Contacts of the helix formed by residues 61 - 71 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203E ASN* 3.6 43.3 - - + +
53F ARG* 5.1 11.4 - - - +
56F GLU* 4.3 6.2 + - - +
57F LEU* 3.0 29.1 + - + +
60F SER* 1.3 90.6 + - - +
62F HIS* 1.3 65.6 + - - +
64F SER* 3.9 0.6 - - - -
65F ALA* 3.0 26.9 + - - +
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Residues in contact with HIS 62 (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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194E GLU* 3.7 9.4 + - - -
197E TYR* 6.0 0.4 - - - -
198E TYR* 2.7 32.0 + + - -
203E ASN* 3.4 26.2 - - + +
57F LEU 3.1 24.7 + - - -
58F HIS* 3.3 20.4 - - + +
61F LYS* 1.3 82.6 - - - +
63F HIS* 1.3 64.6 + - - +
65F ALA* 3.3 9.6 + - - +
66F TYR* 3.1 28.3 + - + -
195F HIS* 3.4 41.5 + + + +
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Residues in contact with HIS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 3.6 8.7 - - + +
36F PRO* 3.5 19.1 - - + -
58F HIS* 2.8 16.4 + - - +
59F TYR* 3.4 14.5 + - - +
62F HIS* 1.3 73.2 - - - +
64F SER* 1.3 64.8 + - - +
66F TYR* 3.2 18.7 + - + +
67F VAL* 3.2 13.3 + - + +
105F HIS* 3.0 40.3 + - + -
108F HIS* 3.5 27.5 - + + +
109F SER* 3.3 19.5 - - - -
112F TRP* 3.0 24.1 + - - +
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Residues in contact with SER 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 3.7 25.8 - - - +
59F TYR 3.1 9.8 + - - -
60F SER 3.0 31.5 + - - -
61F LYS 3.9 0.4 - - - -
62F HIS 3.3 0.6 - - - -
63F HIS* 1.3 76.5 - - - +
65F ALA* 1.3 55.5 + - - +
67F VAL* 3.3 4.1 + - - +
68F ASP* 3.0 42.0 + - - -
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Residues in contact with ALA 65 (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 LYS 3.0 20.2 + - - +
62F HIS* 3.7 6.3 - - - +
63F HIS 3.2 0.2 - - - -
64F SER* 1.3 77.2 - - - +
66F TYR* 1.3 58.5 + - + +
68F ASP* 3.4 6.5 + - - +
69F LYS* 2.9 32.5 + - - +
101F GLN* 4.6 0.9 - - - -
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Residues in contact with TYR 66 (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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152E PHE* 4.0 15.8 - + - -
62F HIS* 3.1 32.8 + - + -
63F HIS* 3.2 11.3 + + - +
65F ALA* 1.3 78.0 - - + +
67F VAL* 1.3 58.0 + - - +
70F LEU* 2.9 33.5 + - - +
101F GLN* 3.2 38.4 - - - +
104F GLN* 3.1 44.3 + - + -
105F HIS* 4.3 9.0 - - - +
108F HIS* 3.6 25.1 - + - -
193F TRP* 3.7 20.3 - - - -
195F HIS* 4.6 3.9 - + - -
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ALA* 3.6 35.5 - - - +
34F GLU* 3.8 7.6 - - - -
35F LEU* 4.0 16.6 - - + +
63F HIS* 3.2 19.3 + - + +
64F SER* 3.3 8.5 + - - +
66F TYR* 1.3 75.6 - - - +
68F ASP* 1.3 71.5 + - - +
70F LEU* 3.7 2.3 - - - +
71F ASN* 3.1 27.8 + - - +
105F HIS* 3.5 34.5 - - + +
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Residues in contact with ASP 68 (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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64F SER* 3.0 28.6 + - - +
65F ALA* 3.9 6.6 - - - +
67F VAL* 1.3 83.0 - - - +
69F LYS* 1.3 62.8 + - - +
71F ASN* 3.2 18.5 + - - +
72F THR* 3.5 15.0 + - - +
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Residues in contact with LYS 69 (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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65F ALA 2.9 14.0 + - - +
68F ASP* 1.3 75.1 - - - +
70F LEU* 1.3 63.0 + - - +
72F THR* 2.6 39.7 + - + +
73F LEU* 3.6 15.3 - - + +
97F VAL* 4.4 18.2 - - - -
101F GLN* 3.3 36.3 - - + +
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Residues in contact with LEU 70 (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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31F TYR* 3.5 16.0 + - + -
33F ALA* 3.9 13.0 - - + -
66F TYR 2.9 18.8 + - - +
67F VAL 3.7 4.3 - - - +
69F LYS* 1.3 75.7 - - - +
71F ASN* 1.3 58.3 + - - +
73F LEU* 3.0 18.6 + - + -
74F GLY 3.2 12.0 + - - +
82F ILE* 3.9 27.1 - - + -
85F ILE* 4.5 7.6 - - + -
98F MET* 4.2 22.4 - - + +
101F GLN* 3.9 10.4 - - + +
102F ALA* 3.9 38.4 - - + +
105F HIS* 4.2 8.5 - - + -
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Residues in contact with ASN 71 (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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31F TYR* 3.6 21.9 + - - -
32F PRO* 3.7 10.1 - - - +
33F ALA* 2.9 46.4 + - - +
67F VAL* 3.1 23.8 + - - +
68F ASP* 3.2 12.6 + - - +
70F LEU* 1.3 76.0 - - - +
72F THR* 1.3 59.4 + - - +
73F LEU 3.3 0.2 - - - -
75F LYS 5.7 0.2 + - - -
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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