Contacts of the helix formed by residues 16 - 32 (chain G) in PDB entry 5TJ4
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 GLY 16 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G ILE* 5.2 2.4 - - - +
15G LYS* 1.3 73.1 - - - +
17G TYR* 1.3 58.9 + - - -
19G GLY 3.5 0.9 + - - -
20G LEU* 3.1 23.6 + - - +
293G VAL* 3.6 19.9 - - - +
296G ASP* 3.2 27.1 - - - -
297G LYS* 3.8 19.7 + - - +
299G LEU* 5.9 0.4 - - - +
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Residues in contact with TYR 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 3.7 26.0 - - + -
12G ASN 4.3 0.9 - - - -
13G GLY* 3.3 29.8 - - - -
15G LYS 3.1 9.4 + - - -
16G GLY* 1.3 69.6 - - - +
18G ASN* 1.3 84.9 + - + +
20G LEU* 3.2 5.9 + - - +
21G ALA* 2.9 27.9 + - - +
37G VAL* 3.8 14.0 - - + +
39G HIS* 3.5 48.6 + + - +
296G ASP* 3.5 1.5 + - - -
297G LYS* 6.5 0.9 - - - -
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Residues in contact with ASN 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G TYR* 1.3 91.2 - - + +
19G GLY* 1.3 60.3 + - - +
21G ALA* 3.1 8.9 + - - +
22G GLU* 2.9 26.5 + - - +
296G ASP* 3.1 14.2 + - - +
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Residues in contact with GLY 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLY 3.5 3.8 + - - -
17G TYR 3.3 0.2 - - - -
18G ASN* 1.3 75.1 - - - +
20G LEU* 1.3 61.2 + - - +
22G GLU* 3.2 10.5 - - - +
23G VAL* 3.2 23.2 + - - +
292G ALA* 3.7 23.1 - - - +
293G VAL* 4.1 7.6 - - - -
296G ASP* 3.0 18.7 + - - -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ILE* 3.9 26.2 - - + -
11G ILE* 3.8 26.7 - - + -
16G GLY 3.1 14.9 + - - +
17G TYR 3.4 9.0 - - - +
19G GLY* 1.3 73.2 - - - +
21G ALA* 1.3 61.4 + - - +
23G VAL* 3.1 9.3 + - + +
24G GLY* 2.8 23.4 + - - -
37G VAL* 4.3 17.1 - - + +
61G PHE* 4.1 7.6 - - + -
279G PHE* 4.1 21.3 - - + -
284G LEU* 4.0 33.0 - - + -
293G VAL* 4.0 10.8 - - + +
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G TYR 2.9 14.0 + - - +
18G ASN* 3.1 12.1 + - - +
20G LEU* 1.3 73.2 - - - +
22G GLU* 1.3 53.7 + - - +
24G GLY* 3.0 3.4 + - - +
25G LYS* 2.7 35.2 + - - +
35G VAL 5.6 3.6 - - - +
37G VAL* 4.0 21.5 - - + +
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Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ASN 2.9 12.6 + - - +
19G GLY* 3.2 15.0 - - - +
21G ALA* 1.3 74.6 - - - +
23G VAL* 1.3 59.9 + - - +
25G LYS* 3.3 9.6 + - - +
26G LYS* 3.1 21.3 + - - +
292G ALA* 4.8 9.2 - - + -
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Residues in contact with VAL 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLY 3.2 13.4 + - - +
20G LEU* 3.1 11.3 + - + +
22G GLU* 1.3 73.3 - - - +
24G GLY* 1.3 66.6 + - - +
26G LYS* 3.2 9.7 + - + +
27G PHE* 3.0 20.6 + - - +
279G PHE* 3.7 21.8 - - + -
283G TYR* 3.8 28.3 - - + +
284G LEU* 4.1 6.5 - - + -
289G GLY* 3.5 30.7 - - - +
292G ALA* 3.9 7.4 - - + -
293G VAL* 4.2 8.3 - - + -
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Residues in contact with GLY 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU 2.8 13.4 + - - -
21G ALA* 3.0 8.2 + - - -
23G VAL* 1.3 76.3 - - - +
25G LYS* 1.3 55.8 + - - +
27G PHE* 3.1 4.9 + - - +
28G GLU* 2.9 25.5 + - - +
35G VAL* 3.3 37.2 - - - +
279G PHE* 4.2 5.8 - - - -
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Residues in contact with LYS 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA 2.7 15.0 + - - +
22G GLU* 3.3 12.1 + - - +
24G GLY* 1.3 71.6 - - - +
26G LYS* 1.3 57.0 + - - +
28G GLU* 3.2 8.7 + - - +
29G LYS* 2.9 30.9 + - - +
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Residues in contact with LYS 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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22G GLU 3.1 12.7 + - - +
23G VAL* 3.2 12.5 + - + +
25G LYS* 1.3 75.3 - - - +
27G PHE* 1.3 61.0 + - - +
29G LYS* 3.7 5.1 + - - +
30G ASP* 3.4 31.0 + - - +
283G TYR* 4.3 5.1 - - + -
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Residues in contact with PHE 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 4.2 17.7 - - + -
23G VAL 3.0 11.2 + - - +
24G GLY 3.2 9.4 - - - +
26G LYS* 1.3 74.5 - - - +
28G GLU* 1.3 60.2 + - - +
30G ASP 3.2 1.0 + - - -
31G THR* 2.8 49.1 + - - -
33G ILE* 4.0 23.1 - - + -
35G VAL* 3.7 19.7 - - + -
275G LEU* 3.9 23.8 - - + -
278G GLU* 4.5 8.7 - - + -
279G PHE* 3.7 32.1 - + + -
283G TYR* 3.0 40.9 - + + -
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Residues in contact with GLU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLY 2.9 15.2 + - - +
25G LYS* 3.2 12.8 + - - +
27G PHE* 1.3 71.0 - - - +
29G LYS* 1.3 58.5 + - - +
32G GLY* 2.8 30.9 + - - -
33G ILE 3.4 25.8 + - - +
34G LYS* 4.9 4.5 - - - -
35G VAL* 4.8 3.4 - - + +
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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
----------------------------------------------------------
25G LYS 2.9 17.1 + - - +
26G LYS* 4.0 7.6 - - - +
27G PHE 3.2 0.2 - - - -
28G GLU* 1.3 79.2 - - - +
30G ASP* 1.3 67.5 + - - +
32G GLY* 4.4 1.2 + - - -
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Residues in contact with ASP 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LYS* 3.4 17.0 + - - +
27G PHE 3.2 2.9 + - - +
29G LYS* 1.3 85.2 - - - +
31G THR* 1.3 60.5 + - - +
283G TYR* 3.1 30.8 + - + +
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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 PHE* 2.8 44.1 + - - -
30G ASP* 1.3 75.0 - - - +
32G GLY* 1.3 63.1 + - - +
33G ILE* 3.6 7.1 + - - +
283G TYR* 5.3 2.2 - - - -
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Residues in contact with GLY 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G GLU* 2.8 25.0 + - - -
29G LYS 4.4 1.3 + - - -
30G ASP 3.5 1.6 - - - -
31G THR* 1.3 74.5 - - - +
33G ILE* 1.3 57.3 + - - +
34G LYS 4.4 0.5 + - - -
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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