Contacts of the helix formed by residues 81 - 98 (chain f) in PDB entry 5T0J
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 VAL 81 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80f TYR* 1.3 70.4 - - + +
82f PRO* 1.3 73.1 - - + +
83f GLU* 3.7 10.3 - - + +
84f PRO* 3.3 34.9 - - + +
85f GLU* 3.4 13.2 - - - +
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Residues in contact with PRO 82 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80f TYR* 3.4 13.7 - - + +
81f VAL* 1.3 86.3 - - + +
83f GLU* 1.3 64.8 + - + +
84f PRO 3.5 0.2 - - - -
85f GLU* 3.1 11.7 + - + +
86f ASN* 3.0 38.7 + - - +
130f VAL* 5.7 8.3 - - + -
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Residues in contact with GLU 83 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81f VAL* 3.2 8.7 - - + -
82f PRO* 1.3 80.2 - - + +
84f PRO* 1.3 64.3 - - + +
86f ASN* 2.8 18.6 + - - +
87f SER* 2.6 42.0 + - - +
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Residues in contact with PRO 84 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81f VAL* 3.3 34.8 - - + +
83f GLU* 1.3 94.3 - - + +
85f GLU* 1.3 66.1 + - + +
87f SER* 3.9 4.9 - - - -
88f ALA* 3.3 24.8 + - - +
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Residues in contact with GLU 85 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56f ASP* 5.4 2.6 - - - +
78f VAL* 3.0 21.3 - - - +
79f ASN* 2.9 30.1 - - - +
80f TYR* 3.5 29.8 - - + +
81f VAL 3.4 16.3 - - - +
82f PRO* 3.1 11.1 + - + +
84f PRO* 1.3 80.8 - - - +
86f ASN* 1.3 62.5 + - - +
88f ALA* 4.7 0.5 - - - +
89f LEU* 3.2 25.9 + - - +
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Residues in contact with ASN 86 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82f PRO* 3.0 23.1 + - - +
83f GLU* 2.8 35.0 + - - +
85f GLU* 1.3 73.1 - - - +
87f SER* 1.3 70.6 + - - +
89f LEU* 4.1 8.5 - - - -
90f LEU* 3.3 28.9 + - - +
130f VAL* 4.8 20.1 - - + +
131f VAL* 4.2 22.2 - - + +
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Residues in contact with SER 87 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83f GLU* 2.6 36.2 + - - +
84f PRO* 4.0 5.2 - - - -
85f GLU 3.2 1.0 - - - -
86f ASN* 1.3 82.3 + - - +
88f ALA* 1.3 66.9 + - - +
89f LEU 3.2 0.9 + - - -
90f LEU* 3.3 13.2 + - - +
91f ARG* 3.3 20.9 + - - +
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Residues in contact with ALA 88 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56f ASP* 3.9 29.7 - - - +
57f MET* 5.0 6.5 - - - +
59f GLU* 4.8 12.4 - - + +
84f PRO 3.3 13.9 + - - +
85f GLU 4.7 0.4 - - - +
87f SER* 1.3 79.6 - - - +
89f LEU* 1.3 51.6 + - - +
90f LEU 3.4 0.2 - - - -
91f ARG* 3.3 9.6 + - - +
92f CYS* 2.7 34.2 + - - +
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Residues in contact with LEU 89 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56f ASP* 5.9 0.4 - - - -
85f GLU 3.2 21.7 + - - +
86f ASN* 4.2 8.5 - - - +
87f SER 3.1 1.0 - - - -
88f ALA* 1.3 74.3 - - - +
90f LEU* 1.3 59.7 + - + +
92f CYS* 2.9 16.8 + - + +
93f ALA* 2.6 37.2 + - + +
122f ILE* 3.8 33.9 - - + -
126f CYS* 3.6 29.2 - - - -
131f VAL* 5.9 2.7 - - + -
134f GLN* 4.7 9.6 - - - +
135f MET* 6.4 1.8 - - - -
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Residues in contact with LEU 90 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86f ASN* 3.3 20.6 + - - +
87f SER 3.3 5.4 + - - +
