Contacts of the helix formed by residues 66 - 81 (chain B) in PDB entry 1EAK
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 ASN 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B LYS* 5.8 7.6 - - - +
63B GLU 3.8 19.0 + - - -
64B SER* 3.2 14.9 + - - +
65B CYS* 1.3 73.0 - - - +
67B LEU* 1.3 74.7 + - - +
68B PHE 2.8 5.2 + - - -
69B VAL* 2.9 5.5 + - - +
70B LEU* 2.6 35.5 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASN* 1.3 77.3 - - + +
68B PHE* 1.3 88.1 + - + +
70B LEU* 4.3 5.8 - - - +
71B LYS* 3.4 36.3 + - - +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASN* 2.8 5.3 + - - -
67B LEU* 1.3 104.7 - - + +
69B VAL* 1.3 63.7 + - + +
71B LYS* 3.1 32.8 + - + +
72B ASP* 3.2 18.4 + - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 3.9 18.2 - - + -
61B PRO* 4.7 6.7 - - + -
64B SER* 3.5 32.1 - - - +
65B CYS* 4.3 1.1 - - - -
66B ASN* 2.9 4.2 + - - +
68B PHE* 1.3 77.2 - - + +
70B LEU* 1.3 63.7 + - - +
72B ASP* 3.5 6.9 + - - +
73B THR* 2.9 40.6 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 4.6 25.8 - - + +
50B ALA* 5.2 5.2 - - + -
51B VAL* 4.8 11.2 - - + -
54B LEU* 3.4 30.3 - - + -
65B CYS* 4.1 14.8 - - - +
66B ASN* 2.6 41.1 + - - +
67B LEU* 4.3 3.8 - - - +
69B VAL* 1.3 73.2 - - - +
71B LYS* 1.3 56.6 + - + +
73B THR* 4.0 0.6 - - - -
74B LEU* 2.9 53.4 + - + +
89B LEU* 5.6 6.1 - - + -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.4 30.6 + - + +
68B PHE* 3.1 29.5 + - + +
70B LEU* 1.3 78.3 - - + +
72B ASP* 1.3 61.1 + - + +
74B LEU* 3.1 19.3 + - - +
75B LYS* 3.2 17.6 + - - +
87B GLY* 3.2 27.1 - - - +
88B ASP* 4.6 13.5 + - - +
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE 3.2 15.3 + - - +
69B VAL* 4.4 6.9 - - - +
71B LYS* 1.3 78.3 - - + +
73B THR* 1.3 63.4 + - - +
75B LYS* 3.8 26.2 - - + +
76B LYS* 3.8 24.1 + - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 3.6 22.4 - - + +
58B TYR* 4.0 18.7 - - + +
60B CYS* 3.7 32.8 - - + +
69B VAL* 2.9 27.0 + - - +
70B LEU* 4.0 3.1 - - - -
72B ASP* 1.3 80.4 + - - +
74B LEU* 1.3 68.0 + - - +
75B LYS 3.1 1.1 - - - -
76B LYS* 3.2 24.4 + - + +
77B MET* 3.4 4.2 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 5.0 4.7 - - + -
54B LEU* 3.3 28.0 - - + +
70B LEU* 2.9 47.7 + - + +
71B LYS 3.2 5.6 - - - +
73B THR* 1.3 78.8 - - - +
75B LYS* 1.3 56.1 + - - +
77B MET* 3.2 9.7 + - + +
78B GLN* 2.8 39.9 + - - +
87B GLY 3.6 17.7 - - - +
88B ASP 3.7 21.5 - - - +
89B LEU* 4.4 7.9 - - + +
93B THR* 4.5 14.8 - - - +
97B MET* 4.9 7.0 - - - -
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 3.2 10.5 + - - +
72B ASP* 4.0 24.6 - - + +
73B THR 3.1 0.6 - - - -
74B LEU* 1.3 80.6 - - - +
76B LYS* 1.3 56.3 + - - +
78B GLN* 2.9 8.5 - - - +
79B LYS* 2.9 30.8 + - - +
85B GLN* 3.2 40.3 - - + +
86B THR 4.3 4.7 - - - -
87B GLY* 3.3 24.0 - - - -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TYR* 3.9 19.3 + - + +
72B ASP* 3.8 16.5 + - - +
73B THR* 3.2 17.9 + - + +
74B LEU 3.2 0.2 - - - -
75B LYS* 1.3 79.0 - - - +
77B MET* 1.3 59.3 + - - +
79B LYS* 3.6 7.0 - - - +
80B PHE* 3.1 24.6 + - - +
107B VAL* 4.4 22.0 - - + +
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Residues in contact with MET 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 4.7 2.5 - - + -
54B LEU* 4.0 17.7 - - + -
58B TYR* 3.2 37.9 - - + -
73B THR 3.4 1.0 + - - -
74B LEU* 3.2 14.7 + - + +
76B LYS* 1.3 75.7 - - - +
78B GLN* 1.3 74.9 + - + +
80B PHE* 3.0 3.1 + - - +
81B PHE* 3.0 47.7 + - - -
83B LEU* 3.7 16.8 - - + -
93B THR* 3.3 44.2 - - - +
96B THR* 4.9 2.5 - - + -
97B MET* 4.3 16.8 - - + -
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 2.8 23.7 + - + +
75B LYS* 2.9 19.9 + - - +
77B MET* 1.3 96.4 - - + +
79B LYS* 1.3 54.8 + - - +
81B PHE 3.7 0.2 + - - -
82B GLY 3.2 4.5 + - - -
83B LEU* 2.5 44.1 + - + +
85B GLN* 3.4 20.6 - - - +
86B THR* 3.1 29.7 + - - +
87B GLY* 2.8 20.1 + - - +
88B ASP 3.2 18.2 + - - -
93B THR* 3.5 15.6 - - + +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LYS 2.9 18.3 + - - +
76B LYS* 3.6 7.4 - - - +
78B GLN* 1.3 75.6 - - - +
80B PHE* 1.3 66.9 + - - +
82B GLY* 3.1 12.1 + - - +
83B LEU 4.7 1.1 - - - -
85B GLN* 3.2 36.7 - - - +
415B GLN* 4.6 15.3 + - - +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TYR* 3.3 22.2 - + + +
76B LYS 3.1 10.6 + - - +
77B MET 3.0 5.2 + - - +
79B LYS* 1.3 81.2 - - - +
81B PHE* 1.3 74.9 + + - +
82B GLY 3.3 2.3 + - - -
106B ASP* 4.0 30.3 - - + -
413B HIS* 3.9 16.6 - - + -
414B SER 3.6 23.1 - - - -
415B GLN* 3.7 52.0 + - + +
423B PRO* 3.7 30.1 - - + -
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 3.6 14.8 - - - -
58B TYR* 3.2 20.6 - + - -
77B MET* 3.0 41.6 + - - +
80B PHE* 1.3 89.9 - + - +
82B GLY* 1.3 62.4 + - - +
83B LEU* 3.3 21.5 + - + +
96B THR* 4.4 12.6 - - + -
101B ARG* 3.5 13.2 - - - -
106B ASP* 3.4 17.7 - - - -
415B GLN 5.9 0.7 - - - -
417B PRO* 5.9 4.2 - - - +
423B PRO* 4.3 7.9 - - + -
424B ILE* 3.8 28.5 - - + -
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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