Contacts of the helix formed by residues 9 - 25 (chain D) in PDB entry 6O81
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 SER 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLY* 1.3 71.2 - - - +
10D GLU* 1.3 67.7 + - - +
12D SER* 3.4 3.9 + - - -
13D GLU* 2.9 33.4 + - - +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLY 3.6 2.0 - - - +
9D SER* 1.3 84.1 + - - +
11D LEU* 1.3 57.7 + - - +
13D GLU* 2.9 27.7 - - - +
14D ARG* 3.0 36.4 + - - +
44D GLN* 3.9 17.5 + - - +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLY* 3.8 22.4 + - - +
9D SER 3.3 0.6 - - - -
10D GLU* 1.3 80.9 - - + +
12D SER* 1.3 56.7 + - - +
14D ARG* 3.4 2.6 + - - +
15D ILE* 2.9 39.5 + - + +
41D LEU* 5.0 4.0 - - + +
44D GLN* 3.3 46.9 - - + +
45D ILE* 3.8 16.8 - - + +
48D ASP* 3.7 29.4 - - + +
49D HIS* 3.6 28.3 - - + +
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Residues in contact with SER 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 4.1 14.1 + - - +
8D GLY 3.2 18.4 + - - -
9D SER* 3.4 4.5 + - - -
11D LEU* 1.3 78.7 - - - +
13D GLU* 1.3 57.7 + - - +
15D ILE* 3.4 8.3 + - - +
16D GLU* 2.9 35.0 + - - +
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 4.2 17.7 + - - +
9D SER 2.9 22.0 + - - +
10D GLU* 2.9 40.3 - - - +
12D SER* 1.3 74.3 - - - +
14D ARG* 1.3 67.6 + - - +
16D GLU* 3.5 2.3 + - - +
17D SER* 2.9 32.4 + - - -
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Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLU* 3.0 24.0 + - - +
11D LEU* 3.8 4.9 - - - +
13D GLU* 1.3 83.1 - - - +
15D ILE* 1.3 58.8 + - - +
17D SER* 2.9 10.4 + - - +
18D PHE* 2.9 33.2 + - + +
37D GLU* 4.1 18.4 + - - +
40D GLY* 4.1 3.2 - - - -
41D LEU* 3.5 46.7 - - + +
44D GLN* 3.4 29.5 + - - +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 2.9 27.3 + - + +
12D SER* 3.8 7.0 - - - +
14D ARG* 1.3 75.7 - - - +
16D GLU* 1.3 61.5 + - - +
18D PHE* 3.3 6.7 + - - +
19D VAL* 2.9 30.8 + - + +
41D LEU* 3.9 23.1 - - + -
45D ILE* 3.8 26.9 - - + -
49D HIS* 6.0 2.0 - - + -
64D GLU* 3.6 25.8 - - + +
67D ARG* 3.5 28.5 - - - +
68D MET* 6.3 2.0 - - + -
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 5.8 1.6 - - - +
113A ARG* 5.7 0.2 + - - -
115A THR* 3.4 35.3 - - + +
329A ASP* 4.3 10.0 - - - +
12D SER* 2.9 24.7 + - - +
13D GLU* 3.9 3.1 - - - +
15D ILE* 1.3 79.6 - - - +
17D SER* 1.3 58.9 + - - +
19D VAL* 3.4 6.8 + - - +
20D GLU* 2.9 50.4 + - - +
67D ARG* 2.6 40.7 + - - -
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 6.3 2.9 - - - -
13D GLU* 2.9 20.9 + - - -
14D ARG* 2.9 22.5 + - - +
16D GLU* 1.3 73.2 - - - +
18D PHE* 1.3 55.4 + - - +
20D GLU* 3.8 7.9 - - - +
21D THR* 2.3 41.2 + - - -
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Residues in contact with PHE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 2.9 20.6 + - + +
15D ILE 3.5 4.7 - - - +
