Contacts of the helix formed by residues 12 - 20 (chain A) in PDB entry 1ORB
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 THR 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 1.3 73.7 - - - +
13A LYS* 1.3 65.8 + - - +
15A LEU* 3.1 4.1 + - - +
16A ALA* 2.8 26.0 + - - +
126A LEU* 3.7 22.4 - - + +
127A ASN 4.3 13.1 + - - +
129A GLY 4.7 1.8 - - - +
132A ASN* 4.5 3.6 - - + -
133A TRP* 3.7 32.4 - - + +
136A GLU* 3.3 32.0 + - - +
138A HIS* 3.9 5.8 - - - -
221A PHE* 5.1 4.5 - - - -
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Residues in contact with LYS 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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11A SER* 3.2 8.6 + - - +
12A THR* 1.3 82.2 + - - +
14A TRP* 1.4 54.1 + - + +
16A ALA* 3.2 6.0 + - - +
17A GLU* 2.9 56.3 + - + +
138A HIS* 4.7 7.5 - - + +
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Residues in contact with TRP 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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7A ARG* 3.6 33.1 - - - +
10A VAL* 3.6 25.4 - - + -
11A SER* 3.2 25.3 + - - +
13A LYS* 1.4 79.8 - - + +
15A LEU* 1.3 68.5 + - + +
17A GLU* 3.6 7.5 + - - +
18A SER* 2.4 47.0 + - - -
28A LEU* 4.1 21.5 - - + -
94A HIS* 3.6 22.0 - + - -
96A VAL* 3.9 22.9 - - + -
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Residues in contact with LEU 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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10A VAL* 5.2 0.2 - - + -
11A SER 3.0 12.4 + - - +
12A THR 3.5 3.1 - - - +
14A TRP* 1.3 91.7 - - + +
16A ALA* 1.3 68.2 + - - +
18A SER* 3.1 5.6 + - - -
19A VAL* 3.0 38.9 + - + +
28A LEU* 5.1 4.3 - - + -
30A VAL* 4.3 35.2 - - + -
52A VAL* 4.8 4.9 - - + -
96A VAL* 4.4 10.8 - - + -
126A LEU* 3.5 36.8 - - + -
133A TRP* 3.4 22.0 - - + -
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Residues in contact with ALA 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 THR 2.8 17.0 + - - +
13A LYS* 3.4 5.4 - - - +
15A LEU* 1.3 76.2 - - - +
17A GLU* 1.3 67.5 + - + +
18A SER 3.0 0.3 + - - -
19A VAL* 3.1 5.4 + - - +
20A ARG* 3.0 29.3 + - + +
133A TRP* 3.6 15.7 - - + -
138A HIS* 3.7 28.7 - - + +
139A PRO* 5.0 5.2 - - + -
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Residues in contact with GLU 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 LYS* 2.9 47.7 + - + +
14A TRP* 4.2 6.7 - - - +
15A LEU 3.4 0.2 - - - -
16A ALA* 1.3 75.4 - - + +
18A SER* 1.3 57.8 + - - +
20A ARG* 3.2 41.9 + - - +
21A ALA* 2.7 30.6 + - + +
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Residues in contact with SER 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 TRP* 2.4 41.5 + - - -
15A LEU* 3.1 6.7 + - - -
16A ALA 3.1 1.0 - - - -
17A GLU* 1.3 74.5 - - - +
19A VAL* 1.3 59.7 - - - +
21A ALA* 3.2 0.4 + - - -
22A GLY 3.1 2.6 + - - -
23A LYS* 2.4 61.7 + - - +
24A VAL* 4.7 1.1 - - - -
28A LEU* 3.9 17.9 - - - -
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Residues in contact with VAL 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 LEU* 3.0 31.6 + - + +
16A ALA* 3.4 6.5 - - - +
18A SER* 1.3 77.2 - - - +
20A ARG* 1.3 55.9 + - + +
22A GLY* 2.5 29.3 + - - -
24A VAL* 4.0 22.2 - - + +
52A VAL* 4.2 16.2 - - + -
53A PRO* 4.3 31.9 - - + +
133A TRP* 4.3 6.1 - - + -
139A PRO* 5.0 10.3 - - + -
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Residues in contact with ARG 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 ALA* 3.0 14.6 + - + +
17A GLU* 3.5 44.6 + - - +
19A VAL* 1.3 85.2 - - + +
21A ALA* 1.3 59.3 + - - +
22A GLY* 3.0 4.3 + - - -
139A PRO* 5.7 8.7 - - + -
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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