Contacts of the helix formed by residues 11 - 26 (chain B) in PDB entry 3GA1
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 ASN 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN* 3.5 10.3 - - - +
14A ASN* 3.0 32.8 + - - +
9B ILE 3.6 0.6 + - - -
10B PRO* 1.3 84.7 - - - +
12B PHE* 1.3 64.2 + - - +
14B ASN* 3.5 22.6 + - + +
15B SER* 3.5 10.9 + - - -
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Residues in contact with PHE 12 (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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14A ASN* 3.7 0.4 + - - -
17A LEU* 3.5 17.0 - - + -
51A SER* 3.6 23.1 - - - -
84A PHE* 3.5 17.9 - + - -
85A CYS 3.4 21.1 - - - -
87A THR 3.5 13.0 - - - +
88A GLY* 3.1 32.3 - - - -
111A GLU* 5.5 6.5 - - + -
9B ILE* 3.6 43.3 + - + +
10B PRO 3.0 3.8 + - - -
11B ASN* 1.3 76.3 - - - +
13B GLY* 1.3 62.1 + - - +
15B SER* 2.8 26.9 + - - -
16B ILE* 3.0 30.1 + - + +
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Residues in contact with GLY 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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13A GLY 3.3 19.8 - - - +
14A ASN* 3.2 10.3 + - - +
17A LEU* 3.8 23.9 - - - +
12B PHE* 1.3 79.6 - - - +
14B ASN* 1.3 55.8 + - - +
16B ILE* 4.4 0.7 - - - -
17B LEU* 2.9 34.8 + - - +
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Residues in contact with ASN 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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11A ASN* 2.8 33.9 + - - +
13A GLY* 3.1 5.9 + - - -
14A ASN* 2.9 37.2 + - - +
11B ASN* 3.6 18.6 + - + +
12B PHE 3.3 0.4 - - - -
13B GLY* 1.3 76.0 - - - +
15B SER* 1.3 61.8 + - - +
17B LEU* 3.9 1.4 + - - +
18B GLU* 3.4 24.6 + - - +
126B NO3 3.0 37.6 + - - +
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Residues in contact with SER 15 (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 ILE* 6.0 0.5 - - - +
11B ASN 3.5 6.7 + - - -
12B PHE* 2.8 27.3 + - - -
14B ASN* 1.3 77.8 - - - +
16B ILE* 1.3 70.8 + - - +
18B GLU* 3.2 12.4 + - - +
19B CYS* 3.2 19.1 + - - +
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Residues in contact with ILE 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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17A LEU* 4.1 21.1 - - + -
47A VAL* 5.2 4.5 - - + -
50A ALA* 4.1 27.6 - - + +
51A SER* 3.7 23.8 - - - +
85A CYS 5.0 3.8 - - - +
12B PHE* 3.0 48.9 + - + +
13B GLY* 3.9 5.6 - - - +
15B SER* 1.3 79.0 - - - +
17B LEU* 1.3 60.8 + - - +
19B CYS* 3.0 9.1 + - + +
20B LEU* 2.8 37.1 + - + +
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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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12A PHE* 3.6 27.1 - - + -
13A GLY* 3.6 18.2 - - - +
16A ILE* 4.0 22.7 - - + -
17A LEU* 6.0 1.3 - - + +
13B GLY 2.9 17.0 + - - +
14B ASN 4.3 1.8 - - - +
16B ILE* 1.3 77.7 - - - +
18B GLU* 1.3 58.0 + - - +
20B LEU* 3.1 24.2 + - + +
21B ASN* 2.9 26.7 + - - +
47B VAL* 4.6 3.1 - - + -
85B CYS 4.4 2.2 - - - +
86B TYR* 3.3 41.1 - - + +
87B THR* 4.0 2.5 - - - +
126B NO3 4.5 3.4 - - - +
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Residues in contact with GLU 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 ASN 3.4 15.3 + - - +
15B SER* 3.2 15.1 + - - +
16B ILE 3.1 0.4 - - - -
17B LEU* 1.3 78.7 - - - +
19B CYS* 1.3 58.1 + - - +
21B ASN* 3.3 10.2 + - + +
22B GLU* 3.2 40.9 + - + +
86B TYR 5.1 2.0 - - - -
89B ARG* 6.3 1.8 - - - +
126B NO3 5.3 3.1 + - - -