17D SER* 1.3 78.3 + - - +
19D VAL* 1.3 57.0 + - + +
21D THR* 3.4 6.2 + - - -
22D LEU* 3.0 61.7 + - + +
34D MET* 4.9 1.6 - - + -
37D GLU* 3.2 40.8 - - + -
38D THR* 3.7 14.1 - - + -
41D LEU* 3.7 26.2 - - + -
68D MET* 3.8 27.1 - - + -
78D VAL* 3.7 23.3 - - + -
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 2.9 23.2 + - + +
16D GLU* 3.8 9.4 - - - +
18D PHE* 1.3 76.2 - - + +
20D GLU* 1.3 60.5 + - + +
22D LEU* 3.4 1.5 + - - -
23D LYS* 2.9 48.7 + - + +
67D ARG* 4.0 45.8 - - + +
68D MET* 4.8 15.3 - - + -
71D ALA* 3.7 21.6 - - + +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 5.9 0.7 - - - +
110A LYS* 4.6 26.1 + - - +
115A THR 5.4 2.6 - - - +
116A SER* 5.8 2.8 - - - -
117A LEU* 3.3 20.0 + - - +
16D GLU* 2.9 38.5 + - - +
17D SER* 4.0 6.8 - - - +
19D VAL* 1.3 80.2 - - + +
21D THR* 1.3 57.2 + - - +
23D LYS* 3.6 10.4 - - + +
24D ARG* 2.9 69.5 + - - +
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Residues in contact with THR 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D SER* 2.3 30.6 + - - -
18D PHE* 3.8 7.1 - - - -
20D GLU* 1.3 75.4 - - - +
22D LEU* 1.3 63.6 + - - +
24D ARG* 4.7 3.4 - - - +
25D GLY 2.9 27.5 + - - +
27D GLY* 3.8 31.7 + - - +
37D GLU* 5.9 0.9 - - - +
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.0 53.2 + - + +
19D VAL* 3.8 3.6 - - - +
21D THR* 1.3 76.4 - - - +
23D LYS* 1.3 59.7 + - - +
25D GLY 4.0 7.2 - - - +
27D GLY 4.0 13.5 - - - +
34D MET* 4.0 28.5 - - + -
68D MET* 4.2 13.5 - - + +
71D ALA* 4.2 10.1 - - + -
72D GLN* 3.0 38.2 + - + +
75D GLU* 4.8 7.9 - - + -
78D VAL* 4.0 22.0 - - + -
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 5.6 1.7 - - - +
319A TYR* 5.8 0.7 + - - -
320A PRO* 4.3 8.0 - - - +
325A ALA* 4.2 16.7 - - + +
326A ASN* 3.3 27.1 + - - +
327A PHE* 4.5 11.6 + - + +
329A ASP* 3.5 20.0 + - - -
19D VAL* 2.9 35.5 + - + +
20D GLU* 3.2 11.9 + - + +
22D LEU* 1.3 77.2 - - - +
24D ARG* 1.3 67.9 + - + +
70D ALA 4.5 3.1 - - - -
71D ALA* 3.4 34.9 - - - +
72D GLN* 4.2 7.3 + - - -
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Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 4.0 18.1 + - - +
84A THR* 2.7 48.9 + - - -
85A ALA* 4.0 21.2 + - + +
110A LYS* 5.7 1.2 - - - +
117A LEU* 3.8 14.5 - - - +
319A TYR* 5.3 4.2 + - - -
320A PRO* 3.3 33.7 - - + +
20D GLU* 2.9 56.3 + - - +
21D THR* 4.7 2.7 - - - +
23D LYS* 1.3 82.7 - - + +
25D GLY* 1.3 58.8 + - - +
72D GLN* 5.5 1.5 + - - -
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Residues in contact with GLY 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D THR 2.9 17.8 + - - +
22D LEU* 4.0 10.6 - - - +
24D ARG* 1.3 82.1 - - - +
26D GLY* 1.3 61.1 + - - -
27D GLY 3.4 1.7 + - - -
72D GLN* 5.1 3.8 + - - -
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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