Contacts of the helix formed by residues 49 - 64 (chain T) in PDB entry 3H3P
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 49 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31M ASN* 4.6 8.5 + - - -
33M LYS* 2.9 30.8 + - - -
46T ASN* 2.7 30.5 + - - +
48T PHE* 1.3 82.7 - - - +
50T ILE* 1.3 63.2 + - - +
51T THR 3.3 2.5 - - - -
52T ALA* 3.2 25.5 + - + +
53T GLN* 3.6 12.6 + - + +
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Residues in contact with ILE 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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52I ILE* 3.6 21.5 - - + -
57I ILE* 4.2 24.7 - - + -
46T ASN 4.3 3.8 - - - +
47T TRP* 3.5 41.7 + - + +
48T PHE 3.5 1.6 - - - -
49T ASP* 1.3 79.3 - - - +
51T THR* 1.3 65.0 + - - +
53T GLN* 3.0 30.0 + - + +
54T LEU* 3.2 22.0 + - + +
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Residues in contact with THR 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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31I THR 3.4 25.2 - - - +
32I TYR* 3.8 2.2 - - - -
33I ALA* 3.6 14.4 - - + +
52I ILE* 4.0 24.9 - - + +
99I GLU* 2.5 36.0 + - - +
110I PRO* 3.7 9.6 - - - +
47T TRP 4.9 0.4 + - - -
48T PHE 4.2 8.8 + - - -
50T ILE* 1.3 78.5 - - - +
52T ALA* 1.3 58.2 + - - +
54T LEU* 3.3 7.7 + - + +
55T TRP* 2.9 29.5 + - - +
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Residues in contact with ALA 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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109I LYS* 4.9 18.3 - - - +
110I PRO* 3.9 15.3 - - + +
48T PHE 5.3 0.4 + - - +
49T ASP* 3.2 19.4 + - + +
50T ILE 3.1 0.4 - - - -
51T THR* 1.3 81.1 + - - +
53T GLN* 1.3 62.0 + - + +
55T TRP* 3.3 7.4 + - - +
56T GLU* 3.3 27.9 + - - +
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Residues in contact with GLN 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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49T ASP* 3.6 14.8 + - - +
50T ILE* 3.0 23.2 + - + +
52T ALA* 1.3 76.0 - - + +
54T LEU* 1.3 65.8 + - + +
56T GLU* 3.3 22.9 + - - +
57T PHE* 3.4 10.6 + - - +
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Residues in contact with LEU 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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31I THR* 4.3 25.5 - - + +
52I ILE* 4.2 25.1 - - + -
54I LEU* 4.1 32.5 - - + +
55I LEU* 6.4 1.8 - - + -
57I ILE* 5.6 2.0 - - + -
50T ILE* 3.2 17.3 + - + +
51T THR* 3.3 11.6 + - - +
53T GLN* 1.3 79.1 - - + +
55T TRP* 1.3 64.2 + - - +
57T PHE* 3.1 25.6 + - + +
58T SER* 3.0 16.1 + - - -
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Residues in contact with TRP 55 (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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31I THR* 5.7 2.2 + - - -
32I TYR* 4.0 11.2 - + + -
107I LEU 3.5 6.2 + - - -
108I GLY* 3.3 27.0 + - - -
109I LYS* 3.3 50.0 - - + -
110I PRO* 3.8 12.8 - - + -
51T THR 2.9 14.5 + - - +
52T ALA 3.4 9.6 - - - +
53T GLN 3.1 0.4 - - - -
54T LEU* 1.3 77.0 - - - +
56T GLU* 1.3 79.8 + - + +
58T SER* 2.8 29.5 + - - -
59T GLN* 2.9 52.1 + - + +
62T ARG* 4.5 1.5 - - - +
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Residues in contact with GLU 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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109I LYS* 5.6 5.0 - - - -
52T ALA* 3.3 14.4 + - - +
53T GLN* 3.3 16.6 + - - +
55T TRP* 1.3 95.4 - - + +
57T PHE* 1.3 57.3 + - - +
59T GLN* 3.6 10.5 + - + +
60T GLU* 3.1 26.5 + - - +
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Residues in contact with PHE 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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53T GLN 3.4 7.3 + - - +
54T LEU* 3.1 21.6 + - + +
56T GLU* 1.3 75.8 - - - +
58T SER* 1.3 66.9 + - - +
60T GLU* 3.3 23.7 + - + +
61T LEU* 3.1 48.3 + - + +
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Residues in contact with SER 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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31I THR* 5.2 10.9 + - - +
54T LEU 3.0 14.8 + - - -
55T TRP* 2.8 15.0 + - - -
57T PHE* 1.3 76.2 - - - +
59T GLN* 1.3 65.2 + - - +
61T LEU* 3.0 24.8 + - - +
62T ARG* 3.2 36.1 + - - -
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Residues in contact with GLN 59 (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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107I LEU 4.5 1.0 - - - +
55T TRP* 2.9 59.0 + - + +
56T GLU* 3.7 11.7 - - + +
58T SER* 1.3 75.4 - - - +
60T GLU* 1.3 57.0 + - - +
62T ARG* 3.1 37.2 + - - +
63T ASN* 2.9 42.4 + - + +
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Residues in contact with GLU 60 (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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56T GLU 3.1 18.0 + - - +
57T PHE* 3.5 26.0 - - + +
58T SER 3.1 0.4 - - - -
59T GLN* 1.3 74.6 - - - +
61T LEU* 1.3 55.7 - - + +
63T ASN* 4.9 2.9 - - - +
64T ARG* 2.8 43.1 + - + +
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Residues in contact with LEU 61 (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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57T PHE* 3.1 46.0 + - + +
58T SER* 3.0 15.1 + - - +
60T GLU* 1.3 78.1 - - + +
62T ARG* 1.3 70.7 + - + +
64T ARG* 3.4 13.5 + - - +
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Residues in contact with ARG 62 (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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107I LEU* 3.9 29.9 + - - +
55T TRP* 4.5 2.4 - - - +
58T SER* 3.2 30.9 + - - +
59T GLN* 3.1 34.0 + - - +
61T LEU* 1.3 83.6 - - + +
63T ASN* 1.3 64.3 + - - +
64T ARG 3.0 6.6 + - - -
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Residues in contact with ASN 63 (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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59T GLN* 2.9 29.6 + - + +
60T GLU* 4.9 2.4 - - - +
62T ARG* 1.3 74.9 - - + +
64T ARG* 1.3 57.9 + - - +
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Residues in contact with ARG 64 (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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60T GLU* 2.8 30.4 + - + +
61T LEU* 3.6 8.4 - - - +
62T ARG 3.1 9.8 - - - -
63T ASN* 1.3 81.0 - - - +
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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