Contacts of the helix formed by residues 6 - 21 (chain B) in PDB entry 3GB9
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 THR 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLY 5.0 3.4 - - - +
5B TYR* 1.3 76.1 - - - +
7B TYR* 1.3 65.6 + - - +
8B GLU* 3.5 8.2 + - - +
9B ASP* 3.1 42.6 + - - +
10B TYR* 3.1 15.0 - - - -
296B SO4 3.7 22.2 - - - +
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Residues in contact with TYR 7 (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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6B THR* 1.3 71.4 - - - +
8B GLU* 1.3 71.4 + - - +
10B TYR* 3.1 12.2 + - - +
11B LYS* 3.0 42.9 + - + +
105B LEU* 3.5 24.0 - - + +
152B ASP* 3.8 7.2 - - - +
154B ARG* 3.3 64.7 + - + +
155B PHE* 3.6 38.8 - + + -
296B SO4 2.9 22.6 + - - +
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.6 9.0 - - - +
7B TYR* 1.3 86.1 - - - +
9B ASP* 1.3 52.3 + - - +
11B LYS* 3.7 26.6 + - - +
12B ASN* 2.8 58.0 + - - +
154B ARG* 5.3 2.6 + - - -
296B SO4 3.3 14.5 + - - +
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Residues in contact with ASP 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY 3.7 6.1 - - - +
5B TYR* 3.6 23.8 - - + -
6B THR* 3.1 40.2 + - - +
8B GLU* 1.3 74.5 - - - +
10B TYR* 1.3 66.1 + - - +
12B ASN* 3.3 8.3 + - - +
13B THR* 3.0 22.2 + - - -
55B ASN* 3.2 30.7 + - - +
98B PHE* 5.0 1.3 - - - -
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Residues in contact with TYR 10 (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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3B ASN* 3.4 23.6 + - - -
5B TYR* 3.6 21.1 - + + +
6B THR 3.1 25.3 + - - -
7B TYR* 3.1 14.3 + - - +
9B ASP* 1.3 76.0 - - - +
11B LYS* 1.3 58.7 + - - +
13B THR* 3.4 3.6 + - - -
14B ALA* 3.0 28.2 + - - +
94B TRP 4.9 2.9 + - - -
98B PHE* 3.5 38.8 - + - -
101B ARG* 3.3 43.9 + - + +
102B VAL* 4.2 6.9 - - + +
105B LEU* 3.6 19.5 - - + +
155B PHE* 3.9 19.1 - + + -
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Residues in contact with LYS 11 (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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7B TYR* 3.0 39.7 + - + +
8B GLU* 3.8 25.6 + - - +
10B TYR* 1.3 74.4 - - - +
12B ASN* 1.3 61.9 + - - +
14B ALA* 3.9 2.6 - - + +
15B GLU* 2.9 65.0 + - + +
105B LEU* 3.8 13.8 - - + +
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Residues in contact with ASN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 2.8 49.1 + - - +
9B ASP* 3.3 12.5 + - - +
11B LYS* 1.3 75.0 - - - +
13B THR* 1.3 55.9 + - - +
15B GLU* 3.5 11.9 + - - +
16B TRP* 3.0 29.5 + - - +
54B PRO* 5.3 5.3 - - + +
55B ASN* 4.4 6.7 + - - +
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Residues in contact with THR 13 (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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9B ASP 3.0 11.2 + - - -
10B TYR 3.7 4.5 - - - -
12B ASN* 1.3 74.4 - - - +
14B ALA* 1.3 64.9 + - - +
16B TRP* 3.2 6.9 + - - +
17B LEU* 3.1 24.1 + - + +
53B ILE* 3.7 19.1 - - + -
54B PRO* 2.7 31.6 + - - +
55B ASN* 3.2 17.0 + - - +
56B PHE* 4.3 3.8 - - + -
98B PHE* 3.6 5.8 - - + -
102B VAL* 3.8 28.0 - - + -
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Residues in contact with ALA 14 (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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10B TYR 3.0 14.3 + - - +
11B LYS* 3.9 5.2 - - + +
13B THR* 1.3 75.3 - - - +
15B GLU* 1.3 59.7 + - + +
17B LEU 3.4 0.5 + - - -
18B LEU* 2.9 36.0 + - + +
102B VAL* 4.1 6.0 - - + +
105B LEU* 3.6 33.7 - - + +
106B LEU* 3.6 26.5 - - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 2.9 51.8 + - + +
12B ASN* 4.0 13.9 - - - +
14B ALA* 1.3 75.2 - - + +
16B TRP* 1.3 63.4 + - - +
18B LEU* 3.9 12.8 - - + +
19B SER* 3.2 25.5 + - - -
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Residues in contact with TRP 16 (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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12B ASN 3.0 18.2 + - - +
13B THR 3.2 4.9 + - - +
15B GLU* 1.3 74.6 - - - +
17B LEU* 1.3 81.5 + - + +
19B SER* 3.1 5.0 + - - -
20B HIS* 2.8 65.9 + + + +
48B PHE* 3.7 37.2 - + - -
52B GLU* 3.6 33.2 - - + -
53B ILE* 4.2 8.7 - - + -
54B PRO* 3.5 35.0 - - + +
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Residues in contact with LEU 17 (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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13B THR* 3.1 13.6 + - + +
14B ALA 3.7 5.6 - - - +
16B TRP* 1.3 102.8 - - + +
18B LEU* 1.3 61.5 + - - +
20B HIS* 3.9 1.2 - - - +
21B THR* 3.1 32.1 + - - +
48B PHE* 3.9 26.2 - - + -
53B ILE* 4.0 20.9 - - + -
56B PHE* 5.4 0.4 - - + -
68B LEU* 4.0 20.0 - - + -
70B PHE* 4.4 10.5 - - + -
102B VAL* 4.1 25.6 - - + -
106B LEU* 4.2 16.2 - - + -
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Residues in contact with LEU 18 (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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14B ALA* 2.9 27.5 + - + +
15B GLU* 3.9 13.5 - - + +
16B TRP 3.3 0.2 - - - -
17B LEU* 1.3 77.6 - - - +
19B SER* 1.3 57.7 + - - +
21B THR* 2.8 19.7 - - + +
23B HIS 4.8 1.3 - - - +
24B ARG* 3.0 55.5 + - - +
25B PRO* 5.8 1.6 - - + -
105B LEU 4.2 17.3 - - - +
106B LEU* 4.1 27.4 - - + +
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Residues in contact with SER 19 (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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15B GLU 3.2 13.8 + - - -
16B TRP* 3.1 13.2 + - - -
18B LEU* 1.3 77.2 - - - +
20B HIS* 1.3 73.0 + - - +
21B THR 3.6 1.3 - - - -
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Residues in contact with HIS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 2.8 72.0 + + + +
17B LEU 3.3 1.5 + - - +
19B SER* 1.3 89.7 + - - +
21B THR* 1.3 58.1 + - - +
46B GLN* 2.8 22.8 + - - -
48B PHE* 3.9 21.1 - + + -
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Residues in contact with THR 21 (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 LEU 3.1 16.8 + - - +
18B LEU* 2.8 21.7 - - + +
19B SER 3.6 1.3 - - - -
20B HIS* 1.3 78.1 - - - +
22B LYS* 1.3 62.4 + - - +
23B HIS* 3.2 38.5 + - + +
24B ARG* 2.9 9.0 + - - +
46B GLN* 2.7 28.2 + - - +
48B PHE* 4.1 12.6 - - + -
70B PHE* 4.3 15.6 - - + +
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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