Contacts of the helix formed by residues 42 - 53 (chain H) in PDB entry 3TGX
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 CYS 42 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H VAL* 4.1 5.6 - - + -
39H GLU* 2.7 57.2 + - - +
41H ASN* 1.3 78.8 - - - +
43H GLU* 1.3 58.4 + - - +
44H TRP 3.3 2.2 - - - -
45H SER* 3.2 14.6 + - - -
46H ALA* 2.8 29.8 + - - +
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Residues in contact with GLU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H VAL* 3.5 24.7 - - + +
39H GLU 3.8 1.1 - - - +
40H THR* 3.2 41.4 + - - +
41H ASN 3.4 2.4 - - - -
42H CYS* 1.3 78.9 - - - +
44H TRP* 1.3 58.4 + - + +
46H ALA* 3.7 2.7 - - - +
47H PHE* 2.7 34.3 + - - +
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Residues in contact with TRP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H HIS* 3.1 39.0 - + - -
10H MET* 4.8 12.1 - - + -
41H ASN 5.0 3.2 + - - +
42H CYS 3.3 0.4 - - - -
43H GLU* 1.3 82.3 - - + +
45H SER* 1.3 65.2 + - - +
47H PHE* 3.7 37.1 - + + +
48H SER* 3.1 23.4 + - - -
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H ASN 5.4 0.6 + - - -
42H CYS* 3.2 21.1 + - - -
44H TRP* 1.3 78.5 - - - +
46H ALA* 1.3 63.2 + - - +
48H SER* 3.3 8.7 + - - -
49H CYS* 3.2 25.1 + - - -
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H PRO* 3.8 27.7 - - + +
38H VAL* 3.8 18.4 - - + -
42H CYS 2.8 19.7 + - - +
43H GLU* 3.7 5.6 - - - +
45H SER* 1.3 71.7 - - - +
47H PHE* 1.3 65.3 + - - +
49H CYS* 2.9 17.7 + - - +
50H PHE* 3.2 20.0 + - + -
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Residues in contact with PHE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H MET* 4.6 20.0 - - + -
13H LEU* 3.7 30.1 - - + -
43H GLU 2.7 22.6 + - - +
44H TRP* 3.7 38.1 - + + +
45H SER 3.3 0.2 - - - -
46H ALA* 1.3 72.4 - - - +
48H SER* 1.3 64.3 + - - +
50H PHE* 3.3 16.3 + + + +
51H GLN* 3.2 59.8 + - + +
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Residues in contact with SER 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H TRP 3.1 17.6 + - - -
45H SER* 3.5 8.1 - - - -
46H ALA 3.1 0.2 - - - -
47H PHE* 1.3 78.2 - - - +
49H CYS* 1.3 58.1 + - - +
51H GLN* 3.6 16.0 + - - +
52H LYS* 3.0 54.4 + - - +
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Residues in contact with CYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H PRO* 4.7 17.2 - - + +
35H PRO* 4.0 17.7 - - + -
45H SER* 3.2 17.4 + - - -
46H ALA* 2.9 13.0 + - - +
48H SER* 1.3 76.7 - - - +
50H PHE* 1.3 65.4 + - - +
52H LYS* 3.5 3.1 + - - +
53H ALA* 3.0 24.4 + - - +
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Residues in contact with PHE 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H PRO 4.6 4.0 - - - -
34H ALA* 3.9 14.6 - - + -
35H PRO* 3.2 52.3 - - + -
46H ALA* 3.2 23.9 + - + -
47H PHE* 3.3 13.7 + + + +
49H CYS* 1.3 78.0 - - - +
51H GLN* 1.3 64.3 + - + +
53H ALA* 3.4 17.6 - - + +
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Residues in contact with GLN 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ARG* 5.9 3.0 - - - +
13H LEU* 5.5 2.6 - - - +
47H PHE* 3.2 53.4 + - + +
48H SER* 3.6 15.9 + - - +
50H PHE* 1.3 80.0 - - + +
52H LYS* 1.3 64.3 + - + +
53H ALA 3.1 6.6 + - - +
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Residues in contact with LYS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H SER* 3.0 34.9 + - - +
49H CYS* 3.9 3.4 - - - +
51H GLN* 1.3 74.6 - - + +
53H ALA* 1.3 66.2 + - - +
54H GLN 3.6 1.2 + - - -
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 4.5 24.9 - - + -
33H PRO* 4.6 15.7 - - + +
49H CYS 3.0 17.6 + - - +
50H PHE* 3.4 15.1 - - + +
51H GLN 3.1 7.2 - - - +
52H LYS* 1.3 81.5 - - - +
54H GLN 1.3 50.3 + - - +
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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