Contacts of the helix formed by residues 42 - 58 (chain T) in PDB entry 4ADV
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 ASP 42 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37T ALA* 3.3 13.1 + - + +
38T ILE* 5.4 0.4 - - - +
40T ALA* 2.7 12.9 + - + +
41T GLY* 1.3 72.4 - - - +
43T LYS* 1.3 63.6 + - - +
44T ALA* 2.8 14.1 + - - +
45T ALA* 2.6 51.7 + - + +
46T ALA* 2.9 13.8 + - - +
85T LEU* 5.5 1.9 - - - +
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Residues in contact with LYS 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41T GLY 3.7 9.2 + - - -
42T ASP* 1.3 72.0 - - - +
44T ALA* 1.3 70.2 + - + +
46T ALA* 3.7 8.0 - - - +
47T GLN* 3.6 24.8 + - - +
85T LEU* 4.7 5.7 - - + +
86T ALA* 3.7 31.4 - - + +
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Residues in contact with ALA 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T ASP* 2.8 9.9 + - - +
43T LYS* 1.3 85.6 - - + +
45T ALA* 1.3 65.6 + - - +
46T ALA 3.3 0.2 + - - -
47T GLN* 4.2 2.9 - - - +
48T LYS* 3.0 26.8 + - - +
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Residues in contact with ALA 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T LYS 5.3 0.4 - - - +
37T ALA* 3.4 21.5 - - + -
42T ASP* 2.6 35.2 + - + +
44T ALA* 1.3 70.2 - - - +
46T ALA* 1.3 55.2 + - - +
48T LYS* 3.5 9.6 - - - +
49T ALA* 2.6 39.8 + - - +
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Residues in contact with ALA 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T VAL* 3.9 8.0 - - + +
37T ALA* 3.8 10.6 - - + +
38T ILE* 4.2 18.4 - - + +
42T ASP 2.9 15.4 + - - +
43T LYS* 3.7 9.2 - - - +
45T ALA* 1.3 77.4 - - - +
47T GLN* 1.3 66.7 + - + +
49T ALA* 2.8 3.8 + - - +
50T PHE* 2.8 22.6 + - - +
82T ILE* 4.1 22.4 - - + -
85T LEU* 5.1 3.8 - - + -
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Residues in contact with GLN 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T LYS 3.6 14.5 + - - +
44T ALA* 4.2 1.8 - - - +
45T ALA 3.5 0.2 - - - -
46T ALA* 1.3 80.4 - - + +
48T LYS* 1.3 65.2 + - - +
50T PHE* 2.9 22.5 + - - +
51T ASN* 2.8 28.8 + - - +
82T ILE* 3.4 37.0 - - + +
86T ALA* 6.4 1.3 - - + -
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Residues in contact with LYS 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ALA 3.0 22.7 + - - +
45T ALA* 3.5 9.4 - - - +
47T GLN* 1.3 76.0 - - - +
49T ALA* 1.3 50.7 + - - +
51T ASN* 2.6 20.1 - - - +
52T GLU* 2.8 51.4 - - - +
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Residues in contact with ALA 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T PHE 4.9 0.4 - - - +
33T LYS* 3.9 10.1 - - + +
34T VAL* 3.5 35.1 - - + +
45T ALA 2.6 22.0 + - - +
46T ALA 2.8 4.2 + - - +
48T LYS* 1.3 72.7 - - - +
50T PHE* 1.3 65.7 + - - +
52T GLU* 2.9 26.6 + - - +
53T MET* 2.9 18.9 + - - +
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Residues in contact with PHE 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A C 4.2 6.3 - - - -
34T VAL* 4.0 6.2 - - + +
46T ALA 2.8 14.8 + - - +
47T GLN* 3.4 19.1 - - - +
49T ALA* 1.3 72.5 - - - +
51T ASN* 1.3 58.2 + - + +
52T GLU 3.0 1.2 + - - -
53T MET* 3.0 21.2 + - + +
54T GLN* 2.7 68.2 + - + +
74T HIS 4.1 1.1 - - - -
75T LYS* 3.3 53.8 - - + -
78T LEU* 4.0 17.3 - - + -
79T THR* 3.6 13.9 - - - -
82T ILE* 5.7 6.7 - - + -
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Residues in contact with ASN 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A A 4.7 9.2 - - - +
