Contacts of the helix formed by residues 58 - 72 (chain F) in PDB entry 2F9K
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 TYR 58 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 4.2 11.2 - - + -
17F PHE* 3.8 19.3 - + + -
18F VAL* 3.8 35.2 - - + +
53F ALA 3.4 20.9 - - - -
54F ILE* 3.4 19.6 - - + +
55F GLY* 2.7 22.9 + - - -
56F GLY* 3.5 25.3 - - - -
57F LYS* 1.3 84.9 - - - +
59F ASN* 1.3 59.1 + - - +
60F ARG 3.2 3.3 + - - -
61F GLY 3.3 0.9 + - - -
62F LEU* 2.8 32.6 + - + +
90F TRP* 3.8 15.5 - + - -
93F GLU* 3.2 26.8 + - - -
113F ARG* 5.6 0.7 - - - -
5001F PO4 4.2 4.2 + - - -
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Residues in contact with ASN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TYR* 3.7 9.2 - - + -
57F LYS* 3.1 40.0 - - + +
58F TYR* 1.3 78.1 - - - +
60F ARG* 1.3 62.8 + - + +
62F LEU* 4.4 6.2 - - - +
63F THR* 2.7 37.7 + - - -
93F GLU* 4.0 0.2 + - - -
344F LEU* 6.4 1.3 - - + -
347F LYS* 3.2 44.7 + - + +
5001F PO4 5.3 0.8 + - - +
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Residues in contact with ARG 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F LYS* 6.0 0.6 - - - +
58F TYR 3.2 0.8 - - - -
59F ASN* 1.3 84.9 - - + +
61F GLY* 1.3 63.7 + - - +
63F THR* 3.3 19.9 + - - -
64F VAL* 3.6 2.6 + - - +
92F VAL* 3.9 17.3 - - + -
93F GLU* 3.5 8.8 + - - +
96F GLN* 3.0 38.5 - - - +
201F THR* 5.6 0.6 - - - +
204F TYR* 3.8 18.4 + - - -
205F SER* 3.0 44.4 + - - +
206F PHE* 6.5 0.2 - - - -
209F PRO* 3.5 16.2 - - + +
239F PHE* 3.3 37.2 - - - -
5001F PO4 3.6 22.6 + - - -
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Residues in contact with GLY 61 (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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17F PHE* 4.0 9.0 - - - -
58F TYR 3.8 0.7 - - - -
60F ARG* 1.3 74.6 - - - +
62F LEU* 1.3 63.4 + - - +
64F VAL* 3.1 20.3 + - - +
65F VAL* 3.4 6.8 + - - +
89F GLY* 3.4 32.8 - - - -
92F VAL* 4.5 1.7 - - - +
93F GLU* 2.8 20.2 + - - -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TYR* 3.6 32.1 - - + +
13F GLU* 3.9 11.2 - - + +
14F LYS* 3.5 39.9 - - + +
17F PHE* 3.5 38.3 - - + -
57F LYS 4.0 14.1 - - - +
58F TYR* 2.8 21.5 + - + +
59F ASN* 3.8 4.9 - - - +
61F GLY* 1.3 75.0 - - - +
63F THR* 1.3 57.9 + - - +
65F VAL* 3.1 7.0 + - + +
66F VAL* 2.8 35.0 + - + +
347F LYS* 5.8 0.4 - - - -
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Residues in contact with THR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TYR* 3.0 27.7 + - - +
59F ASN* 2.7 19.6 + - - +
60F ARG* 3.4 12.3 - - - -
61F GLY 3.1 0.2 - - - -
62F LEU* 1.3 78.2 - - - +
64F VAL* 1.3 58.0 + - - +
66F VAL* 3.9 0.8 - - - +
67F ALA* 2.9 30.0 + - - +
206F PHE 5.7 0.2 - - - +
209F PRO* 3.9 15.0 - - + -
210F ILE* 3.5 29.6 - - + +
340F VAL 6.0 0.2 - - - +
344F LEU* 3.4 19.1 - - + +
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ARG 3.9 2.2 - - - +
61F GLY 3.1 10.9 + - - +
63F THR* 1.3 78.5 - - - +
65F VAL* 1.3 56.6 + - - +
68F PHE* 3.0 29.2 + - + +
85F ALA* 3.6 21.3 - - + +
88F VAL* 4.1 13.0 - - + +
89F GLY* 3.8 10.8 - - - +
92F VAL* 3.7 23.1 - - + -
209F PRO* 3.6 37.9 - - + +
212F ALA* 4.6 2.7 - - + -
213F ALA* 3.7 12.3 - - + +
216F MET* 4.8 6.1 - - - -
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Residues in contact with VAL 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 3.8 34.3 - - + +
