Contacts of the helix formed by residues 73 - 87 (chain T) in PDB entry 2KFX
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 73 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24T PHE* 4.1 1.6 - - - -
34T GLY 5.4 4.5 - - - -
35T SER* 6.2 1.3 - - - +
71T THR* 4.1 5.1 - - - +
72T VAL* 1.3 75.7 - - - +
74T PHE* 1.3 56.8 + - - +
75T ASP* 2.6 40.0 + - - +
76T GLU* 3.2 30.6 + - - +
77T PHE* 3.1 20.3 + - - +
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Residues in contact with PHE 74 (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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17T LYS* 4.0 29.6 - - + -
20T PHE* 5.0 6.3 - - + -
21T LYS* 4.4 18.8 - - + -
24T PHE* 3.7 41.6 - + + -
73T ASP* 1.3 71.9 - - - +
75T ASP* 1.3 66.4 + - - +
77T PHE* 3.8 5.1 - + - +
78T LEU* 3.4 50.3 - - + +
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Residues in contact with ASP 75 (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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73T ASP* 2.6 32.8 + - - +
74T PHE* 1.3 77.7 + - - +
76T GLU* 1.3 57.4 + - - +
77T PHE 2.5 16.1 + - - -
78T LEU* 3.0 21.6 + - - +
79T VAL* 3.9 4.6 + - - +
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Residues in contact with GLU 76 (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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64T VAL* 3.5 26.7 - - + +
65T ASP* 2.7 37.2 + - - +
66T GLU* 4.9 3.4 - - + +
67T ASP* 3.9 6.6 - - - +
71T THR* 3.1 8.1 + - - +
72T VAL* 4.1 4.9 - - + -
73T ASP* 3.2 25.7 + - - +
75T ASP* 1.3 78.2 - - - +
77T PHE* 1.3 66.3 + - - +
79T VAL* 3.3 28.0 - - + +
80T MET* 3.3 6.6 + - - +
90T CA 2.8 17.7 - - - -
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Residues in contact with PHE 77 (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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20T PHE* 3.8 30.7 - + + -
24T PHE* 3.5 22.4 - + + -
64T VAL* 6.2 0.2 - - - -
72T VAL* 3.9 12.6 - - + -
73T ASP 3.1 21.5 + - - +
74T PHE* 3.8 9.4 - + - -
75T ASP 2.5 5.9 + - - -
76T GLU* 1.3 72.8 - - - +
78T LEU* 1.3 82.1 + - + +
80T MET* 2.8 21.0 + - + +
81T MET* 3.0 52.5 - - + +
91T WW7 3.1 50.9 - + + -
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Residues in contact with LEU 78 (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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9T VAL* 4.8 23.8 - - + -
12T LEU* 5.2 14.1 - - + -
20T PHE* 6.0 4.9 - - + -
74T PHE* 3.4 56.5 - - + +
75T ASP* 3.8 5.8 - - - +
77T PHE* 1.3 85.1 - - + +
79T VAL* 1.3 66.0 + - + +
81T MET* 3.1 9.5 + - + +
82T VAL* 2.9 32.3 + - + +
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Residues in contact with VAL 79 (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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2T ASP* 6.2 1.1 - - + +
5T TYR* 3.6 42.4 - - + +
64T VAL* 6.2 0.4 - - + -
66T GLU* 6.5 0.9 - - + -
75T ASP 4.2 3.6 - - - +
76T GLU* 3.3 26.0 - - + +
77T PHE 3.0 0.2 + - - -
78T LEU* 1.3 78.0 - - + +
80T MET* 1.3 64.2 + - - +
82T VAL* 3.2 7.8 + - - +
83T ARG* 2.8 43.4 + - - +
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Residues in contact with MET 80 (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 MET* 4.6 6.7 - - + +
61T ILE* 6.1 1.6 - - + -
63T GLU* 4.9 7.2 - - - +
64T VAL* 3.8 41.7 - - + +
72T VAL* 4.9 9.4 - - + -
76T GLU 3.3 3.1 + - - +
77T PHE* 2.8 28.5 + - + +
79T VAL* 1.3 75.9 - - - +
81T MET* 1.3 78.5 + - + +
83T ARG* 3.2 9.1 + - - +
84T SER* 3.1 30.8 + - - +
91T WW7 3.2 48.0 - - + -
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Residues in contact with MET 81 (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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20T PHE* 4.3 22.9 - - + -
77T PHE* 3.0 60.1 - - + +
78T LEU* 3.1 7.4 + - + +
80T MET* 1.3 96.6 - - + +
82T VAL* 1.3 59.2 + - + +
83T ARG 2.9 0.7 + - - -
84T SER* 3.9 3.8 - - - -
85T MET* 2.7 52.8 + - + +
91T WW7 3.4 26.0 - - + -
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Residues in contact with VAL 82 (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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4T ILE 5.0 2.2 - - - +
5T TYR* 3.9 33.9 - - + +
8T ALA* 3.9 31.0 - - + -
9T VAL* 5.2 5.8 - - + +
12T LEU* 5.4 8.7 - - + -
78T LEU* 2.9 30.1 + - + +
79T VAL* 3.5 8.3 - - - +
81T MET* 1.3 72.5 - - + +
83T ARG* 1.3 57.7 + - - +
85T MET* 4.1 5.4 - - - -
86T LYS* 2.9 38.5 + - + +
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Residues in contact with ARG 83 (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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5T TYR* 4.0 19.3 - - + +
63T GLU* 4.1 33.4 + - - +
64T VAL* 4.1 20.0 - - - +
66T GLU* 5.8 1.0 + - - +
79T VAL* 2.8 38.3 + - + +
80T MET* 3.3 9.0 - - - +
81T MET 2.9 0.6 + - - -
82T VAL* 1.3 72.8 - - - +
84T SER* 1.3 58.1 + - - +
85T MET 2.8 1.6 + - - -
86T LYS* 3.6 1.5 - - - +
87T ASP* 2.6 42.3 + - - +
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Residues in contact with SER 84 (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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80T MET* 3.1 20.2 + - - +
81T MET* 3.9 3.8 - - - -
83T ARG* 1.3 77.5 - - - +
85T MET* 1.3 61.0 + - - +
87T ASP 3.1 8.3 - - - -
88T ASP* 2.9 34.7 + - - +
89T SER* 5.1 4.8 + - - +
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Residues in contact with MET 85 (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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20T PHE* 5.8 7.0 - - + -
81T MET* 2.7 44.2 + - + +
82T VAL* 3.5 6.5 - - - +
83T ARG 2.8 0.6 + - - -
84T SER* 1.3 74.0 - - - +
86T LYS* 1.3 61.1 + - - +
87T ASP* 2.8 10.8 + - - -
88T ASP* 4.1 1.7 + - - +
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Residues in contact with LYS 86 (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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4T ILE 5.8 3.8 - - - +
82T VAL* 2.9 25.0 + - + +
83T ARG* 4.1 1.6 - - - +
85T MET* 1.3 76.6 - - - +
87T ASP* 1.3 85.2 + - - +
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Residues in contact with ASP 87 (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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83T ARG* 2.6 24.8 + - - +
84T SER* 3.0 10.2 - - - -
85T MET 2.8 1.8 + - - -
86T LYS* 1.3 108.6 + - - +
88T ASP* 1.3 66.2 + - - +
89T SER* 3.9 5.0 + - - -
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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