Contacts of the helix formed by residues 21 - 35 (chain G) in PDB entry 6A5T
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 GLN 21 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17G TYR 5.8 0.4 - - - -
19G GLY* 3.5 1.0 - - - -
20G PRO* 1.3 90.1 - - + +
22G MET* 1.3 66.8 + - - +
23G ASN 3.7 1.1 - - - -
24G GLN* 3.4 19.5 + - - +
25G TYR* 2.8 24.3 + - + +
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Residues in contact with MET 22 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1448A ILE* 4.2 20.0 - - + +
1449A ASP 4.2 1.1 - - - +
1450A GLU* 3.4 37.7 - - + +
1453A LEU* 3.6 26.9 - - + -
1454A THR* 5.9 2.2 - - + -
13G LEU* 5.1 2.9 - - + -
17G TYR 4.9 14.1 - - - +
18G PHE* 4.6 8.7 - - + -
19G GLY 4.2 12.3 + - - +
20G PRO 3.0 6.3 + - - +
21G GLN* 1.3 74.6 - - - +
23G ASN* 1.3 86.6 + - - +
25G TYR* 2.8 19.5 + - - +
26G LEU* 2.9 29.0 + - + +
70G PHE* 5.1 6.1 - - + -
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Residues in contact with ASN 23 (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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1450A GLU* 3.9 22.7 - - - +
1454A THR* 4.6 13.1 - - - +
22G MET* 1.3 90.4 - - - +
24G GLN* 1.3 57.5 + - - +
26G LEU* 3.2 23.2 - - - +
27G ARG* 3.0 54.7 + - - +
56G VAL* 3.9 17.1 - - + +
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Residues in contact with GLN 24 (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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21G GLN* 3.4 20.7 + - - +
22G MET 2.8 1.2 + - - -
23G ASN* 1.3 76.3 - - - +
25G TYR* 1.3 65.1 + - - +
26G LEU 3.1 1.3 - - - -
27G ARG* 2.6 47.0 + - - +
28G GLU* 2.6 63.7 + - + +
52G MET* 4.2 20.0 - - - +
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Residues in contact with TYR 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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13G LEU* 5.1 7.9 - - + -
17G TYR* 4.0 45.7 + + + +
21G GLN* 2.8 21.5 + - + +
22G MET* 2.8 9.9 + - - +
24G GLN* 1.3 73.3 - - - +
26G LEU* 1.3 65.4 + - + +
28G GLU* 3.7 10.1 - - + +
29G LYS* 2.9 43.9 + - + +
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Residues in contact with LEU 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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11G LEU* 5.2 9.6 - - + +
13G LEU* 3.8 21.1 - - + -
22G MET* 2.9 19.9 + - + +
23G ASN* 3.2 33.7 - - - +
25G TYR* 1.3 83.9 - - + +
27G ARG* 1.3 58.4 + - - +
29G LYS* 3.2 7.6 + - - +
30G LEU* 2.9 27.0 + - - +
56G VAL* 4.4 21.1 - - + -
70G PHE* 3.4 46.7 - - + -
72G VAL* 6.1 1.8 - - + +
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Residues in contact with ARG 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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23G ASN* 3.0 40.0 + - - +
24G GLN* 2.6 54.7 + - - +
26G LEU* 1.3 77.6 - - + +
28G GLU* 1.3 59.1 + - - +
30G LEU* 3.3 9.2 + - - +
31G LEU* 2.9 32.8 + - - +
51G GLY 3.8 14.4 - - - +
52G MET 3.6 11.4 + - - -
53G ASN* 5.4 0.6 - - - -
54G ILE* 3.3 59.1 + - + +
56G VAL* 5.5 5.7 - - + +
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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
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71D ARG* 5.8 1.9 + - - -
24G GLN* 2.6 52.6 + - + +
25G TYR* 3.7 12.1 - - + +
27G ARG* 1.3 74.6 - - - +
29G LYS* 1.3 56.2 + - - +
31G LEU* 3.4 18.1 + - - +
32G THR* 2.7 39.7 + - - +
52G MET* 4.3 13.5 - - - +
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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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11G LEU* 4.6 25.1 - - + -
25G TYR* 2.9 33.8 + - + +
26G LEU* 3.5 10.8 - - - +
28G GLU* 1.3 77.2 - - - +
30G LEU* 1.3 63.4 + - - +
32G THR* 3.2 7.0 + - + -
33G ASP* 3.0 50.2 + - + +
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Residues in contact with LEU 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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9G LEU* 3.6 19.1 - - + -
11G LEU* 5.1 5.3 - - + +
26G LEU 2.9 13.8 + - - +
27G ARG* 3.5 10.5 - - - +
28G GLU 3.3 0.2 - - - -
29G LYS* 1.3 76.6 - - - +
31G LEU* 1.3 57.7 - - + +
34G VAL* 2.7 60.6 + - + +
48G VAL* 5.7 5.4 - - + -
54G ILE* 3.9 28.5 - - + -
72G VAL* 3.5 38.8 - - + -
74G TYR* 4.2 18.8 - - + -
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Residues in contact with LEU 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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67D ARG* 4.0 12.1 - - - +
71D ARG* 4.5 13.2 - - - +
94D SER* 3.4 26.4 - - - +
27G ARG 2.9 19.5 + - - +
28G GLU* 3.7 20.6 - - - +
30G LEU* 1.3 80.3 - - + +
32G THR* 1.3 65.0 + - - +
33G ASP 2.9 1.4 + - - -
34G VAL* 3.1 8.0 + - - -
35G GLU* 3.3 40.1 + - - +
48G VAL* 4.0 15.7 - - + -
51G GLY* 4.8 8.3 - - - +
52G MET* 3.9 24.7 - - + -
54G ILE* 5.2 3.8 - - + -
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Residues in contact with THR 32 (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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94D SER* 3.7 25.5 + - - +
95D GLY* 5.1 2.8 - - - -
28G GLU* 2.7 27.8 + - - +
29G LYS* 3.2 8.7 + - + -
31G LEU* 1.3 73.0 - - - +
33G ASP* 1.3 73.2 + - - +
35G GLU 5.2 1.0 - - - +
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Residues in contact with ASP 33 (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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29G LYS* 3.0 46.1 + - + +
32G THR* 1.3 97.7 - - - +
34G VAL* 1.3 63.7 + - + +
35G GLU 5.1 0.7 - - - -
37G THR* 3.9 16.2 - - - +
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Residues in contact with VAL 34 (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 LEU* 3.8 17.3 - - + -
30G LEU* 2.7 50.4 + - + +
31G LEU* 4.8 0.4 - - - -
33G ASP* 1.3 82.5 - - + +
35G GLU* 1.3 72.1 + - + +
37G THR* 3.3 17.2 + - - -
45G ILE* 3.2 28.8 - - + +
48G VAL* 5.1 5.4 - - + -
74G TYR* 3.5 28.0 - - + +
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Residues in contact with GLU 35 (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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67D ARG* 2.6 26.9 + - - -
93D THR* 3.2 32.7 - - - -
94D SER* 3.3 24.3 + - - +
98D ALA* 3.7 5.1 + - + +
31G LEU* 3.3 23.1 + - + +
32G THR 5.2 0.9 - - - +
33G ASP 5.1 0.5 - - - -
34G VAL* 1.3 80.4 + - + +
36G GLY* 1.3 59.3 + - - +
37G THR* 3.6 4.7 + - - +
45G ILE* 3.8 6.1 - - + -
46G VAL 3.8 6.1 - - - +
47G THR* 3.9 13.2 - - - -
48G VAL* 3.1 37.3 + - + +
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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