Contacts of the helix formed by residues 21 - 30 (chain K) in PDB entry 5T0G
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 LEU 21 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K ASN* 3.4 32.3 - - - +
14K THR 4.4 1.1 - - - -
15K PHE* 3.6 17.7 - - + -
20K ARG* 1.3 77.9 - - - +
22K PHE* 1.3 64.9 - - - +
23K GLN* 4.8 0.9 - - + +
24K VAL* 3.8 23.7 - - + +
25K GLU* 3.0 25.8 + - - +
121K LEU* 3.9 28.5 - - + -
123K PHE* 4.2 9.9 - - + -
77L LEU* 4.8 19.0 - - + +
126L ARG* 3.6 23.8 - - - +
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Residues in contact with PHE 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K TYR* 4.4 9.4 - - + -
9K ASP* 6.1 0.4 - - - -
10K ARG* 3.6 40.6 - - + -
12K VAL* 5.1 8.6 + - - +
14K THR 3.6 16.8 + - - +
15K PHE 4.1 2.9 - - - -
16K SER* 3.1 39.5 - - - -
17K PRO* 4.0 11.4 - - + -
20K ARG 3.3 3.6 + - - -
21K LEU* 1.3 68.2 - - - +
23K GLN* 1.3 66.3 + - - +
25K GLU* 3.0 9.4 + - + +
26K TYR* 2.9 58.2 + + + -
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Residues in contact with GLN 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J VAL* 3.4 18.5 - - + +
10J PHE* 3.2 48.1 - - + +
12K VAL* 3.6 38.8 + - + +
21K LEU* 3.5 1.4 - - + +
22K PHE* 1.3 78.5 - - - +
24K VAL* 1.3 56.7 + - - +
26K TYR* 3.7 10.9 - - - +
27K ALA* 2.9 28.8 + - - +
123K PHE* 4.5 3.3 - - + -
134K SER 4.1 2.8 + - - +
135K ARG* 3.4 15.0 - - - +
136K PRO* 3.4 26.7 - - + +
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K ARG* 6.4 1.1 - - - -
21K LEU* 3.5 35.6 + - + -
22K PHE 3.1 1.2 - - - -
23K GLN* 1.3 76.5 - - - +
25K GLU* 1.3 67.4 + - - +
27K ALA* 2.9 16.5 + - - +
28K ILE* 3.0 24.0 + - + +
121K LEU* 4.1 23.8 - - + -
123K PHE* 4.4 3.6 - - + -
136K PRO* 4.2 13.0 - - + -
158K PRO* 5.0 2.2 - - + +
159K SER* 3.8 33.2 - - - +
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Residues in contact with GLU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 3.1 42.9 + - + +
21K LEU 3.0 13.5 + - - +
22K PHE* 3.0 11.3 + - + +
24K VAL* 1.3 77.7 - - - +
26K TYR* 1.3 72.6 + - + +
28K ILE* 3.4 22.1 + - - +
29K GLU* 3.9 4.5 + - - +
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Residues in contact with TYR 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J PHE* 3.4 23.1 - - - +
11J SER 3.5 16.1 - - - +
12J PRO* 3.4 44.8 - - + +
14J GLY* 3.9 8.7 - - - -
22K PHE* 2.9 60.2 + + + +
23K GLN* 3.8 6.3 - - - +
25K GLU* 1.3 89.3 - - + +
27K ALA* 1.3 62.3 + - - +
29K GLU* 3.1 19.7 + - - +
30K ALA 3.8 3.1 + - - -
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J PHE* 4.0 23.1 - - + +
23K GLN 2.9 19.2 + - - +
24K VAL* 2.9 9.1 + - - +
26K TYR* 1.3 74.9 - - - +
28K ILE* 1.3 67.5 + - - +
30K ALA* 3.3 16.4 + - - +
136K PRO* 4.5 9.0 - - + +
137K PHE 4.8 2.0 - - - +
138K GLY* 3.9 31.8 - - - +
158K PRO* 5.1 3.1 - - + -
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Residues in contact with ILE 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K VAL* 3.0 20.8 + - + +
25K GLU* 3.6 17.7 - - - +
26K TYR 3.2 1.0 - - - -
27K ALA* 1.3 77.9 - - - +
29K GLU* 1.3 60.0 + - - +
31K ILE* 3.1 27.9 + - + +
32K LYS* 4.1 1.4 + - - +
157K ASP* 5.2 5.4 - - + +
158K PRO* 3.8 37.0 - - + -
159K SER* 4.6 9.2 - - - +
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Residues in contact with GLU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J PRO 3.7 13.9 - - - +
13J ASP* 3.4 25.9 - - - +
14J GLY* 4.2 1.3 - - - +
25K GLU 3.9 3.9 + - - +
26K TYR* 3.1 14.4 + - - +
28K ILE* 1.3 78.3 - - - +
30K ALA* 1.3 56.5 + - - +
31K ILE 3.1 0.4 - - - -
32K LYS* 3.0 40.3 + - - +
33K LEU* 3.8 4.5 + - - +
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Residues in contact with ALA 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J PHE* 4.6 13.7 - - + -
14J GLY* 3.4 23.0 - - - +
26K TYR 3.8 2.2 + - - -
27K ALA* 3.3 14.5 + - - +
28K ILE 3.2 0.6 - - - -
29K GLU* 1.3 77.5 - - - +
31K ILE* 1.3 58.4 + - - +
32K LYS 3.3 0.2 - - - -
33K LEU* 3.1 37.6 + - + +
34K GLY 3.7 2.6 + - - -
80K GLY* 4.2 7.3 - - - -
81K LEU* 5.0 8.9 - - + +
138K GLY* 4.8 6.7 - - - +
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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