193A C 5.7 2.2 - - - +
47T GLN* 2.8 26.2 + - - +
48T LYS* 2.6 33.9 - - - +
50T PHE* 1.3 79.6 - - + +
52T GLU* 1.3 56.9 + - - +
53T MET 3.3 0.4 - - - -
54T GLN* 4.0 15.7 - - - +
55T PRO* 2.9 22.6 - - - +
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Residues in contact with GLU 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T PHE* 3.1 38.3 - - + -
33T LYS* 3.2 34.6 + - - +
48T LYS* 2.8 49.2 + - - +
49T ALA* 3.0 21.2 - - - +
50T PHE 2.9 0.6 - - - -
51T ASN* 1.3 80.2 - - - +
53T MET* 1.3 56.3 + - - +
55T PRO* 3.9 3.6 - - - +
56T ILE* 3.1 11.6 - - - +
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Residues in contact with MET 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T PHE* 3.4 28.9 - - + +
31T ILE* 4.4 9.0 - - - +
34T VAL* 3.7 14.6 - - + -
49T ALA 2.9 14.8 + - - +
50T PHE* 3.3 39.0 - - + +
52T GLU* 1.3 77.8 - - - +
54T GLN* 1.3 56.5 + - + +
55T PRO* 3.2 2.7 - - - -
56T ILE* 2.7 13.5 + - + +
57T VAL* 2.6 64.2 + - + +
74T HIS* 4.2 11.0 - - + +
75T LYS* 5.4 2.0 - - + -
78T LEU* 3.7 27.4 - - + -
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Residues in contact with GLN 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A C 5.9 1.6 - - - -
192A A 3.3 35.2 + - - +
193A C 2.6 40.7 + - - -
50T PHE* 2.7 48.9 + - + +
51T ASN* 4.0 5.3 - - - +
53T MET* 1.3 81.5 - - + +
55T PRO* 1.3 59.8 - - + +
56T ILE 3.0 5.2 + - - -
57T VAL* 3.5 6.7 + - - -
58T ASP* 2.7 29.7 + - - +
75T LYS* 3.8 28.2 - - + +
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Residues in contact with PRO 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A C 3.4 37.7 - - - +
194A C 3.3 26.8 + - - +
51T ASN* 2.9 26.5 - - - +
52T GLU 4.1 9.9 - - - +
53T MET 3.3 2.0 - - - -
54T GLN* 1.3 94.5 - - + +
56T ILE* 1.3 62.6 + - + +
58T ASP 4.6 0.7 - - - -
59T ARG* 4.3 8.0 + - - -
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Residues in contact with ILE 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T MET* 4.1 29.6 - - + -
27T MET* 5.2 7.4 - - + -
30T PHE* 3.4 35.4 - - + -
52T GLU 3.1 26.0 - - - +
53T MET* 2.7 9.8 + - + +
55T PRO* 1.3 87.3 - - + +
57T VAL* 1.3 51.2 + - + +
58T ASP 2.7 7.8 + - - -
59T ARG* 2.9 15.5 + - + +
60T GLN* 2.5 42.9 + - - +
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Residues in contact with VAL 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T MET* 4.5 17.1 - - + +
31T ILE* 4.5 12.6 - - + -
53T MET* 2.6 52.5 + - + +
54T GLN* 3.5 6.3 + - - +
56T ILE* 1.3 66.4 - - + +
58T ASP* 1.3 60.0 + - - +
60T GLN* 2.8 20.6 + - - +
61T ALA* 2.8 15.4 - - - +
66T ILE* 5.1 1.3 - - + +
71T ALA* 4.0 17.1 - - + +
74T HIS* 3.5 31.4 - - + +
75T LYS* 5.6 3.4 - - + -
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Residues in contact with ASP 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A G 5.7 2.5 - - - -
193A C 3.1 17.3 + - - +
194A C 3.2 25.4 - - - +
54T GLN* 2.7 21.1 - - - +
56T ILE 2.7 2.4 + - - -
57T VAL* 1.3 83.5 - - - +
59T ARG* 1.3 68.1 + - - +
60T GLN* 3.4 1.6 - - - -
61T ALA* 3.2 4.9 + - - +
62T ALA* 2.9 22.7 + - - +
71T ALA* 4.7 6.9 - - - +
75T LYS* 3.0 35.9 + - - -
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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
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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) + - + + + + + -
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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