Contacts of the helix formed by residues 12 - 21 (chain B) in PDB entry 1S13
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 ASP 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B PRO 4.3 0.3 - - - -
11B GLN* 1.3 106.8 + - - +
13B LEU* 1.3 60.5 + - - +
14B SER* 4.2 6.3 - - - +
15B GLU* 3.3 20.5 + - + +
16B ALA* 2.9 24.4 + - - +
187B ASN* 3.6 31.1 + - - +
196B ARG* 3.3 3.3 + - - -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN 3.8 0.2 + - - -
12B ASP* 1.3 71.0 - - - +
14B SER* 1.3 63.5 + - - +
16B ALA* 3.1 3.7 + - + +
17B LEU* 3.1 48.1 + - + +
130B VAL* 5.1 4.0 - - + -
186B MET* 3.2 36.6 - - + +
187B ASN* 3.0 14.6 + - - +
189B LEU* 4.5 8.5 - - + +
191B MET* 4.3 22.4 - - + -
196B ARG* 3.6 39.0 - - + +
199B VAL* 4.6 13.5 - - + -
200B ILE* 4.9 5.6 - - + -
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP* 4.2 3.1 - - - +
13B LEU* 1.3 77.2 - - - +
15B GLU* 1.3 61.0 + - - +
17B LEU* 3.1 12.8 + - - +
18B LYS* 3.0 30.3 + - - +
134B TYR* 4.6 3.2 + - - -
183B ARG* 3.8 38.4 - - - +
186B MET* 4.0 11.4 - - - +
187B ASN* 2.9 26.4 + - - -
300B 2FH 4.9 1.3 - - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 3.5 27.5 - - + +
11B GLN* 4.9 3.3 + - - +
12B ASP* 3.3 26.4 + - + +
14B SER* 1.3 84.6 + - - +
16B ALA* 1.3 61.7 + - - +
17B LEU 3.2 0.7 + - - -
18B LYS* 3.4 13.7 + - + +
19B GLU* 3.4 23.9 + - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.2 23.5 - - + +
12B ASP 2.9 7.4 + - - +
13B LEU* 3.1 6.3 + - - +
15B GLU* 1.3 75.8 - - - +
17B LEU* 1.3 58.1 + - - +
19B GLU* 4.2 1.5 - - - +
20B ALA* 3.3 25.0 + - - +
196B ARG* 3.4 30.5 - - - +
200B ILE* 3.7 22.9 - - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.1 39.9 + - + +
14B SER* 3.5 7.2 - - - +
15B GLU 3.0 0.6 - - - -
16B ALA* 1.3 78.6 - - - +
18B LYS* 1.3 52.5 + - - +
19B GLU 2.8 10.6 + - - -
20B ALA* 4.4 1.3 - - - +
21B THR* 2.5 37.4 + - + -
130B VAL* 6.4 1.1 - - + -
131B ALA* 5.8 2.7 - - + -
134B TYR* 3.8 37.0 - - + +
186B MET* 4.3 11.9 - - - -
199B VAL* 4.8 8.3 - - + +
200B ILE* 4.2 23.3 - - + +
203B ALA* 3.8 29.2 - - + -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B SER 3.0 15.5 + - - +
15B GLU* 3.4 14.3 + - + +
17B LEU* 1.3 74.6 - - - +
19B GLU* 1.3 57.2 + - - +
21B THR* 4.1 5.8 - - - -
22B LYS* 3.5 15.9 + - - +
134B TYR* 3.8 6.7 + - - -
183B ARG* 4.8 10.3 - - - +
300B 2FH 2.7 79.6 + - + +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.0 35.0 - - + +
15B GLU 3.4 13.4 + - - +
16B ALA 4.5 0.4 - - - +
17B LEU 2.8 0.2 - - - -
18B LYS* 1.3 79.9 - - - +
20B ALA* 1.3 61.6 + - - +
21B THR 3.0 8.4 + - - -
22B LYS* 3.4 15.9 + - + +
23B GLU* 4.2 4.7 + - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.3 19.3 + - - +
17B LEU* 3.4 4.1 + - - +
19B GLU* 1.3 78.2 - - - +
21B THR* 1.3 60.4 + - + +
23B GLU* 4.6 9.7 - - - +
24B VAL* 4.7 1.0 - - - +
200B ILE* 3.4 13.5 - - + -
204B LYS* 3.1 48.7 - - - +
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 2.5 25.9 + - - +
18B LYS* 4.1 4.9 - - - -
20B ALA* 1.3 86.0 - - + +
22B LYS* 1.3 63.4 + - - +
23B GLU 2.7 6.6 + - - -
24B VAL* 3.2 8.5 + - + +
25B HIS* 2.8 27.6 + - - +
134B TYR* 4.5 8.4 + - + -
203B ALA* 3.9 28.3 - - + -
204B LYS* 4.5 2.2 - - + +
207B PHE* 3.6 36.0 - - + -
300B 2FH 5.5 1.4 - - - +
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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