Contacts of the helix formed by residues 44 - 51 (chain P) in PDB entry 1DFU
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 HIS 44 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24P ASN* 3.2 29.0 + - - +
25P LYS 4.3 2.2 + - - +
26P PHE* 3.6 21.1 - - + +
42P LEU 3.4 4.0 + - - -
43P ASP* 1.3 73.6 + - - +
45P ASP* 1.3 84.7 + - - +
47P VAL* 3.3 1.7 + - - +
48P MET* 2.8 50.1 + - + +
84P PRO 4.3 1.8 + - - -
85P LYS* 3.4 35.5 + - + +
86P LEU* 2.9 47.0 + - + +
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Residues in contact with ASP 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P ASN* 4.7 8.4 + - - +
43P ASP* 3.3 6.9 + - - +
44P HIS* 1.3 96.0 - - - +
46P LYS* 1.3 65.3 + - + +
48P MET* 3.3 4.0 + - - +
49P ASN* 3.0 35.5 + - - +
85P LYS* 4.9 2.1 + - - -
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Residues in contact with LYS 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P ASP* 3.1 40.8 + - + +
45P ASP* 1.3 76.5 - - + +
47P VAL* 1.3 64.2 + - + +
49P ASN* 3.3 8.6 + - - +
50P MET* 3.1 38.0 + - + +
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Residues in contact with VAL 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P ILE* 4.2 18.2 - - + -
5P ASN 5.9 0.2 - - - +
26P PHE* 4.0 20.4 - - + -
42P LEU* 4.0 25.8 - - + -
43P ASP* 3.3 18.1 + - + +
44P HIS 3.3 3.4 + - - +
46P LYS* 1.3 73.2 - - + +
48P MET* 1.3 60.3 + - - +
50P MET* 3.1 14.0 + - + +
51P GLN* 2.8 29.3 + - + +
56P PHE* 4.2 17.7 - - + -
86P LEU* 4.0 3.8 - - + -
89P ILE* 4.0 16.6 - - + -
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Residues in contact with MET 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P HIS* 2.8 32.2 + - + +
45P ASP* 3.6 6.5 - - - +
47P VAL* 1.3 77.4 - - - +
49P ASN* 1.3 66.0 + - - +
51P GLN* 3.0 52.1 + - - -
52P ALA* 3.3 7.4 + - - +
84P PRO* 3.1 31.6 - - + +
85P LYS* 3.3 25.4 - - - -
86P LEU* 3.7 16.7 - - + +
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Residues in contact with ASN 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P ASP* 3.0 28.5 + - - +
46P LYS* 3.7 8.1 - - - +
48P MET* 1.3 80.0 - - - +
50P MET* 1.3 66.1 + - + +
52P ALA* 3.1 21.8 - - - +
53P LYS* 4.2 6.9 + - - +
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Residues in contact with MET 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P PHE* 3.6 37.7 - - + -
3P THR 3.9 20.6 - - - +
4P ILE* 3.8 31.0 - - + -
5P ASN 5.6 0.7 - - - +
46P LYS* 3.1 37.2 + - + +
47P VAL* 3.1 17.9 + - + +
49P ASN* 1.3 78.2 - - - +
51P GLN* 1.3 57.8 + - - +
52P ALA 3.0 4.7 + - - -
53P LYS* 3.2 16.8 + - - +
56P PHE* 3.8 12.2 - - + +
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Residues in contact with GLN 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P VAL* 2.8 23.2 + - + +
48P MET* 3.0 42.0 + - - +
50P MET* 1.3 68.2 - - - +
52P ALA* 1.3 69.0 + - - +
53P LYS 3.1 6.1 + - - +
56P PHE* 3.4 37.0 - - + -
57P TYR* 2.9 35.0 + - - +
79P ARG* 3.2 19.7 + - - +
86P LEU* 3.8 16.7 - - + +
89P ILE* 5.9 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