Contacts of the helix formed by residues 15 - 27 (chain F) in PDB entry 3KHU
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 VAL 15 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F TYR* 1.3 78.4 - - - +
16F GLY* 1.3 64.0 + - - +
17F GLY 3.5 0.2 - - - -
18F PRO* 3.8 0.5 - - - +
19F THR* 2.8 34.5 + - - +
88F SER* 3.9 4.9 - - - +
129F LYS* 3.8 24.9 - - + +
130F SER* 4.0 4.3 - - - +
161F GLN* 3.6 53.2 - - + +
163F LEU* 4.2 7.8 - - + +
502F UPG 2.9 37.8 + - - +
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Residues in contact with GLY 16 (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 CYS* 3.9 9.6 - - - -
11F GLY 3.6 15.9 - - - -
13F GLY 3.6 4.4 + - - +
15F VAL* 1.3 79.2 - - - +
17F GLY* 1.3 63.7 + - - +
19F THR* 4.1 2.0 - - - -
20F CYS* 3.0 30.7 + - - +
34F VAL* 4.7 1.1 - - - +
88F SER* 3.1 19.9 + - - -
129F LYS* 4.9 1.8 - - - -
502F UPG 4.2 1.0 + - - -
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Residues in contact with GLY 17 (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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12F ALA* 4.3 1.2 - - - +
13F GLY 3.3 8.9 + - - +
16F GLY* 1.3 75.7 - - - +
18F PRO* 1.3 64.2 - - - +
20F CYS* 3.8 0.7 - - - +
21F SER* 2.8 37.1 + - - -
34F VAL* 4.6 12.1 - - - +
45F TRP* 3.7 25.4 - - - -
71F PHE* 4.7 2.8 - - - -
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Residues in contact with PRO 18 (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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13F GLY 3.4 6.5 - - - +
14F TYR* 3.1 28.9 - - - +
15F VAL 3.8 0.9 - - - +
17F GLY* 1.3 89.1 - - - +
19F THR* 1.3 62.1 + - - +
21F SER* 3.3 1.2 + - - -
22F VAL* 3.0 28.6 + - - +
45F TRP* 3.9 6.2 - - + -
52F ILE* 4.8 6.7 - - + -
54F GLU* 5.3 2.0 - - + -
57F LEU* 4.0 34.8 - - + -
163F LEU* 4.7 3.8 - - + -
168F ALA* 4.8 12.3 - - + -
169F ILE* 4.9 2.9 - - + +
172F LEU* 3.7 15.0 - - + -
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Residues in contact with THR 19 (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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15F VAL* 2.8 28.8 + - - +
16F GLY 4.1 1.3 - - - -
18F PRO* 1.3 78.1 - - - +
20F CYS* 1.3 60.3 + - - +
22F VAL* 3.2 3.5 + - - +
23F ILE* 3.1 40.7 + - + +
86F PHE* 5.6 0.2 - - + -
129F LYS* 4.0 22.4 - - + +
161F GLN* 5.2 2.1 - - - +
163F LEU* 3.9 9.9 - - - +
172F LEU* 3.7 30.1 - - + +
199F TYR* 4.6 12.1 - - + +
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Residues in contact with CYS 20 (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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7F ILE* 4.5 1.6 - - - -
9F CYS* 3.4 32.5 - - - -
16F GLY 3.0 15.0 + - - +
19F THR* 1.3 75.3 - - - +
21F SER* 1.3 64.2 + - - +
23F ILE* 3.5 6.9 + - - +
24F ALA* 3.1 24.6 + - - +
32F VAL* 3.6 26.0 - - + +
34F VAL* 3.7 13.2 - - + -
69F LEU* 4.5 1.3 - - - -
86F PHE* 3.7 27.1 - - - -
129F LYS* 5.1 4.3 - - - -
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Residues in contact with SER 21 (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 GLY 2.8 24.8 + - - -
18F PRO* 3.6 7.4 - - - -
20F CYS* 1.3 77.9 - - - +
22F VAL* 1.3 62.1 + - - +
