Contacts of the helix formed by residues 61 - 74 (chain E) in PDB entry 4F2N
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 LYS 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E ARG* 5.3 11.7 - - - +
56E GLU* 4.3 4.9 - - - +
57E LEU* 3.0 26.0 + - + +
60E SER* 1.3 89.0 + - - +
62E HIS* 1.3 67.7 + - - +
63E HIS 3.6 0.2 - - - -
64E SER* 4.0 0.4 - - - -
65E ALA* 3.1 25.6 + - - +
203F ASN* 3.9 39.7 - - + +
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Residues in contact with HIS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E LEU 2.9 30.9 + - - -
58E HIS* 3.3 20.2 - - + +
61E LYS* 1.3 73.5 - - - +
63E HIS* 1.3 67.9 + - - +
65E ALA* 3.3 9.7 + - - +
66E TYR* 3.2 27.5 + - + -
108E HIS* 5.0 0.4 - - - +
195E HIS* 3.5 42.2 + + + +
194F GLU* 3.8 8.7 + - - -
197F TYR* 6.1 0.2 - - - -
198F TYR* 2.7 32.3 + + - -
203F ASN* 3.4 27.7 - - + +
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Residues in contact with HIS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 3.6 7.7 - - + +
36E PRO* 3.4 18.2 - - + -
58E HIS 2.8 17.3 + - - +
59E TYR* 3.4 14.1 + - - +
62E HIS* 1.3 71.3 - - - +
64E SER* 1.3 64.6 + - - +
66E TYR* 3.1 20.7 + - + +
67E VAL* 3.2 13.4 + - + +
105E HIS* 2.7 40.1 + - + -
108E HIS* 3.5 18.0 - + + +
109E SER* 3.3 33.0 - - - -
112E TRP* 2.9 21.8 + - - +
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Residues in contact with SER 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 3.6 26.0 - - - +
59E TYR 3.1 10.0 + - - -
60E SER 3.1 29.9 + - - -
61E LYS 4.0 0.7 - - - -
62E HIS 3.3 0.6 - - - -
63E HIS* 1.3 74.9 - - - +
65E ALA* 1.3 56.1 + - - +
67E VAL* 3.3 4.1 + - - +
68E ASP* 3.0 42.2 + - - +
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LYS 3.1 19.9 + - - +
62E HIS* 3.7 5.4 - - - +
63E HIS 3.2 0.4 - - - -
64E SER* 1.3 72.9 - - - +
66E TYR* 1.3 61.6 + - + +
68E ASP* 3.4 7.4 + - - +
69E LYS* 2.9 32.3 + - - +
101E GLN* 4.7 0.7 - - - -
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Residues in contact with TYR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E HIS* 3.2 32.9 + - + -
63E HIS* 3.1 12.1 + + - +
65E ALA* 1.3 74.6 - - + +
67E VAL* 1.3 62.2 + - - +
70E LEU* 2.9 33.1 + - - +
100E ASN 4.8 0.2 - - - -
101E GLN* 3.4 38.8 - - - +
104E GLN* 3.0 42.7 + - + -
105E HIS* 4.4 8.7 - - + +
108E HIS* 3.6 26.5 - + - -
193E TRP* 3.7 21.1 - - - -
195E HIS* 4.5 3.7 - + - -
152F PHE* 4.0 16.4 - + - -
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Residues in contact with VAL 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 3.5 35.7 - - - +
34E GLU* 3.8 6.1 - - - +
35E LEU* 4.0 18.8 - - + +
63E HIS* 3.2 16.5 + - + +
64E SER* 3.3 8.7 + - - +
66E TYR* 1.3 78.4 - - - +
68E ASP* 1.3 71.5 + - - +
70E LEU* 3.4 3.1 + - - +
71E ASN* 3.1 27.0 + - - +
105E HIS* 3.6 36.3 - - + +
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E SER* 3.0 32.6 + - - +
65E ALA* 3.9 6.7 - - - +
67E VAL* 1.3 82.9 - - - +
69E LYS* 1.3 63.7 + - - +
71E ASN* 3.4 16.7 + - - +
72E THR* 3.4 17.1 + - - +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ALA 2.9 14.5 + - - +
68E ASP* 1.3 74.1 - - - +
70E LEU* 1.3 65.4 + - - +
72E THR* 2.5 38.4 + - + +
73E LEU* 3.6 14.6 + - + +
97E VAL* 4.2 18.1 - - - +
101E GLN* 3.2 36.3 - - + +
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TYR* 3.7 16.7 + - + -
33E ALA* 3.9 21.1 - - + -
66E TYR 2.9 18.4 + - - +
67E VAL 3.6 4.5 - - - +
69E LYS* 1.3 76.6 - - - +
71E ASN* 1.3 57.1 + - - +
72E THR 3.1 0.2 - - - -
73E LEU* 2.8 20.4 + - - -
74E GLY* 3.0 12.9 + - - -
82E ILE* 4.0 17.9 - - + -
85E ILE* 4.7 4.7 - - + -
98E MET* 4.0 30.3 - - + +
101E GLN* 3.9 12.4 - - + +
102E ALA* 3.8 33.0 - - + +
105E HIS* 4.4 7.6 - - + -
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Residues in contact with ASN 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E TYR* 3.4 25.0 + - - +
32E PRO* 3.6 9.2 - - - +
33E ALA* 2.8 47.6 + - - +
67E VAL* 3.1 26.4 + - - +
68E ASP* 3.7 9.5 + - - +
69E LYS 3.2 0.6 - - - -
70E LEU* 1.3 74.5 - - - +
72E THR* 1.3 60.3 + - - +
73E LEU 3.2 0.2 - - - -
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Residues in contact with THR 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ASP 3.5 15.3 - - - +
69E LYS* 2.5 35.0 + - + +
71E ASN* 1.3 78.9 - - - +
73E LEU* 1.3 70.5 + - - +
74E GLY 3.9 0.2 - - - -
75E LYS* 5.6 1.3 - - - +
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Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 3.7 22.0 - - + +
70E LEU* 2.8 6.1 + - - +
72E THR* 1.3 94.0 - - - +
74E GLY* 1.3 58.9 + - - +
75E LYS* 3.4 10.2 + - - +
77E TYR* 5.5 0.2 - - - -
97E VAL* 3.8 29.8 - - + -
98E MET* 3.6 43.8 - - + +
101E GLN* 4.3 8.3 - - + -
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Residues in contact with GLY 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E TYR* 3.0 37.5 + - - -
70E LEU* 3.0 9.5 + - - -
72E THR 3.9 0.4 - - - -
73E LEU* 1.3 76.0 - - - +
75E LYS* 1.3 66.3 + - - +
77E TYR* 3.0 24.4 + - - +
85E ILE* 5.6 0.4 - - - -
98E MET* 4.0 13.5 - - - -
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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