Contacts of the helix formed by residues 6 - 21 (chain K) in PDB entry 5O6I
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 6 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5K GLU* 1.3 76.7 - - - +
7K VAL* 1.3 63.1 + - + +
8K SER 3.4 1.1 - - - -
9K GLY* 3.4 0.3 + - - -
10K ILE* 3.1 38.3 + - - +
58K PHE* 4.2 19.6 - - - -
104K ARG* 2.7 20.3 + - - +
182K LEU 3.5 4.3 - - - +
183K ASN* 3.3 36.5 + - - +
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Residues in contact with VAL 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K GLU* 2.5 35.2 + - + +
6K ASN* 1.3 73.6 - - + +
8K SER* 1.3 53.0 + - - +
10K ILE* 3.4 2.6 + - - +
11K SER* 2.7 36.9 + - - +
58K PHE* 4.5 15.5 - - + -
59K LEU* 4.2 22.0 - - + +
62K GLU* 4.1 36.6 - - + +
63K LEU* 5.2 5.8 - - + -
90K TYR* 4.4 5.2 - - - +
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Residues in contact with SER 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K GLU* 3.4 25.5 - - - +
7K VAL* 1.3 77.2 - - - +
9K GLY* 1.3 61.8 + - - +
11K SER* 3.6 10.2 - - - -
12K ALA* 3.0 27.7 + - - +
90K TYR* 4.9 2.2 - - - -
94K MET* 4.0 4.6 - - - +
102K ASN* 5.2 2.1 + - - -
104K ARG* 3.9 2.9 + - - -
105K GLU* 3.3 31.2 + - - +
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Residues in contact with GLY 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ASN 3.8 0.4 - - - -
7K VAL 3.2 0.2 - - - -
8K SER* 1.3 74.3 + - - +
10K ILE* 1.3 64.7 + - - +
12K ALA* 3.3 2.2 + - - -
13K TYR* 3.1 19.1 + - - +
104K ARG* 2.9 35.0 - - - +
105K GLU* 5.0 3.4 - - - -
108K ALA* 3.3 20.6 - - - +
182K LEU* 5.1 8.1 - - - -
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Residues in contact with ILE 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ASN* 3.1 28.9 + - - +
7K VAL 3.9 3.1 - - - +
9K GLY* 1.3 74.2 - - - +
11K SER* 1.3 57.3 + - - +
13K TYR* 3.4 6.8 + - + +
14K LEU* 2.9 46.1 + - + +
55K LEU* 3.8 42.2 - - + +
58K PHE* 3.6 35.9 - - + -
59K LEU* 5.5 3.8 - - + -
182K LEU 5.2 1.1 + - - +
183K ASN* 4.6 14.1 - - + -
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Residues in contact with SER 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K VAL 2.7 24.6 + - - -
8K SER* 3.6 8.5 - - - -
9K GLY 3.2 0.2 - - - -
10K ILE* 1.3 78.2 - - - +
12K ALA* 1.3 56.5 + - - +
14K LEU* 3.4 1.5 + - - -
15K LEU* 2.9 28.4 + - - +
59K LEU* 3.6 13.6 - - - +
90K TYR* 2.6 35.1 + - - -
91K PHE* 3.7 11.5 - - - -
94K MET* 3.8 17.4 - - - +
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Residues in contact with ALA 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K SER 3.0 17.8 + - - +
9K GLY 3.3 4.7 + - - +
11K SER* 1.3 73.9 - - - +
13K TYR* 1.3 66.0 + - - +
15K LEU* 3.2 5.3 + - - +
16K GLY 3.0 18.0 + - - -
94K MET* 3.5 13.0 - - + +
101K CYS* 5.7 1.8 - - - -
105K GLU* 3.3 37.7 - - + +
108K ALA* 3.9 2.7 - - + -
109K PHE* 3.5 17.3 - - + +
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Residues in contact with TYR 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K GLY 3.1 16.3 + - - +
10K ILE* 3.8 7.9 - - + +
12K ALA* 1.3 77.0 - - - +
14K LEU* 1.3 65.5 + - + +
16K GLY* 3.2 3.5 + - - -
17K LEU* 3.2 43.9 + - + +
52K PHE* 4.0 17.5 - + - -
55K LEU* 3.7 30.3 - - + -
108K ALA* 3.3 20.8 + - + +
111K LYS* 3.9 36.6 - - + -
112K GLY* 3.6 30.3 - - - -
115K VAL* 4.0 14.0 - - + +
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Residues in contact with LEU 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ILE* 2.9 30.1 + - + +
