Contacts of the helix formed by residues 49 - 59 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31L ASN* 5.1 9.5 + - - -
33L LYS* 3.3 26.3 + - - -
46S ASN* 2.7 33.3 + - - +
48S PHE* 1.3 76.5 - - - +
50S ILE* 1.3 67.7 + - - +
51S THR 3.3 2.2 - - - -
52S ALA* 3.0 25.4 + - + +
53S GLN* 3.5 13.9 + - + +
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Residues in contact with ILE 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H ILE* 3.4 17.9 - - + -
57H ILE* 4.2 28.0 - - + -
46S ASN 4.5 2.7 - - - +
47S TRP* 3.3 43.8 + - + +
49S ASP* 1.3 77.9 - - - +
51S THR* 1.3 63.9 + - - +
53S GLN* 3.2 24.2 + - - +
54S LEU* 3.1 27.4 + - + +
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Residues in contact with THR 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H THR 3.2 28.9 - - - +
33H ALA* 3.8 13.0 - - + +
52H ILE* 4.1 24.0 - - + -
99H GLU* 2.8 38.2 + - - +
110H PRO* 3.6 9.8 - - - +
47S TRP 4.8 1.2 + - - +
48S PHE 4.3 4.9 + - - -
50S ILE* 1.3 73.6 - - - +
52S ALA* 1.3 61.2 + - - +
54S LEU* 3.1 10.5 + - + +
55S TRP* 2.8 29.8 + - - +
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Residues in contact with ALA 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H LYS* 4.5 21.8 - - - +
110H PRO* 3.8 14.9 - - + +
48S PHE 5.2 1.1 + - - +
49S ASP* 3.0 20.5 + - + +
51S THR* 1.3 78.9 + - - +
53S GLN* 1.3 58.3 + - + +
55S TRP* 3.2 5.9 + - - +
56S GLU* 3.0 32.2 + - - +
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Residues in contact with GLN 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S ASP* 3.8 14.1 + - + +
50S ILE* 3.2 28.1 + - + +
51S THR 3.1 0.6 - - - -
52S ALA* 1.3 73.9 - - + +
54S LEU* 1.3 66.6 + - + +
55S TRP 3.1 1.1 - - - -
56S GLU* 3.3 8.1 + - - +
57S PHE* 3.0 25.2 + - - +
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Residues in contact with LEU 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H THR* 4.0 35.0 - - + +
52H ILE* 4.2 21.5 - - + -
54H LEU* 4.0 25.8 - - + +
55H LEU* 6.5 0.7 - - + -
57H ILE* 5.7 3.1 - - + -
50S ILE* 3.1 17.6 + - + +
51S THR* 3.1 17.1 + - + +
53S GLN* 1.3 79.2 - - - +
55S TRP* 1.3 59.5 + - - +
57S PHE* 3.5 17.4 - - + +
58S SER* 2.8 24.8 + - - -
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Residues in contact with TRP 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TYR* 4.4 5.4 - + - -
107H LEU 3.4 24.0 + - - -
108H GLY* 4.0 4.9 - - - -
109H LYS* 3.4 48.2 - - + +
110H PRO* 3.8 15.0 - - + -
51S THR 2.8 12.6 + - - +
52S ALA* 3.4 7.9 - - - +
53S GLN 3.1 0.2 - - - -
54S LEU* 1.3 73.4 - - - +
56S GLU* 1.3 94.4 + - + +
57S PHE 2.9 4.0 - - - -
58S SER* 2.9 21.9 + - - -
59S GLN* 3.2 52.4 + - + +
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Residues in contact with GLU 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H LYS* 5.5 7.2 - - - -
52S ALA 3.0 19.2 + - - +
53S GLN* 3.8 7.6 - - - +
55S TRP* 1.3 98.4 - - + +
57S PHE* 1.3 61.7 + - - +
59S GLN* 3.6 14.2 + - - +
60S GLU* 3.8 7.8 + - - +
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Residues in contact with PHE 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S GLN 3.0 15.6 + - - +
54S LEU* 3.5 20.6 - - + +
55S TRP 2.9 0.6 + - - -
56S GLU* 1.3 74.1 - - - +
58S SER* 1.3 60.1 + - - +
60S GLU* 2.7 40.9 + - + +
61S LEU* 3.1 26.0 + - + -
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Residues in contact with SER 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H THR* 6.1 1.2 - - - +
54S LEU 2.8 16.1 + - - -
55S TRP* 2.9 11.4 + - - -
57S PHE* 1.3 77.6 - - - +
59S GLN* 1.3 62.4 + - - +
60S GLU 2.7 14.9 + - - -
61S LEU* 2.8 31.4 + - - +
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Residues in contact with GLN 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H LEU 5.4 1.2 + - - -
55S TRP* 3.2 65.1 + - + +
56S GLU* 3.8 12.1 - - - +
57S PHE 3.2 0.2 - - - -
58S SER* 1.3 79.5 - - - +
60S GLU* 1.3 58.2 + - - +
61S LEU 5.2 0.2 - - - -
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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