Contacts of the helix formed by residues 21 - 31 (chain G) in PDB entry 3TDD
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A MET* 3.9 22.0 - - + -
130A ARG* 3.8 25.1 - - - +
12G ILE 6.1 0.7 - - - -
13G THR* 4.0 9.2 - - - +
14G ILE 3.2 40.8 - - - +
15G PHE* 3.9 11.7 - - + +
19G GLY 5.3 0.4 - - - +
20G ARG* 1.3 77.9 - - - +
22G TYR* 1.3 66.0 + - - +
23G GLN* 3.2 2.9 - - - -
24G VAL* 2.8 31.7 + - + +
25G GLU* 3.2 14.2 + - - +
124G THR* 3.9 17.0 - - + +
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Residues in contact with TYR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ASP* 4.3 5.9 + - - -
10G ARG* 3.1 64.8 + - + -
12G ILE 5.9 0.2 + - - -
16G SER* 3.6 29.8 - - - -
18G GLU* 3.4 13.7 + - - -
20G ARG* 3.1 39.8 + - - -
21G LEU* 1.3 71.7 - - - +
23G GLN* 1.3 52.6 + - - +
25G GLU* 2.7 35.6 + - - +
26G TYR* 2.7 54.7 + + + -
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Residues in contact with GLN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F SER 4.4 2.3 - - - +
14F VAL* 3.4 10.1 - - - +
15F PHE* 2.9 61.9 + - - +
10G ARG 2.8 23.5 + - - +
11G HIS 3.2 31.2 - - - +
12G ILE* 3.9 11.0 + - - +
13G THR* 4.0 21.5 - - + -
21G LEU 3.1 1.0 + - - -
22G TYR* 1.3 76.1 - - - +
24G VAL* 1.3 57.7 + - - +
26G TYR* 3.7 4.9 + - - -
27G ALA* 3.1 26.3 + - - +
130G ARG* 5.7 0.5 - - - +
131G PRO* 4.4 7.7 - - + +
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G THR* 4.5 7.9 - - + -
21G LEU* 2.8 32.7 + - + +
23G GLN* 1.3 74.3 - - - +
25G GLU* 1.3 68.6 + - + +
27G ALA* 3.2 7.6 + - - +
28G PHE* 3.1 33.7 + - + -
124G THR* 3.6 21.3 - - - +
131G PRO* 4.4 10.3 - - + -
153G PRO 3.9 7.6 - - - +
154G ALA* 3.8 29.4 - - + -
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Residues in contact with GLU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ARG* 2.9 55.1 + - - +
21G LEU 3.6 10.5 + - - +
22G TYR* 2.7 23.7 + - - +
24G VAL* 1.3 80.8 - - + +
26G TYR* 1.3 69.0 + - + +
28G PHE* 3.0 21.4 + - + +
29G LYS* 3.2 13.9 + - - +
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Residues in contact with TYR 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F TYR* 3.4 35.3 + + - -
15F PHE* 3.3 31.0 - - + -
16F SER 3.4 18.4 - - - +
17F PRO* 3.6 31.9 - - + +
19F GLY* 3.5 6.6 - - - -
10G ARG* 3.8 10.6 + - - -
22G TYR* 2.7 56.6 + + + +
23G GLN* 3.8 7.0 - - - +
25G GLU* 1.3 76.6 - - + +
27G ALA* 1.3 66.2 + - - +
29G LYS* 3.0 24.6 + - + +
30G ALA* 3.1 6.1 + - - +
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PHE* 3.6 29.1 - - + -
23G GLN 3.1 19.5 + - - +
24G VAL 3.3 8.1 - - - +
25G GLU 3.1 0.2 - - - -
26G TYR* 1.3 77.8 - - - +
28G PHE* 1.3 60.9 + - - +
30G ALA* 3.2 17.0 + - - +
31G THR* 3.4 10.4 + - - +
131G PRO* 4.0 8.5 - - + -
133G GLY* 3.5 5.5 - - - -
153G PRO* 3.8 20.9 - - + -
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Residues in contact with PHE 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G VAL* 3.1 36.6 + - + -
25G GLU* 3.0 13.3 + - + +
27G ALA* 1.3 75.6 - - - +
29G LYS* 1.3 66.4 + - + +
31G THR* 2.7 30.2 + - - -
32G ASN* 4.1 3.3 + - - -
135G ILE* 4.4 15.5 - - + -
152G ASP* 3.4 42.0 - - + -
153G PRO* 3.9 8.5 - - + -
154G ALA* 3.9 23.1 - - + -
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Residues in contact with LYS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PRO 3.9 16.6 - - - +
18F ASP* 4.2 9.6 - - - +
19F GLY* 4.0 11.7 - - - +
25G GLU 3.2 8.4 + - - +
26G TYR* 3.0 19.4 + - + +
28G PHE* 1.3 81.2 - - + +
30G ALA* 1.3 60.7 + - - +
31G THR 3.1 1.2 + - - -
32G ASN* 3.1 25.5 + - - +
33G GLN* 4.0 2.8 + - - +
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PHE* 3.7 19.5 - - + -
18F ASP 5.4 0.4 - - - -
19F GLY* 3.5 24.8 - - - +
26G TYR 3.1 7.7 + - - +
27G ALA 3.2 11.0 + - - +
29G LYS* 1.3 76.8 - - - +
31G THR* 1.3 61.8 + - - +
33G GLN* 2.9 26.7 + - - +
81G PRO* 3.5 16.8 - - + +
133G GLY* 3.9 10.8 - - - +
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Residues in contact with THR 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ALA 3.5 11.2 - - - +
28G PHE* 2.7 27.6 + - - +
30G ALA* 1.3 76.8 - - - +
32G ASN* 1.3 69.0 + - - +
33G GLN 3.8 0.2 + - - -
34G THR* 4.2 4.3 + - - -
35G ILE 5.7 0.2 - - - +
79G ASN* 3.3 34.6 + - - +
80G GLY* 3.5 5.0 + - - -
133G GLY 3.5 23.3 + - - +
134G VAL* 3.7 5.6 - - - +
135G ILE* 3.8 31.7 - - + +
153G PRO* 4.2 2.9 - - + -
165G THR* 5.7 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