11K SER 3.8 3.6 - - - +
13K TYR* 1.3 81.5 - - + +
15K LEU* 1.3 58.1 + - - +
17K LEU* 3.1 22.4 + - + +
18K ILE* 2.8 36.0 + - + +
40K ILE* 4.4 5.7 - - + +
52K PHE 4.5 5.8 - - - +
55K LEU* 4.0 24.7 - - + +
56K MET* 4.0 37.9 - - + +
59K LEU* 3.9 25.8 - - + -
91K PHE* 4.1 10.1 - - + -
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Residues in contact with LEU 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K SER 2.9 18.1 + - - +
12K ALA* 3.6 6.1 - - - +
14K LEU* 1.3 76.3 - - - +
16K GLY* 1.3 57.1 + - - +
18K ILE* 4.1 8.7 - - + +
19K ILE* 2.8 58.6 + - + +
24K LEU* 4.6 5.8 - - + -
91K PHE* 4.0 32.3 - - + +
94K MET* 4.0 30.1 - - + +
95K LEU* 4.2 18.4 - - + +
98K ILE* 4.7 7.6 - - + -
101K CYS* 6.5 0.4 - - - -
109K PHE* 4.1 15.3 - - + -
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Residues in contact with GLY 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ALA 3.0 10.9 + - - -
13K TYR 3.2 4.2 + - - -
15K LEU* 1.3 77.4 - - - +
17K LEU* 1.3 55.7 + - - +
19K ILE* 4.7 0.7 - - - -
20K GLY* 3.0 24.8 + - - -
109K PHE* 3.7 21.9 - - - -
112K GLY 3.6 11.6 - - - +
113K LEU* 3.7 22.1 - - - +
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Residues in contact with LEU 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K TYR* 3.2 31.3 + - + +
14K LEU* 3.1 14.5 + - + +
16K GLY* 1.3 74.8 - - - +
18K ILE* 1.3 58.9 + - - +
21K ASP* 2.6 37.7 + - + +
22K GLY 3.5 0.5 + - - -
40K ILE* 3.8 23.5 - - + +
52K PHE* 3.5 39.9 - - + -
112K GLY* 3.4 22.0 - - - +
115K VAL* 3.7 26.5 - - + -
116K ALA* 4.3 7.4 - - + +
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Residues in contact with ILE 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LEU 2.8 24.1 + - - +
15K LEU* 3.8 5.6 - - + +
17K LEU* 1.3 75.1 - - - +
19K ILE* 1.3 65.8 + - + +
22K GLY 2.9 29.5 + - - +
23K GLY* 3.1 27.8 + - - +
24K LEU* 3.7 20.2 - - + -
38K VAL* 3.6 23.8 - - + -
39K VAL 3.7 10.8 - - - +
40K ILE* 3.6 19.3 - - + -
56K MET* 4.4 5.6 - - + -
91K PHE* 3.7 31.0 - - + -
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Residues in contact with ILE 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 2.8 43.9 + - + +
16K GLY* 4.2 2.7 - - - +
18K ILE* 1.3 77.8 - - + +
20K GLY* 1.3 63.8 + - - +
22K GLY 4.5 3.8 - - - +
23K GLY* 5.5 2.5 - - - -
24K LEU* 4.8 5.6 - - + +
95K LEU* 3.7 34.3 - - + -
109K PHE* 4.4 9.6 - - + -
113K LEU* 4.4 6.3 - - + -
117K GLU* 4.4 0.3 - - - +
129K ASN* 4.7 5.2 + - - +
131K ASN* 6.3 0.2 - - - +
134K LEU* 3.6 31.2 - - + -
202K MN 4.0 6.1 + - - -
15L G 5.2 0.5 - - - +
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Residues in contact with GLY 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K GLY 3.0 17.6 + - - -
17K LEU 3.6 1.3 - - - -
19K ILE* 1.3 78.3 - - - +
21K ASP* 1.3 62.4 - - - +
113K LEU* 4.2 1.8 - - - +
116K ALA* 3.6 5.6 - - - -
117K GLU* 3.5 23.8 - - - -
202K MN 2.4 27.4 + - - -
15L G 3.0 8.0 + - - +
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Residues in contact with ASP 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K LEU* 2.6 17.2 + - + +
20K GLY* 1.3 73.1 - - - +
22K GLY* 1.3 53.1 + - - -
40K ILE* 4.4 6.3 - - + -
41K THR* 2.6 48.5 + - - +
42K GLN* 2.6 22.0 + - - +
115K VAL* 5.9 0.2 - - - +
116K ALA* 3.3 22.3 - - + +
117K GLU* 4.0 0.2 - - - +
201K MN 2.6 35.3 + - - -
14L A 3.6 11.3 - - - +
15L G 3.5 10.2 + - - -
16N C 3.4 5.7 + - - -
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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