Contacts of the helix formed by residues 59 - 71 (chain C) in PDB entry 2F4N
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 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ILE* 3.6 9.0 - - - +
56C LYS* 2.8 31.5 + - + +
57C PRO 3.1 2.8 - - - +
58C PHE* 1.3 75.4 - - - +
60C ILE* 1.3 59.9 + - - +
61C TYR* 3.1 19.7 + - - +
62C HIS* 3.0 24.9 + - + +
63C GLY 3.3 15.4 + - - -
83C ILE* 3.8 3.1 - - - +
257C TYR* 3.3 39.1 - - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE 3.2 11.0 + - - +
59C ASN* 1.3 70.1 + - - +
61C TYR* 1.3 92.4 + - + +
63C GLY 3.7 0.7 - - - -
64C ALA* 2.7 36.8 + - - +
83C ILE* 3.8 19.7 - - + +
85C PRO* 4.1 10.8 - - + -
109C ASN* 3.4 47.8 - - + +
111C LEU* 3.6 15.9 - - + +
168C ILE* 4.5 10.3 - - + +
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Residues in contact with TYR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN* 3.1 14.1 + - - +
60C ILE* 1.3 95.4 - - + +
62C HIS* 1.3 67.5 + - - +
64C ALA* 3.3 6.1 + - - +
65C TYR* 3.0 23.9 + - - +
114C TYR* 4.6 7.0 - - - +
168C ILE* 3.5 42.6 - - + +
174C ARG* 4.5 6.5 + - - -
176C ILE* 3.9 11.5 - - - +
257C TYR* 3.7 19.3 - + + -
258C LEU* 3.6 48.4 - - + +
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Residues in contact with HIS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 2.8 37.1 + - - -
54C GLU 3.7 3.8 - - - -
55C ILE* 3.6 20.6 - - + +
56C LYS* 3.0 53.1 + - + +
59C ASN* 3.0 25.3 + - + +
61C TYR* 1.3 77.1 - - - +
63C GLY* 1.3 61.9 + - - +
65C TYR* 3.2 4.3 + - - +
66C VAL* 3.1 20.0 + - + +
177C HIS* 3.4 19.8 - + - -
257C TYR* 3.3 18.7 - - - +
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 5.2 0.9 - - - -
55C ILE* 3.6 24.9 - - - +
59C ASN 3.3 8.8 + - - -
60C ILE 3.7 2.5 - - - -
62C HIS* 1.3 80.1 - - - +
64C ALA* 1.3 63.5 + - - +
66C VAL* 3.1 3.1 + - - +
67C LEU* 2.9 27.0 + - - +
83C ILE* 4.7 4.0 - - - -
111C LEU* 3.8 14.4 - - - -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE 2.7 22.5 + - - +
61C TYR 3.6 2.2 - - - +
63C GLY* 1.3 72.0 - - - +
65C TYR* 1.3 57.3 + - - +
67C LEU* 3.5 4.2 + - - +
68C LEU* 3.1 22.2 + - - +
110C GLY 4.5 0.2 - - - +
111C LEU* 3.3 26.5 - - - +
114C TYR* 3.5 37.5 - - + +
115C VAL* 5.1 1.2 + - - +
168C ILE* 3.8 13.9 - - + -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU* 5.4 8.7 - - + -
26A GLY 6.1 0.4 - - - -
27A TYR* 5.9 0.4 - - - -
61C TYR 3.0 12.7 + - - +
62C HIS 3.5 8.3 - - - +
64C ALA* 1.3 75.0 - - - +
66C VAL* 1.3 66.5 + - + +
68C LEU* 3.3 8.8 + - + +
69C THR* 2.9 34.0 + - - -
114C TYR* 4.0 6.2 - + - -
176C ILE* 3.1 32.5 - - + -
177C HIS* 3.4 35.0 - + + -
185C ILE* 3.9 10.0 - - + +
235C ASN* 3.2 22.3 + - - -
237C GLU* 2.8 40.5 + - + +
239C PHE* 3.7 24.4 - + - -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR 5.2 0.9 - - - +
24A ASN 3.5 22.7 - - - +
25A GLU* 3.9 12.1 - - - +
26A GLY* 3.9 12.1 - - - +
18C THR* 4.6 5.8 - - + -
51C ILE* 3.6 28.5 - - + -
52C SER* 4.5 4.0 - - - -
55C ILE* 3.5 28.9 - - + -
62C HIS* 3.1 11.3 + - + +
63C GLY 3.1 7.4 + - - +
65C TYR* 1.3 78.4 - - + +
67C LEU* 1.3 63.6 + - - +
69C THR* 3.1 7.9 + - - -
70C ALA* 3.0 22.5 + - - +
177C HIS* 5.5 0.4 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR* 5.9 0.2 - - - +
18C THR* 3.6 33.7 - - + +
51C ILE* 4.7 3.4 - - + -
63C GLY 2.9 19.7 + - - +
64C ALA 3.7 4.3 - - - +
66C VAL* 1.3 75.4 - - - +
68C LEU* 1.3 62.2 + - - +
70C ALA* 5.3 1.1 - - - -
71C ILE* 3.2 56.5 + - + +
72C PRO* 3.7 0.7 - - - +
79C HIS* 5.6 1.3 - - + -
80C VAL 6.0 0.4 - - - -
81C ALA* 3.7 26.5 - - + -
111C LEU* 3.9 23.8 - - + +
112C PHE* 3.8 17.3 - - + -
115C VAL* 4.3 12.3 - - + +
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA 3.1 17.2 + - - +
65C TYR* 3.6 11.7 - - + +
66C VAL 3.2 0.2 - - - -
67C LEU* 1.3 76.9 - - - +
69C THR* 1.3 62.1 + - - +
72C PRO* 3.4 17.6 - - + +
73C TYR* 5.1 2.3 - - - -
114C TYR* 3.9 42.2 - - + +
115C VAL* 4.6 6.7 - - - +
118C LYS* 4.5 23.1 - - + -
237C GLU* 4.9 9.0 - - + +
239C PHE* 3.8 33.7 - - + -
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 3.6 30.8 + - - +
27A TYR* 4.0 14.1 - - + +
30A ALA* 3.5 4.6 - - + +
65C TYR* 2.9 23.1 + - - -
66C VAL 3.1 7.2 + - - -
68C LEU* 1.3 79.7 - - - +
70C ALA* 1.3 57.4 + - - +
73C TYR* 3.1 30.5 - - + -
237C GLU* 3.7 38.0 - - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 3.5 14.1 - - - +
29A GLY* 3.7 11.0 - - - -
30A ALA* 3.6 17.1 - - - +
51C ILE* 4.0 23.6 - - + -
66C VAL 3.0 15.1 + - - +
67C LEU 4.7 0.2 - - - +
69C THR* 1.3 77.1 - - - +
71C ILE* 1.3 64.8 + - - +
72C PRO 3.6 0.4 - - - -
73C TYR* 3.2 19.2 + - - +
74C PHE* 3.4 12.2 - - + -
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.0 10.5 - - + -
67C LEU* 3.2 42.8 + - + +
70C ALA* 1.3 72.0 - - - +
72C PRO* 1.3 62.1 - - + +
73C TYR 2.7 12.2 + - - -
74C PHE* 2.8 25.1 + - - +
79C HIS* 3.5 51.8 - - + +
102C TYR* 4.2 3.6 - - + -
104C LEU* 4.6 3.1 - - + -
112C PHE* 5.0 2.2 - - + -
115C VAL* 3.8 27.4 - - + -
119C LEU* 3.9 16.6 - - + -
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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