Contacts of the helix formed by residues 58 - 69 (chain A) in PDB entry 1F9Q
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 PRO 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLN 4.0 4.0 - - - +
57A ALA* 1.3 86.6 - - + +
59A LEU* 1.3 65.0 + - - +
60A TYR 3.3 0.9 - - - -
61A LYS* 3.1 39.9 + - + +
62A LYS* 3.4 5.4 + - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR 4.9 0.7 - - - +
17A SER* 4.0 27.8 - - - +
19A VAL* 4.1 20.6 - - + +
21A PRO* 4.1 25.6 - - + -
53A LEU* 4.6 11.2 - - + -
54A ASP 5.8 1.8 - - - +
57A ALA* 3.1 13.1 - - + +
58A PRO* 1.3 78.8 - - - +
60A TYR* 1.3 58.8 + - - +
62A LYS* 2.8 39.6 + - + +
63A ILE* 3.1 15.0 + - + +
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.8 1.4 - - + +
41A LEU* 3.4 26.9 - - + -
53A LEU* 4.2 14.5 - - + +
54A ASP 3.6 13.6 + - - +
55A LEU* 3.3 24.8 + - - -
57A ALA 3.4 22.4 + - - -
59A LEU* 1.3 79.2 - - - +
61A LYS* 1.3 99.0 + - + +
63A ILE* 3.2 12.8 + - - +
64A ILE* 2.9 46.6 + - + +
164B ILE* 5.2 0.7 - - + -
168B LEU* 3.3 34.9 - - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU 5.4 0.7 - - - -
56A GLN 5.1 5.6 + - - -
57A ALA 4.8 0.4 - - - -
58A PRO* 3.1 27.6 + - + +
60A TYR* 1.3 121.3 - - + +
62A LYS* 1.3 61.4 + - - +
64A ILE* 3.5 7.2 + - - +
65A LYS* 3.3 28.5 + - + +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 4.8 15.3 - - + +
58A PRO 3.4 4.3 + - - +
59A LEU* 2.8 29.6 + - + +
61A LYS* 1.3 77.6 - - - +
63A ILE* 1.3 63.9 + - - +
65A LYS* 3.0 17.4 - - + +
66A LYS* 3.0 27.0 + - + +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.7 2.9 - - + -
21A PRO* 3.9 27.5 - - + +
24A ILE* 3.3 48.7 - - + -
27A LEU* 4.6 12.8 - - + -
53A LEU* 3.4 25.6 - - + -
59A LEU* 3.1 29.8 + - + +
60A TYR* 3.2 6.0 + - - +
62A LYS* 1.3 77.2 - - - +
64A ILE* 1.3 62.7 - - - +
66A LYS* 3.4 7.1 + - - +
67A LEU* 3.0 26.2 + - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 23.3 - - + -
29A VAL* 5.0 5.2 - - + -
41A LEU* 5.3 0.7 - - + -
60A TYR* 2.9 44.5 + - + +
61A LYS* 3.7 7.4 - - - +
62A LYS 3.2 0.4 - - - -
63A ILE* 1.3 75.9 - - - +
65A LYS* 1.3 60.8 + - - +
67A LEU* 2.8 24.8 + - - +
68A LEU* 3.0 35.4 + - + +
129B VAL* 5.4 5.6 - - + -
160B TYR* 4.8 3.4 - - + -
164B ILE* 3.8 36.3 - - + -
165B LYS* 5.9 1.3 - - - +
168B LEU* 5.1 0.4 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.3 16.0 + - + +
62A LYS* 3.0 30.5 - - + +
64A ILE* 1.3 82.2 - - - +
66A LYS* 1.3 61.3 + - + +
68A LEU* 4.6 5.8 - - - +
69A GLU* 3.2 47.4 + - - +
160B TYR* 5.4 5.2 - - - +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 4.0 26.7 - - + +
22A ARG* 3.7 32.9 - - - +
62A LYS* 3.0 20.8 + - + +
63A ILE* 3.8 6.3 - - - +
64A ILE 3.1 0.2 - - - -
65A LYS* 1.3 79.6 - - + +
67A LEU* 1.3 61.3 + - + +
69A GLU* 4.3 3.2 + - - +
70A SER 3.4 19.1 - - - +
131B LYS* 5.8 5.7 - - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO 5.5 2.0 - - - +
24A ILE* 3.4 26.9 - - + +
25A THR 4.5 0.4 - - - -
26A SER 4.3 3.1 - - - -
27A LEU* 3.8 26.0 - - + +
63A ILE* 3.0 15.6 + - + +
64A ILE* 2.8 10.8 + - - +
66A LYS* 1.3 79.9 - - + +
68A LEU* 1.3 63.4 + - - +
70A SER* 3.4 12.0 + - - -
129B VAL* 3.6 38.6 - - + +
131B LYS* 3.4 41.3 - - + +
139B ALA* 3.8 11.7 - - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.0 33.0 + - + +
65A LYS* 4.4 4.5 - - - +
66A LYS 3.6 0.2 - - - -
67A LEU* 1.3 72.2 - - - +
69A GLU* 1.3 58.8 + - + +
70A SER* 2.9 11.4 + - - -
129B VAL* 3.6 15.3 - - + -
139B ALA* 3.7 19.2 - - + +
141B LEU* 3.3 38.8 - - + -
155B LEU* 4.8 10.4 - - + +
160B TYR* 3.2 52.7 - - + +
164B ILE* 4.9 2.2 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.2 34.5 + - - +
66A LYS* 4.3 2.4 + - - +
67A LEU 3.4 0.4 - - - -
68A LEU* 1.3 76.0 - - + +
70A SER* 1.3 72.9 + - - +
160B TYR* 6.0 1.3 - - - +
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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