Contacts of the helix formed by residues 55 - 67 (chain I) in PDB entry 5DPW
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 THR 55 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I GLU 3.8 8.5 - - - +
54I LEU* 1.3 80.2 - - - +
56I MET* 1.3 54.7 + - - +
57I THR* 3.8 4.9 + - - -
58I GLN* 2.7 45.3 + - - +
59I PHE* 2.7 35.0 + - - +
87I MET 4.1 7.2 - - - -
88I SER* 3.7 17.9 - - - +
89I ALA 3.1 12.1 - - - +
90I THR* 4.3 5.8 - - + -
91I MET* 4.1 3.6 - - - -
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Residues in contact with MET 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I THR* 1.3 74.1 - - - +
57I THR* 1.3 58.2 + - - +
59I PHE* 3.1 11.0 + - - +
60I LEU* 2.8 29.3 + - - +
77I LEU* 4.2 26.3 - - + +
79I VAL* 3.9 14.8 - - + -
85I VAL* 3.7 18.2 - - + -
86I SER 3.7 14.8 - - - +
87I MET* 3.7 38.3 - - + +
89I ALA 3.1 8.7 + - - +
91I MET* 3.6 27.8 - - - +
94I ILE* 3.8 22.2 - - + -
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Residues in contact with THR 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I THR* 3.8 6.7 + - - -
56I MET* 1.3 76.4 - - - +
58I GLN* 1.3 61.2 + - - +
60I LEU* 3.4 19.4 - - + +
61I SER* 3.4 10.0 + - - -
87I MET* 2.3 53.5 + - + -
88I SER* 4.4 2.4 - - - -
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Residues in contact with GLN 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I GLU 4.4 3.4 + - - +
54I LEU* 4.0 25.2 - - + +
55I THR* 2.7 52.4 + - - +
57I THR* 1.3 77.2 - - - +
59I PHE* 1.3 60.1 + - - +
61I SER* 3.8 6.0 + - - -
62I ILE* 3.1 31.4 + - - +
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Residues in contact with PHE 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I VAL* 3.7 24.7 - - + -
31I VAL* 4.0 5.8 - - + -
48I PHE* 4.0 33.0 - + + -
50I VAL* 4.0 14.1 - - + -
54I LEU* 4.2 17.7 - - + +
55I THR 2.7 16.3 + - - +
56I MET* 3.1 13.4 + - - +
58I GLN* 1.3 73.8 - - - +
60I LEU* 1.3 59.2 + - - +
62I ILE* 3.1 15.2 + - + -
63I ILE* 2.8 63.5 + - + +
77I LEU* 4.0 13.2 - - + -
91I MET* 4.5 17.0 - - + -
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I MET 2.8 12.9 + - - +
57I THR* 3.4 17.0 - - + +
59I PHE* 1.3 77.4 - - - +
61I SER* 1.3 57.5 + - - +
63I ILE* 3.3 4.8 + - - +
64I ARG* 2.8 62.9 + - + +
75I PHE* 3.5 38.3 - - + +
76I TYR* 5.0 0.4 - - - -
77I LEU* 3.8 28.0 - - + +
87I MET* 5.1 10.8 - - + -
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Residues in contact with SER 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I THR 3.4 9.1 + - - -
58I GLN* 4.1 8.7 - - - -
59I PHE 3.3 0.4 - - - -
60I LEU* 1.3 78.6 - - - +
62I ILE* 1.3 59.0 + - - +
64I ARG* 3.2 15.7 - - - +
65I SER* 2.8 28.6 + - - -
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Residues in contact with ILE 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I PHE* 5.4 6.7 - - + -
54I LEU* 3.7 34.5 - - + -
58I GLN* 3.1 19.9 + - + +
59I PHE* 3.1 19.0 + - + +
61I SER* 1.3 76.1 - - - +
63I ILE* 1.3 66.2 + - - +
65I SER* 2.3 31.9 + - - +
66I ARG* 3.4 12.8 + - + +
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Residues in contact with ILE 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I VAL* 3.8 20.6 - - + -
43I LEU* 4.0 18.6 - - + +
48I PHE* 4.3 13.9 - - + -
59I PHE* 2.8 55.5 + - + +
60I LEU* 3.8 3.8 - - - +
62I ILE* 1.3 76.3 - - - +
64I ARG* 1.3 62.8 + - - +
66I ARG* 3.3 21.7 + - - +
67I MET* 3.7 12.1 - - - +
75I PHE* 3.6 22.7 - - + -
77I LEU* 3.8 20.4 - - + -
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Residues in contact with ARG 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I LEU* 2.8 34.0 + - + +
61I SER* 3.2 18.2 - - - +
63I ILE* 1.3 73.3 - - - +
65I SER* 1.3 59.2 + - - +
66I ARG 2.9 10.6 + - - -
67I MET* 3.0 24.4 + - - +
69I LEU* 3.6 15.2 - - + +
70I ARG 4.8 1.2 + - - -
71I ALA* 5.0 4.0 + - - +
73I GLU 2.5 30.5 + - - -
74I ALA* 3.5 23.8 - - - +
75I PHE* 3.5 33.4 + - + +
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Residues in contact with SER 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I SER 2.8 16.1 + - - -
62I ILE* 2.3 33.4 + - - +
64I ARG* 1.3 72.1 - - - +
66I ARG* 1.3 62.7 + - - +
67I MET 3.7 3.0 + - - +
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Residues in contact with ARG 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LEU* 3.7 18.1 - - + +
44I ASP* 3.6 34.4 + - - +
45I LYS* 4.0 24.9 - - - +
48I PHE* 4.6 20.2 - - + -
62I ILE* 3.4 20.0 - - + +
63I ILE* 3.4 15.3 - - - +
64I ARG 2.9 1.0 + - - -
65I SER* 1.3 82.4 - - - +
67I MET* 1.3 61.2 + - - +
68I VAL* 4.2 1.0 + - - +
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Residues in contact with MET 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LEU* 4.6 10.5 - - + -
41I PRO* 3.3 37.2 - - + +
42I PRO 4.0 7.4 - - - +
43I LEU* 3.4 31.0 - - + -
63I ILE* 3.7 15.5 - - - +
64I ARG* 3.0 15.9 + - - +
65I SER 4.4 2.8 - - - +
66I ARG* 1.3 79.9 - - - +
68I VAL* 1.3 62.3 + - - +
69I LEU* 3.7 32.2 + - + +
75I PHE* 4.0 22.7 - - + -
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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