Contacts of the helix formed by residues 10 - 26 (chain A) in PDB entry 6OZE
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PRO* 1.3 93.1 - - + +
11A GLU* 1.3 65.5 + - + +
12A GLU* 4.1 10.5 - - + +
13A THR* 3.1 27.9 + - - +
14A LEU* 3.3 11.1 + - - +
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Residues in contact with GLU 11 (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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9A PRO 3.7 1.0 + - - -
10A PRO* 1.3 73.3 - - + +
12A GLU* 1.3 62.1 + - + +
14A LEU* 3.3 9.1 + - - +
15A SER* 2.9 29.7 + - - -
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Residues in contact with GLU 12 (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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10A PRO* 3.2 7.8 - - + +
11A GLU* 1.3 85.5 - - + +
13A THR* 1.3 57.1 + - - +
15A SER* 3.4 7.3 + - - -
16A LEU* 3.0 47.7 + - + +
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Residues in contact with THR 13 (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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9A PRO* 4.2 14.6 - - + -
10A PRO* 3.1 31.4 + - - +
12A GLU* 1.3 75.9 + - - +
14A LEU* 1.3 61.5 + - - +
16A LEU* 3.3 6.1 + - - +
17A TRP* 2.8 59.3 + - + +
90A PRO* 5.0 2.7 - - + -
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Residues in contact with LEU 14 (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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9A PRO* 4.2 12.1 - - + +
10A PRO 3.3 9.3 + - - +
11A GLU* 3.8 10.1 - - - +
13A THR* 1.3 78.6 - - - +
15A SER* 1.3 58.0 + - - +
17A TRP* 3.3 27.9 + - + +
18A LYS* 2.8 48.9 + - - +
92A VAL* 3.9 38.8 - - + -
95A PHE* 4.0 13.6 - - + -
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Residues in contact with SER 15 (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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11A GLU 2.9 17.5 + - - -
12A GLU* 3.7 8.1 - - - -
14A LEU* 1.3 77.9 - - - +
16A LEU* 1.3 62.7 + - - +
18A LYS* 3.4 12.0 + - - +
19A ARG* 3.0 27.0 + - - +
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Residues in contact with LEU 16 (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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12A GLU* 3.0 39.2 + - + +
13A THR* 4.0 4.9 - - - +
15A SER* 1.3 77.6 - - - +
17A TRP* 1.3 64.9 + - + +
19A ARG* 3.3 29.7 + - + +
20A GLU* 2.9 28.8 + - - +
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Residues in contact with TRP 17 (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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13A THR* 2.8 33.4 + - + +
14A LEU* 3.6 29.6 - - + +
16A LEU* 1.3 76.1 - - + +
18A LYS* 1.3 60.7 + - - +
20A GLU* 3.2 1.9 + - + -
21A GLN* 2.9 32.6 + - - +
89A ALA* 4.2 13.0 - - + -
90A PRO* 3.5 44.0 - - + -
92A VAL* 4.3 6.7 - - + -
95A PHE* 3.7 36.8 - - + -
98A PHE* 3.3 53.7 - + + -
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Residues in contact with LYS 18 (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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14A LEU* 2.8 35.7 + - - +
15A SER* 3.5 9.3 - - - +
17A TRP* 1.3 71.4 - - - +
19A ARG* 1.3 63.8 + - - +
21A GLN* 3.3 11.7 + - - +
22A ALA* 3.0 22.2 + - - +
95A PHE* 3.5 23.1 - - + -
134A ARG* 3.7 34.3 - - - +
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Residues in contact with ARG 19 (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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15A SER 3.0 16.9 + - - +
16A LEU* 3.6 26.8 - - + +
17A TRP 3.2 0.2 - - - -
18A LYS* 1.3 76.7 - - - +
20A GLU* 1.3 57.7 + - - +
22A ALA* 3.3 8.3 + - + +
23A ARG* 2.9 27.5 + - - +
302A ACT 2.9 46.6 + - + +
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Residues in contact with GLU 20 (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 LEU 2.9 16.8 + - - +
17A TRP* 3.2 5.1 + - + +
19A ARG* 1.3 76.5 - - - +
21A GLN* 1.3 65.8 + - - +
23A ARG* 2.7 49.7 + - - +
24A LEU* 3.0 41.9 + - + +
98A PHE* 4.1 20.9 - - + -
141A HIS* 5.2 0.2 - - - +
145A LEU* 5.6 0.7 - - - +
302A ACT 5.3 0.5 - - - +
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Residues in contact with GLN 21 (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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17A TRP 2.9 12.6 + - - +
18A LYS* 3.3 7.6 + - - +
20A GLU* 1.3 76.1 - - - +
22A ALA* 1.3 56.9 + - - +
24A LEU* 3.3 0.8 + - - -
25A LYS* 2.8 33.9 + - - +
94A GLY 3.0 25.9 + - - -
95A PHE* 3.4 23.0 - - - +
97A ALA* 5.8 2.2 - - - +
98A PHE* 3.6 18.3 - - + -
132A HIS* 4.1 1.6 - - - -
134A ARG* 3.0 40.0 + - + -
136A PHE* 3.9 41.5 + - + -
141A HIS* 4.9 2.2 + - + -
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Residues in contact with ALA 22 (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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18A LYS 3.0 13.3 + - - +
19A ARG* 3.6 11.7 - - + +
21A GLN* 1.3 76.0 - - - +
23A ARG* 1.3 64.5 + - - +
25A LYS* 3.9 8.8 - - - +
26A ALA* 3.4 20.4 + - - +
134A ARG* 5.6 2.4 - - - +
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Residues in contact with ARG 23 (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 ARG 2.9 17.5 + - - +
20A GLU* 2.7 43.9 + - - +
22A ALA* 1.3 78.5 - - - +
24A LEU* 1.3 78.2 + - + +
26A ALA* 3.6 9.9 + - - +
27A HIS* 3.2 29.0 + - + -
145A LEU* 5.5 3.8 - - - +
302A ACT 3.6 37.7 - - + +
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Residues in contact with LEU 24 (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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20A GLU* 3.0 35.0 + - - +
23A ARG* 1.3 101.4 - - - +
25A LYS* 1.3 61.4 + - - +
26A ALA 3.1 2.2 - - - -
27A HIS* 2.9 34.6 + - + +
28A VAL 3.7 2.4 + - - -
136A PHE* 3.4 20.6 - - + -
141A HIS* 3.5 37.7 - - + +
144A VAL* 4.0 10.6 - - + +
145A LEU* 4.3 23.3 - - + -
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Residues in contact with LYS 25 (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 GLN 2.8 23.2 + - - +
22A ALA* 3.9 8.3 - - - +
23A ARG 3.4 0.4 - - - -
24A LEU* 1.3 72.7 - - - +
26A ALA* 1.3 61.5 + - - +
27A HIS 3.0 0.2 - - - -
28A VAL* 3.1 21.2 + - + +
130A VAL* 6.2 0.2 - - - -
134A ARG* 3.0 28.7 + - + +
135A GLY* 3.6 23.2 - - - +
136A PHE* 3.7 24.6 - - + -
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Residues in contact with ALA 26 (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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22A ALA 3.4 9.5 + - - +
23A ARG* 3.7 12.8 - - - +
24A LEU 3.1 1.2 - - - -
25A LYS* 1.3 76.8 - - - +
27A HIS* 1.3 63.2 + - + +
28A VAL 3.5 3.6 + - - +
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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