Contacts of the helix formed by residues 13 - 31 (chain G) in PDB entry 3DBL
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 TYR 13 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G LYS* 2.8 46.4 + - + +
10G GLU* 5.4 0.2 - - - -
12G LYS* 1.3 93.0 - - + +
14G ASP* 1.3 64.6 + - - +
15G ARG 3.4 2.9 - - - -
16G GLN* 3.0 36.1 - - + +
17G LEU* 3.1 21.7 + - + +
25G GLN* 3.9 13.0 - - + -
29G GLU* 3.4 21.0 + - - -
51G LEU 3.5 16.6 - - - -
52G PRO 3.3 22.9 - - - -
53G GLY* 3.8 6.8 - - - -
97G ASN* 2.9 20.7 + - - -
99G ASP* 3.3 16.5 + - - +
89H ASN* 4.3 6.3 - - + -
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Residues in contact with ASP 14 (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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10G GLU* 3.5 18.3 + - - +
11G GLN* 3.9 11.0 - - - +
12G LYS 3.3 3.2 - - - -
13G TYR* 1.3 77.3 - - - +
15G ARG* 1.3 83.7 + - - +
16G GLN 3.1 1.2 + - - -
17G LEU* 3.4 15.5 + - + +
18G ARG* 3.0 51.4 + - - +
86H SER* 5.2 5.2 - - - -
279H ARG* 3.5 14.9 + - - -
282H GLN* 3.8 10.3 - - - +
288H ILE* 5.2 0.4 - - - -
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Residues in contact with ARG 15 (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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12G LYS 5.0 0.4 + - - -
13G TYR 3.4 1.0 - - - -
14G ASP* 1.3 91.6 + - - +
16G GLN* 1.3 56.5 + - - +
18G ARG* 4.1 4.4 - - - +
19G LEU* 4.0 0.7 - - - +
86H SER* 3.4 35.3 + - - +
87H ASN* 5.3 0.4 + - - -
89H ASN* 3.9 4.1 - - - +
90H ARG* 3.3 44.4 - - - +
286H LYS* 3.8 17.0 - - - +
288H ILE* 3.4 38.0 - - - +
289H ILE 3.5 21.7 - - - +
290H PRO* 3.5 13.0 - - - +
291H ALA* 3.0 38.0 + - + +
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Residues in contact with GLN 16 (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 TYR* 3.0 30.3 - - + +
15G ARG* 1.3 78.0 - - - +
17G LEU* 1.3 54.1 + - - +
18G ARG 2.8 5.4 - - - -
19G LEU* 2.5 30.2 + - - +
20G TRP* 3.1 42.9 + - + +
25G GLN* 2.7 29.0 + - - +
52G PRO* 2.8 42.3 + - - +
89H ASN* 3.3 23.7 + - - +
291H ALA 3.9 1.6 - - - -
292H VAL* 4.0 9.4 - - + +
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Residues in contact with LEU 17 (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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10G GLU* 4.0 27.6 - - + +
13G TYR* 3.1 34.9 + - + +
14G ASP* 3.4 7.2 + - - +
16G GLN* 1.3 76.6 - - + +
18G ARG* 1.3 58.1 + - - +
19G LEU 2.9 1.1 + - - -
20G TRP* 4.7 1.1 - - - +
21G GLY* 2.9 41.9 + - - +
22G ASP* 3.9 11.2 - - - +
25G GLN* 3.5 38.4 - - + +
279H ARG* 3.8 34.2 + - - +
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Residues in contact with ARG 18 (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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14G ASP* 3.0 45.8 + - - +
15G ARG* 4.1 7.4 - - - +
16G GLN 2.8 0.6 - - - -
17G LEU* 1.3 77.8 - - - +
19G LEU* 1.3 64.2 + - - +
279H ARG* 2.9 48.9 + - + +
280H LEU* 4.7 2.6 - - - +
282H GLN* 3.5 13.3 + - - +
283H GLY* 3.9 9.5 - - - +
288H ILE* 3.3 43.9 - - - +
290H PRO* 4.0 24.3 - - + +
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Residues in contact with LEU 19 (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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15G ARG 4.0 6.3 - - - +
16G GLN* 2.5 18.1 + - - +
18G ARG* 1.3 75.6 - - - +
20G TRP* 1.3 65.4 + - + +
21G GLY 3.7 0.7 - - - -
175G HIS* 4.0 12.8 - - - -
513G PHE* 3.7 18.9 - - + -
184H GLY* 4.3 14.8 - - - -
185H PHE* 3.7 30.1 - - + -
290H PRO* 3.5 31.0 - - + -
291H ALA 4.1 4.5 - - - +
292H VAL* 3.5 30.3 - - + -
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Residues in contact with TRP 20 (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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16G GLN* 3.1 48.5 + - + +
17G LEU* 4.7 0.6 - - - +
19G LEU* 1.3 78.2 - - + +
21G GLY* 1.3 62.9 + - - +
23G HIS* 3.5 6.1 - - - -
24G GLY* 3.0 18.2 + - - -
25G GLN* 2.9 40.3 + - + +
28G LEU* 3.9 14.6 - - + -
52G PRO* 4.2 9.9 - - + -
175G HIS* 5.5 0.2 - - - -
503G GLN* 4.2 7.4 - - - -
506G ILE* 3.7 32.8 - - + -
510G THR* 4.9 5.6 - - + -
512G GLN* 2.8 42.1 + - - +
513G PHE* 4.6 8.3 - + + -
185H PHE* 4.3 14.8 - + - -
292H VAL* 4.0 21.3 - - + -
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Residues in contact with GLY 21 (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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17G LEU* 2.9 32.5 + - - +
