Contacts of the helix formed by residues 21 - 27 (chain B) in PDB entry 6THQ
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 SER 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.8 11.6 - - - +
18B THR* 3.0 21.7 + - - +
19B VAL 3.3 0.8 - - - -
20B LEU* 1.3 77.6 - - - +
22B PRO* 1.3 62.7 - - - +
23B SER* 3.0 17.5 + - - -
24B LEU* 2.8 24.1 + - - -
25B ASN* 2.9 15.6 + - - -
98B ILE 2.5 29.3 + - - -
100B LYS 3.8 5.2 - - - -
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Residues in contact with PRO 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 3.4 1.3 - - - +
21B SER* 1.3 85.6 - - - +
23B SER* 1.3 55.7 + - - +
25B ASN* 4.2 0.9 - - + +
26B TYR* 2.9 56.0 + - + +
28B PHE* 3.8 7.0 + - + +
98B ILE* 3.8 23.8 - - + -
100B LYS 3.4 16.6 - - - +
102B GLN* 3.6 28.9 - - + +
104B SER 4.8 4.9 - - - +
107B VAL* 4.5 12.3 - - + -
110B LEU* 4.5 7.0 - - + -
159C ILE* 5.5 0.7 - - + -
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Residues in contact with SER 23 (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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21B SER* 3.0 10.0 + - - -
22B PRO* 1.3 76.6 - - - +
24B LEU* 1.3 62.0 - - - +
27B GLY* 3.5 15.9 + - - -
28B PHE 2.7 33.1 + - - +
29B GLY* 4.7 0.7 - - - -
97B TYR* 3.4 20.0 - - - -
98B ILE* 2.7 27.7 + - - +
152B THR* 4.8 0.7 + - - -
23C SER 4.9 2.3 - - - +
24C LEU* 3.8 18.7 - - - +
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Residues in contact with LEU 24 (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 VAL* 5.3 0.7 - - + -
18B THR 4.5 1.1 - - - +
19B VAL* 3.6 43.1 - - + +
21B SER* 2.8 19.1 + - - +
23B SER* 1.3 81.9 - - - +
25B ASN* 1.3 61.0 + - - +
27B GLY 4.5 0.3 + - - -
17C VAL* 4.2 17.5 - - + -
23C SER* 3.9 40.2 - - - +
24C LEU* 3.9 17.4 - - + +
27C GLY* 5.8 0.2 - - - -
95C VAL* 4.3 15.7 - - + -
97C TYR* 4.5 9.6 - - + -
152C THR* 3.4 20.5 + - + +
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Residues in contact with ASN 25 (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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19B VAL 3.0 26.9 + - - -
20B LEU* 3.5 10.6 - - - +
21B SER 2.9 24.1 + - - +
22B PRO* 4.4 0.4 - - + -
24B LEU* 1.3 82.3 - - - +
26B TYR* 1.3 82.2 + - + +
102B GLN 5.5 0.2 - - - +
31C PHE* 3.4 13.6 - - + +
93C ARG* 2.8 47.5 + - - +
95C VAL* 4.0 11.0 - - - +
152C THR* 3.3 23.9 - - - +
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Residues in contact with TYR 26 (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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22B PRO* 2.9 29.0 + - + +
25B ASN* 1.3 94.2 - - + +
27B GLY* 1.3 62.4 + - - +
28B PHE 3.2 1.9 + - - -
102B GLN 4.0 13.9 - - - -
103B ILE 2.5 29.4 + - - -
104B SER 4.1 6.1 - - - -
105B LEU* 3.6 25.0 - - + +
31C PHE* 3.7 23.6 - + - -
93C ARG* 3.0 29.1 + - - -
152C THR 3.2 11.0 - - - -
155C TYR* 3.3 20.6 - + + -
156C LEU* 3.0 24.6 + - - -
159C ILE* 3.5 18.9 - - + +
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Residues in contact with GLY 27 (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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23B SER 3.5 11.7 + - - -
24B LEU 4.5 1.4 + - - -
25B ASN 3.8 0.6 - - - -
26B TYR* 1.3 76.4 - - - +
28B PHE* 1.3 55.9 + - - +
29B GLY 3.4 1.2 + - - -
152B THR* 2.9 19.0 + - - -
153B GLY* 3.0 32.8 + - - -
27C GLY* 4.8 5.2 - - - -
152C THR* 3.5 8.8 + - - -
153C GLY* 4.1 2.5 - - - -
156C LEU* 3.8 13.3 - - - +
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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