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Residues in contact with CYS 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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49A ALA 5.4 0.4 - - - -
50A ALA* 3.7 37.2 - - + +
56A ARG* 5.6 3.4 - - - -
15B SER 3.2 10.7 + - - +
16B ILE* 3.0 13.2 + - + +
18B GLU* 1.3 70.5 - - - +
20B LEU* 1.3 61.0 + - - +
22B GLU* 3.2 18.6 + - - +
23B GLN* 2.9 42.7 + - - +
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Residues in contact with LEU 20 (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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17A LEU* 5.6 0.2 - - + -
20A LEU* 3.8 28.3 - - + -
46A ALA* 3.7 29.2 - - + +
47A VAL* 4.3 7.6 - - + +
50A ALA* 4.6 4.5 - - + -
16B ILE* 2.8 24.7 + - + +
17B LEU* 3.4 19.3 - - + +
19B CYS* 1.3 77.1 - - - +
21B ASN* 1.3 62.4 + - - +
23B GLN* 3.4 22.7 + - - +
24B ARG* 3.0 19.4 + - - +
44B HIS* 3.5 11.8 - - + +
47B VAL* 3.8 16.8 - - + -
86B TYR* 3.7 13.6 - - + -
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Residues in contact with ASN 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 2.9 12.2 + - - +
18B GLU* 3.5 12.8 - - + +
19B CYS 3.2 0.2 - - - -
20B LEU* 1.3 78.2 - - - +
22B GLU* 1.3 57.9 + - + +
24B ARG* 3.0 36.9 + - - +
25B LEU* 3.0 46.6 + - - +
83B SER* 5.3 0.6 + - - -
86B TYR* 3.3 28.1 - - + +
87B THR* 3.7 19.8 - - + +
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Residues in contact with GLU 22 (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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18B GLU* 3.2 30.7 + - + +
19B CYS* 3.2 18.2 + - - +
21B ASN* 1.3 72.9 - - + +
23B GLN* 1.3 66.1 + - + +
25B LEU* 3.3 13.0 + - + +
26B GLN* 3.1 39.4 + - - +
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Residues in contact with GLN 23 (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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46A ALA* 3.1 46.4 + - - +
49A ALA* 3.9 2.2 - - - +
50A ALA* 3.7 14.5 - - - +
56A ARG* 6.0 0.4 - - - +
19B CYS* 2.9 33.4 + - - +
20B LEU* 3.5 11.5 - - - +
22B GLU* 1.3 76.4 - - + +
24B ARG* 1.3 62.9 + - - +
26B GLN* 3.0 4.6 + - - +
27B GLY 3.0 4.9 + - - -
28B LEU* 2.8 46.3 + - + +
29B TYR* 3.5 26.8 - - + -
44B HIS* 3.4 6.7 + - - +
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Residues in contact with ARG 24 (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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20B LEU 3.0 10.5 + - - +
21B ASN* 3.0 37.3 + - - +
23B GLN* 1.3 76.8 - - - +
25B LEU* 1.3 83.7 + - - +
27B GLY* 2.8 21.0 + - - -
30B CYS* 3.9 14.7 - - - -
41B PHE* 5.5 2.6 - - - -
42B LYS* 3.5 27.2 + - - +
44B HIS* 4.0 10.5 - - + -
79B GLN* 5.8 4.4 + - - +
82B LEU* 3.6 29.4 - - - +
83B SER* 4.0 22.4 + - - +
86B TYR* 3.5 29.1 - - + +
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Residues in contact with LEU 25 (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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21B ASN* 3.0 39.2 + - - +
22B GLU* 3.7 11.4 - - + +
23B GLN 3.2 0.2 - - - -
24B ARG* 1.3 108.0 - - - +
26B GLN* 1.3 62.6 + - + +
27B GLY 3.8 0.2 + - - -
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Residues in contact with GLN 26 (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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22B GLU* 3.1 27.5 + - - +
23B GLN* 3.0 9.0 + - - +
25B LEU* 1.3 81.4 - - + +
27B GLY* 1.3 59.8 + - - +
28B LEU* 3.4 29.0 + - + +
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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
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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