
57B GLN* 3.4 24.0 - - - +
59B LEU* 4.4 4.7 - - + -
84B LEU* 4.1 16.6 - - + -
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Residues in contact with ALA 47 (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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43B LYS 3.1 16.8 + - - +
44B GLU* 3.6 10.7 + - - +
45B HIS 3.4 1.8 - - - -
46B ILE* 1.3 75.8 - - - +
48B ALA* 1.3 57.8 + - - +
50B VAL* 4.1 0.7 - - - -
51B SER* 2.9 26.5 + - - -
52B ILE 3.4 30.4 + - - +
53B PRO* 4.5 2.2 - - + -
54B SER* 4.0 11.2 - - - +
57B GLN* 3.5 5.2 - - - +
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Residues in contact with ALA 48 (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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44B GLU 4.9 1.0 + - - -
45B HIS 4.8 3.7 + - - +
46B ILE 3.3 0.6 - - - -
47B ALA* 1.3 80.0 - - - +
49B SER* 1.3 64.7 + - - +
51B SER* 3.5 13.8 + - - +
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Residues in contact with SER 49 (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 ARG* 3.2 30.8 + - - -
31B PHE* 3.8 30.0 - - - -
45B HIS 4.9 3.2 + - - -
46B ILE 3.1 9.9 + - - -
48B ALA* 1.3 80.3 - - - +
50B VAL* 1.3 59.5 + - - +
51B SER* 4.4 3.1 + - - -
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Residues in contact with VAL 50 (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 VAL* 4.7 6.7 - - + +
23B THR* 4.6 7.9 - - + +
29B ARG* 3.9 30.0 + - + +
31B PHE* 4.3 12.8 - - + -
46B ILE* 3.0 28.4 + - + +
47B ALA* 3.8 5.2 - - - +
49B SER* 1.3 77.3 - - - +
51B SER* 1.3 70.9 + - - +
52B ILE* 3.3 22.1 + - + +
57B GLN* 4.1 4.3 - - - +
84B LEU* 3.6 33.0 - - + -
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Residues in contact with SER 51 (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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47B ALA 2.9 11.0 + - - -
48B ALA* 3.5 9.9 + - - +
49B SER 3.4 3.8 + - - -
50B VAL* 1.3 80.5 - - - +
52B ILE* 1.3 62.7 + - - +
53B PRO* 4.3 4.1 - - - +
86B GLU* 4.6 3.8 - - - +
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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