24F ALA* 3.3 3.3 + - - +
25F HIS* 3.0 22.7 + - - +
45F TRP* 4.6 0.2 - - - -
57F LEU* 4.5 1.8 - - - -
60F VAL* 3.8 11.8 - - - +
61F VAL* 3.5 27.3 - - - +
64F CYS* 4.2 2.6 - - - -
69F LEU* 3.6 23.0 - - - +
71F PHE* 3.7 9.0 - - - -
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Residues in contact with VAL 22 (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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18F PRO 3.0 17.9 + - - +
19F THR 3.7 6.7 - - - +
21F SER* 1.3 72.0 - - - +
23F ILE* 1.3 67.6 + - - +
25F HIS* 3.1 9.7 + - + +
26F MET* 2.9 36.8 + - + +
60F VAL* 4.2 9.2 - - + -
169F ILE* 3.9 19.3 - - + -
172F LEU* 3.9 34.5 - - + -
173F LYS* 4.4 18.6 - - + -
202F TRP* 4.2 15.9 - - + -
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Residues in contact with ILE 23 (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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7F ILE* 3.9 17.7 - - + -
19F THR* 3.1 29.9 + - + +
20F CYS* 3.7 12.8 - - - +
22F VAL* 1.3 76.0 - - - +
24F ALA* 1.3 56.9 + - - +
26F MET 3.2 0.7 + - - -
27F CYS* 2.8 37.1 + - + +
30F ILE* 5.2 0.4 - - + -
32F VAL* 4.3 7.9 - - + -
86F PHE* 3.7 34.8 - - + -
195F LEU* 6.2 0.2 - - + -
198F VAL* 3.9 26.5 - - + -
199F TYR* 4.8 8.1 - - + +
202F TRP* 3.9 25.4 - - + -
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Residues in contact with ALA 24 (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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20F CYS 3.1 17.9 + - - +
21F SER 3.6 4.7 - - - +
23F ILE* 1.3 78.1 - - - +
25F HIS* 1.3 62.0 + - - +
27F CYS 3.3 10.4 + - - -
28F PRO* 3.8 1.7 - - - +
32F VAL* 3.8 19.7 - - + +
64F CYS* 4.0 2.8 - - - +
68F ASN* 3.0 33.8 + - - +
69F LEU* 3.8 28.0 - - + -
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Residues in contact with HIS 25 (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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21F SER 3.0 13.7 + - - +
22F VAL* 3.1 9.2 + - - +
24F ALA* 1.3 75.9 - - - +
26F MET* 1.3 86.1 + - + +
28F PRO* 4.7 7.4 - - - +
59F GLU 5.6 0.2 - - - -
60F VAL* 3.9 20.3 + - + +
63F SER* 2.9 31.1 + - - -
64F CYS* 3.9 11.3 - - - +
173F LYS* 4.3 19.6 + - - -
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Residues in contact with MET 26 (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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22F VAL* 2.9 23.4 + - + +
23F ILE 4.0 1.3 - - - +
25F HIS* 1.3 92.7 - - + +
27F CYS* 1.3 61.9 + - - +
28F PRO* 3.5 9.1 - - - +
173F LYS* 3.7 43.3 - - + +
201F HIS* 3.8 14.3 - - - +
202F TRP* 3.5 56.5 - - + -
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Residues in contact with CYS 27 (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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23F ILE* 2.8 19.0 + - + +
24F ALA* 3.3 3.8 + - - +
26F MET* 1.3 82.7 - - - +
28F PRO* 1.3 66.9 - - - +
29F GLU* 3.1 9.2 - - - +
30F ILE* 3.0 40.1 + - + +
68F ASN* 3.0 10.0 + - - -
198F VAL* 3.8 15.5 - - - -
201F HIS* 3.6 29.4 - - + -
202F TRP* 4.1 10.1 - - - -
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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