Contacts of the helix formed by residues 14 - 22 (chain A) in PDB entry 5TKM
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 ARG 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 1.3 75.5 - - - +
15A ASP* 1.3 67.8 + - - +
17A PHE* 3.3 1.9 + - - +
18A TYR* 3.0 33.7 + - + -
157A TRP* 3.5 31.9 - - + -
161A VAL* 3.8 12.1 - - + +
162A ASP 3.4 15.5 + - - +
163A ASN* 3.5 18.3 + - - -
164A GLU* 3.0 43.9 + - - +
166A GLN* 4.0 16.1 - - - +
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Residues in contact with ASP 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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13A ASP* 3.3 9.1 + - - +
14A ARG* 1.3 81.4 + - - +
16A THR* 1.3 63.3 + - - +
18A TYR* 3.3 7.5 + - - +
19A ASP* 2.9 26.4 + - - +
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Residues in contact with THR 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 MET* 4.0 13.5 - - + -
13A ASP* 2.8 38.5 + - - -
15A ASP* 1.3 73.2 - - - +
17A PHE* 1.3 62.1 + - - +
19A ASP* 3.2 3.3 + - - -
20A ASN* 3.0 39.3 + - - +
34A TRP* 3.5 44.2 - - + -
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Residues in contact with PHE 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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12A MET* 3.7 15.9 - - + -
13A ASP 3.1 11.3 + - - +
14A ARG 3.3 6.0 + - - +
16A THR* 1.3 76.9 - - - +
18A TYR* 1.3 68.5 + + - +
21A PHE* 3.0 55.8 + + + +
148A MET* 5.5 0.2 - - + -
153A PHE* 3.9 37.0 - + - -
156A CYS* 3.9 21.3 - - + -
157A TRP* 3.7 27.6 - + - -
161A VAL* 3.5 30.5 - - + -
168A PHE* 3.9 20.0 - + - -
171A TRP* 4.5 5.1 - + - -
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Residues in contact with TYR 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 ARG* 3.0 27.5 + - + +
15A ASP* 3.9 6.7 - - - +
17A PHE* 1.3 80.5 - + - +
19A ASP* 1.3 62.4 + - - +
20A ASN 3.3 0.9 + - - -
22A GLU* 3.8 11.3 + - - +
30A ARG* 5.4 0.2 + - - -
157A TRP* 3.6 24.7 - + - -
167A GLN 3.8 4.9 + - - -
168A PHE* 3.8 20.8 - + - -
169A MET* 2.9 50.5 + - + +
171A TRP* 3.7 38.9 + + - +
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Residues in contact with ASP 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 ASP 2.9 18.8 + - - +
16A THR* 3.8 4.9 - - - +
18A TYR* 1.3 76.3 - - - +
20A ASN* 1.3 69.6 + - - +
22A GLU* 4.9 1.7 + - - +
27A LEU* 4.8 1.4 - - - +
30A ARG* 2.9 59.4 + - - +
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Residues in contact with ASN 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 THR* 3.0 31.9 + - - +
19A ASP* 1.3 93.5 + - - +
21A PHE* 1.3 68.3 + - + +
22A GLU 3.6 1.6 - - - -
30A ARG* 4.1 17.1 - - - +
32A TYR* 4.2 16.4 - - - +
34A TRP* 3.4 40.4 + - + +
93A SER* 3.2 10.1 + - - -
122A ARG* 2.8 28.3 + - - -
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Residues in contact with PHE 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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12A MET* 3.7 22.7 - - + -
17A PHE* 3.0 45.6 + + + +
20A ASN* 1.3 83.2 - - + +
22A GLU* 1.3 66.7 + - - +
23A ASN 3.2 3.1 + - - -
34A TRP* 3.7 34.1 - + + -
36A CYS* 4.2 11.2 - - - -
91A PHE* 3.9 13.9 - - + -
92A VAL 3.7 19.7 - - - -
93A SER* 3.8 3.8 - - - -
121A ALA* 3.4 21.8 - - + +
122A ARG* 3.9 2.5 - - - +
148A MET* 4.1 19.3 - - + -
153A PHE* 3.2 25.6 - - + -
156A CYS* 5.5 0.4 - - - -
171A TRP* 3.6 4.3 - - + -
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Residues in contact with GLU 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 TYR 3.8 7.6 + - - +
19A ASP 5.2 2.0 - - - +
20A ASN 3.6 1.4 - - - -
21A PHE* 1.3 73.8 - - - +
23A ASN* 1.3 62.4 + - - +
24A GLU* 3.0 39.5 + - + +
27A LEU* 4.0 12.9 - - + +
30A ARG* 4.1 16.3 + - - -
122A ARG* 2.8 24.9 + - - -
171A TRP* 3.4 53.7 + - + +
177A ASN* 5.6 0.7 - - - +
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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