19G LEU 3.7 0.8 - - - -
20G TRP* 1.3 77.9 - - - +
22G ASP* 1.3 65.6 + - - -
23G HIS* 3.2 8.5 - - - -
25G GLN* 3.0 24.1 + - - +
279H ARG* 5.0 3.1 - - - -
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Residues in contact with ASP 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLU* 4.8 3.7 - - - +
17G LEU* 3.9 14.4 - - - +
21G GLY* 1.3 71.6 - - - -
23G HIS* 1.3 59.7 + - - +
25G GLN* 3.3 5.1 + - - +
26G GLU* 3.1 33.7 + - - +
279H ARG* 2.9 30.4 + - - +
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Residues in contact with HIS 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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20G TRP 3.5 14.3 + - - -
21G GLY* 4.3 6.3 - - - -
22G ASP* 1.3 81.5 + - - +
24G GLY* 1.3 66.7 + - - +
26G GLU* 3.1 20.7 + - - +
27G ALA* 3.2 14.6 + - - +
173G GLU* 2.8 34.3 + - - -
382G LEU* 5.6 4.4 - - + +
512G GLN* 3.2 18.5 + - + -
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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 TRP* 3.0 36.4 + - - -
23G HIS* 1.3 78.2 - - - +
25G GLN* 1.3 62.9 + - - +
26G GLU 3.1 0.3 + - - -
27G ALA* 3.2 5.6 + - - +
28G LEU* 3.1 22.5 + - - +
510G THR* 3.7 11.7 - - - +
512G GLN* 3.5 12.8 - - - -
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Residues in contact with GLN 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 TYR* 3.9 13.5 - - + -
16G GLN* 2.7 25.9 + - - +
17G LEU* 3.5 18.6 - - + +
20G TRP* 2.9 16.6 + - - +
21G GLY 3.0 13.1 + - - +
22G ASP* 3.4 9.9 - - - +
24G GLY* 1.3 77.4 - - - +
26G GLU* 1.3 56.5 + - - +
28G LEU* 3.6 7.4 - - - +
29G GLU* 2.9 71.8 + - - +
52G PRO 3.0 22.2 + - - -
53G GLY* 4.3 1.0 - - - -
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Residues in contact with GLU 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 ASP* 3.1 21.8 + - - +
23G HIS* 3.4 15.2 - - - +
24G GLY 3.1 0.6 - - - -
25G GLN* 1.3 73.6 - - - +
27G ALA* 1.3 67.3 + - - +
28G LEU 3.1 1.3 - - - -
29G GLU* 3.0 7.8 + - - +
30G SER* 3.0 29.6 + - - +
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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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23G HIS 3.2 9.0 + - - +
24G GLY* 3.2 8.5 + - - +
26G GLU* 1.3 78.8 - - - +
28G LEU* 1.3 62.2 + - - +
30G SER* 3.3 6.0 + - - -
31G ALA* 3.1 18.5 + - - +
509G ILE* 3.4 32.1 - - - +
510G THR* 4.1 11.2 - - - +
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Residues in contact with LEU 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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20G TRP* 3.9 23.3 - - + -
24G GLY 3.1 13.2 + - - +
25G GLN* 3.6 11.4 - - - +
27G ALA* 1.3 75.7 - - - +
29G GLU* 1.3 57.7 + - - +
30G SER 3.0 8.6 + - - -
31G ALA* 3.1 10.9 + - - +
52G PRO* 4.0 26.5 - - + +
53G GLY 4.5 0.2 - - - -
54G ILE* 3.6 24.4 - - + +
55G GLY 2.9 18.9 + - - -
506G ILE* 3.5 34.8 - - + -
509G ILE* 3.8 21.9 - - + +
510G THR* 4.6 6.7 - - + -
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Residues in contact with GLU 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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9G LYS* 3.6 28.4 + - - +
13G TYR* 3.4 31.2 + - - -
25G GLN* 2.9 48.2 + - - +
26G GLU* 3.0 7.5 + - - +
28G LEU* 1.3 73.2 - - - +
30G SER* 1.3 57.8 + - - +
31G ALA 3.6 0.4 - - - -
53G GLY 3.8 9.8 - - - +
55G GLY* 3.4 21.0 - - - +
99G ASP* 5.5 1.4 - - - +
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Residues in contact with SER 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLU* 3.0 18.4 + - - +
27G ALA* 3.7 6.7 - - - -
29G GLU* 1.3 77.7 + - - +
31G ALA* 1.3 63.8 + - - +
32G HIS* 5.2 1.4 - - - +
55G GLY* 4.9 0.2 - - - -
124G THR* 4.9 0.5 + - - -
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Residues in contact with ALA 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 3.1 14.8 + - - +
28G LEU 3.1 1.6 + - - -
30G SER* 1.3 80.7 - - - +
32G HIS* 1.3 61.1 + - - +
33G VAL 4.1 0.4 - - - -
54G ILE* 3.6 25.1 - - + +
55G GLY* 3.4 6.2 + - - -
56G SER* 3.1 23.3 + - - +
124G THR* 3.7 15.0 - - + +
509G ILE* 3.7 20.0 - - + -
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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
------------------------------------------------------------
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