89f LEU* 1.3 85.2 - - + +
91f ARG* 1.3 79.0 + - - +
93f ALA* 3.7 9.7 - - + +
94f LEU* 3.4 28.1 + - - +
131f VAL* 4.0 32.8 - - + -
132f GLN 5.7 2.7 - - - +
134f GLN* 5.3 5.8 - - - +
138f MET* 5.8 4.2 - - + +
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Residues in contact with ARG 91 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59f GLU* 3.5 41.1 + - + +
61f ASP* 3.8 1.8 - - - +
87f SER* 3.3 16.5 + - - +
88f ALA* 3.6 7.6 - - - +
89f LEU 3.1 0.4 - - - -
90f LEU* 1.3 105.3 + - - +
92f CYS* 1.3 58.4 + - - +
94f LEU* 3.7 11.2 + - - +
95f GLY* 3.1 23.4 + - - -
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Residues in contact with CYS 92 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56f ASP* 5.1 10.3 - - - +
59f GLU* 5.5 2.2 - - - +
61f ASP* 3.4 25.6 - - - +
64f GLU* 5.1 11.9 - - - -
88f ALA 2.7 20.6 + - - +
89f LEU* 2.9 17.2 + - + +
91f ARG* 1.3 72.0 - - - +
93f ALA* 1.3 66.4 + - - +
96f VAL* 3.0 44.4 + - - +
118f LEU* 6.0 4.3 - - - -
135f MET* 4.4 2.6 - - - +
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Residues in contact with ALA 93 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89f LEU* 2.6 20.8 + - + +
90f LEU* 3.7 12.1 - - + +
91f ARG 3.3 0.2 - - - -
92f CYS* 1.3 77.6 - - - +
94f LEU* 1.3 59.4 + - - +
97f PHE* 3.7 17.7 + - - +
134f GLN* 5.3 7.4 - - - +
135f MET* 3.7 38.4 - - + +
138f MET* 3.9 22.3 - - + +
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Residues in contact with LEU 94 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90f LEU 3.4 17.4 + - - +
91f ARG* 4.3 12.3 - - - +
93f ALA* 1.3 75.7 - - - +
95f GLY* 1.3 60.7 + - - +
97f PHE* 4.2 10.5 - - + +
98f ARG* 3.5 26.0 + - - +
138f MET* 3.7 32.8 - - + -
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Residues in contact with GLY 95 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61f ASP* 3.1 21.5 - - - +
91f ARG 3.1 13.3 + - - -
93f ALA 3.3 0.2 - - - -
94f LEU* 1.3 77.0 - - - +
96f VAL* 1.3 59.7 + - - +
98f ARG* 3.1 36.0 + - - +
99f LYS* 3.2 16.8 - - - +
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Residues in contact with VAL 96 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61f ASP* 3.8 14.6 - - + -
62f ILE* 5.1 4.5 - - - +
65f ASN* 5.7 9.0 - - + +
92f CYS* 3.0 37.9 + - - +
95f GLY* 1.3 75.1 - - - +
97f PHE* 1.3 65.1 + - - +
98f ARG 3.2 0.2 - - - -
99f LYS* 3.1 16.9 + - + +
100f PHE* 3.4 39.3 + - + -
118f LEU* 6.3 2.7 - - + -
119f VAL* 5.8 4.3 - - + -
135f MET* 3.7 23.6 - - + -
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Residues in contact with PHE 97 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93f ALA 3.7 16.6 + - - +
94f LEU* 4.5 11.4 - - + +
95f GLY 3.5 0.2 - - - -
96f VAL* 1.3 80.7 - - - +
98f ARG* 1.3 62.2 + - + +
100f PHE* 2.9 28.1 + - - +
101f SER* 5.5 7.9 - - - -
135f MET* 4.2 3.7 - - + +
138f MET* 3.3 33.2 - - + -
139f LEU* 3.5 41.3 - - + +
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Residues in contact with ARG 98 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59f GLU 5.2 5.7 + - - -
60f LYS* 6.1 0.6 - - - +
61f ASP* 5.1 8.1 + - - +
94f LEU 3.5 14.6 + - - +
95f GLY* 3.1 33.2 + - - +
97f PHE* 1.3 83.9 - - + +
99f LYS* 1.3 77.0 + - - +
100f PHE 3.3 1.7 + - - +
102f ARG* 2.6 50.1 + - - +
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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