17F PHE* 3.9 25.6 - - + -
61F GLY 3.4 12.5 + - - +
62F LEU* 3.1 9.3 + - + +
64F VAL* 1.3 74.5 - - - +
66F VAL* 1.3 66.8 + - - +
68F PHE* 3.2 7.9 + - + +
69F ARG* 3.0 27.8 + - + +
82F LEU* 6.1 2.5 - - + -
85F ALA* 4.2 8.3 - - + +
86F TRP* 4.0 24.9 - - + +
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 3.8 40.6 - - + +
10F TYR* 4.1 32.5 - - + +
13F GLU* 4.2 13.0 - - + -
62F LEU 2.8 23.6 + - - +
63F THR* 3.9 3.6 - - - +
65F VAL* 1.3 74.0 - - - +
67F ALA* 1.3 62.8 + - - +
69F ARG* 3.3 8.1 + - - +
70F GLU* 3.1 45.2 + - - +
340F VAL* 6.0 1.6 - - - +
343F GLY* 6.3 0.4 - - - -
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Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F THR 2.9 19.4 + - - +
66F VAL* 1.3 76.8 - - - +
68F PHE* 1.3 58.5 + - - +
70F GLU* 3.2 10.9 + - - -
71F LEU* 2.9 42.2 + - + +
210F ILE* 3.9 23.8 - - + -
213F ALA* 3.5 20.4 - - + -
340F VAL* 4.5 6.7 - - + -
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Residues in contact with PHE 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 VAL* 3.0 21.9 + - + +
65F VAL* 3.4 6.5 - - + +
66F VAL 3.2 0.2 - - - -
67F ALA* 1.3 77.0 - - - +
69F ARG* 1.3 62.4 + - + +
71F LEU* 4.7 2.9 - - - -
72F VAL* 2.9 64.7 + - + +
77F GLN* 4.4 10.3 - - + -
81F SER* 3.7 32.5 - - - -
82F LEU* 3.9 24.9 - - + -
85F ALA* 3.5 26.5 - - + -
213F ALA* 3.7 10.5 - - + +
216F MET* 4.1 32.1 - - + -
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Residues in contact with ARG 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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9F VAL* 6.4 2.0 - - + -
13F GLU* 2.9 40.6 + - - +
16F ASP* 5.4 4.8 + - - -
65F VAL* 3.0 15.5 + - + +
66F VAL* 3.3 8.3 + - - +
68F PHE* 1.3 78.3 - - + +
70F GLU* 1.3 61.9 + - + +
72F VAL 3.6 2.6 - - - +
74F PRO* 5.8 0.5 - - - +
77F GLN* 3.0 44.2 + - - +
82F LEU* 3.2 45.2 - - + +
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Residues in contact with GLU 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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9F VAL* 4.2 14.4 - - + +
66F VAL* 3.1 36.7 + - + +
67F ALA* 3.2 5.2 + - - +
69F ARG* 1.3 79.0 - - + +
71F LEU* 1.3 60.2 + - - +
72F VAL 4.7 0.7 - - - -
337F PRO* 3.7 22.2 - - + +
339F ALA* 4.3 17.2 - - + +
340F VAL* 3.1 42.4 - - + +
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Residues in contact with LEU 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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67F ALA* 2.9 32.4 + - + +
68F PHE* 4.1 2.0 - - - +
70F GLU* 1.3 80.1 - - - +
72F VAL* 1.3 63.4 + - - +
73F GLU 3.9 1.2 + - - -
210F ILE* 5.5 1.8 - - + -
213F ALA* 4.1 4.7 - - + -
214F MET* 3.9 39.9 - - + +
217F ALA* 3.8 18.9 - - + +
219F ILE* 4.0 8.0 - - + +
336F LEU* 3.7 30.3 - - + -
337F PRO* 3.8 19.3 - - + -
340F VAL* 4.3 11.2 - - + -
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Residues in contact with VAL 72 (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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68F PHE* 2.9 49.5 + - + +
69F ARG 3.6 4.0 - - - +
70F GLU 4.7 0.9 - - - -
71F LEU* 1.3 77.2 - - - +
73F GLU* 1.3 70.7 + - - +
74F PRO* 3.5 1.9 - - - +
76F LYS* 3.6 21.5 - - + +
77F GLN* 2.7 40.7 + - + -
216F MET 4.4 1.8 - - - +
217F ALA* 3.9 26.0 - - + -
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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