Contacts of the helix formed by residues 12 - 25 (chain A) in PDB entry 2GB0
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY 3.4 7.3 + - - -
11A ALA* 1.3 75.8 - - - +
13A SER* 1.3 66.9 + - - -
14A MET 3.3 2.2 - - - -
15A GLY 4.2 1.2 - - - +
16A MET* 2.9 26.9 + - - +
44A HIS* 4.2 9.0 - - - -
153A ILE* 3.9 7.6 - - - +
400A FAD 3.4 28.5 + - - -
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 1.3 72.8 - - - +
14A MET* 1.3 62.0 + - - +
16A MET* 4.8 0.2 - - - +
17A ALA* 3.6 13.9 + - - +
44A HIS* 3.5 7.1 - - - +
153A ILE* 3.6 14.8 - - - +
156A TYR* 5.3 1.9 - - - -
347A PHE* 3.3 26.9 - - - -
350A SER* 3.5 20.6 + - - -
400A FAD 2.8 52.5 + - - -
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Residues in contact with MET 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 1.3 75.7 - - - +
15A GLY* 1.3 66.4 + - - +
17A ALA* 3.4 4.4 + - - +
18A ALA* 3.0 23.2 + - - +
200A SER* 4.2 9.2 - - - -
339A ALA* 4.6 0.9 - - + -
342A PHE* 3.6 41.5 - - + -
346A GLY 3.3 34.8 - - - +
350A SER* 3.6 26.9 - - - -
353A VAL* 3.8 18.6 - - + -
354A GLY* 4.3 1.2 - - - -
357A LEU* 4.0 20.4 - - + +
400A FAD 3.0 31.6 + - - +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.7 8.4 - - - +
10A GLY 3.4 22.0 + - - -
11A ALA* 4.3 1.1 - - - -
12A GLY 3.5 3.2 + - - +
14A MET* 1.3 80.3 - - - +
16A MET* 1.3 58.2 + - - +
18A ALA* 3.3 5.8 + - - +
19A GLY 2.8 23.0 + - - -
31A LEU* 3.3 14.0 - - - +
200A SER* 3.4 13.3 + - - -
357A LEU* 5.3 0.9 - - - -
400A FAD 4.4 0.2 + - - -
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Residues in contact with MET 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.3 34.5 - - + +
12A GLY 2.9 23.1 + - - +
13A SER 4.8 0.4 - - - +
15A GLY* 1.3 68.6 - - - -
17A ALA* 1.3 65.2 + - - +
19A GLY* 3.3 1.6 + - - -
20A TYR* 3.0 23.0 + - - +
31A LEU* 4.2 21.8 - - - -
37A PRO* 4.0 14.8 - - + -
153A ILE* 3.6 18.2 - - + +
156A TYR* 3.8 6.6 - - + +
157A ARG* 3.6 60.1 - - + +
160A ALA* 5.1 2.4 - - - +
167A VAL* 4.8 6.7 - - + -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER 3.6 15.8 + - - +
14A MET 3.4 3.9 + - - +
16A MET* 1.3 74.7 - - - +
18A ALA* 1.3 65.5 + - - +
20A TYR* 3.3 3.5 + - - +
21A GLN* 3.0 27.0 + - - +
156A TYR* 3.6 32.4 - - + -
350A SER 3.3 26.5 - - - +
351A SER* 4.4 1.8 - - - +
354A GLY* 3.8 5.6 - - - -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.8 2.7 - - + -
14A MET 3.0 14.5 + - - +
15A GLY* 3.5 9.9 - - - +
16A MET 3.2 0.2 - - - -
17A ALA* 1.3 75.4 - - - +
19A GLY* 1.3 58.5 + - - +
21A GLN* 3.2 2.8 + - - +
22A LEU* 2.9 34.4 + - - +
198A ILE* 4.1 16.2 - - + -
354A GLY* 3.6 13.6 - - - +
357A LEU* 4.0 28.3 - - + -
358A SER 4.9 1.1 - - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.7 1.0 - - - +
15A GLY 2.8 14.7 + - - -
16A MET 3.3 3.1 + - - -
17A ALA 3.3 0.4 - - - -
18A ALA* 1.3 77.4 - - - +
20A TYR* 1.3 56.5 + - - +
22A LEU* 3.8 2.4 - - - +
23A ALA* 2.9 32.4 + - - +
29A THR* 4.5 10.5 - - - +
31A LEU* 3.9 23.1 - - - -
160A ALA* 4.0 7.1 - - - +
165A ALA* 4.8 1.6 - - - +
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET 3.0 12.4 + - - +
17A ALA 3.6 8.1 - - - +
19A GLY* 1.3 73.9 - - - +
21A GLN* 1.3 82.9 + - + +
23A ALA* 4.0 0.7 - - - +
24A LYS* 3.0 71.5 + - + +
71A LEU* 6.2 1.6 - - + -
74A GLU* 5.4 1.6 + - - +
75A LEU* 5.4 0.8 - - + -
78A GLU* 2.6 34.7 + - - -
156A TYR* 3.4 43.7 - + + +
159A LEU* 3.8 33.7 - - + -
160A ALA* 3.7 12.4 - - - +
163A ARG* 5.3 5.1 - - - -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 3.0 17.9 + - - +
18A ALA 3.2 6.7 + - - +
20A TYR* 1.3 96.4 - - + +
22A LEU* 1.3 62.8 + - - +
24A LYS* 3.6 24.2 + - - +
25A GLN* 3.4 28.1 + - - +
71A LEU* 4.3 18.4 - - - +
156A TYR* 5.2 3.0 + - + -
351A SER 4.6 3.4 - - - +
354A GLY* 3.8 1.3 - - - +
355A GLU* 3.8 42.3 + - - +
358A SER* 3.7 19.0 - - - -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.6 33.4 - - + -
8A VAL* 4.3 4.7 - - + -
18A ALA 2.9 20.1 + - - +
19A GLY 3.8 2.5 - - - +
21A GLN* 1.3 75.2 - - - +
23A ALA* 1.3 66.9 + - - +
25A GLN* 3.0 13.2 + - - +
26A GLY 3.5 0.2 + - - -
27A VAL* 3.1 29.2 + - + +
29A THR* 3.4 22.2 - - + +
198A ILE* 3.9 15.9 - - + -
358A SER* 3.3 25.6 - - - +
361A ALA* 4.9 1.8 - - + -
362A LEU* 3.8 31.9 - - + -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 2.9 21.3 + - - +
20A TYR 4.0 2.9 - - - +
22A LEU* 1.3 73.0 - - - +
24A LYS* 1.3 61.9 + - - +
26A GLY* 3.0 14.7 + - - -
27A VAL 4.0 11.4 + - - +
29A THR* 4.3 1.1 + - - +
160A ALA* 3.7 31.2 - - - +
163A ARG* 3.9 24.2 - - + +
165A ALA* 4.1 12.8 - - + +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.0 60.2 + - + +
21A GLN* 3.6 25.4 + - - +
23A ALA* 1.3 77.2 - - - +
25A GLN* 1.3 61.7 + - + +
26A GLY 3.3 0.7 + - - -
71A LEU* 5.8 2.2 - - - +
74A GLU* 4.8 10.3 + - - -
78A GLU* 5.1 2.9 + - - +
163A ARG* 3.7 28.2 - - - +
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 3.4 17.7 + - - +
22A LEU* 3.0 8.8 + - - +
24A LYS* 1.3 81.4 - - + +
26A GLY* 1.3 61.8 + - - +
27A VAL* 3.5 10.2 + - + +
358A SER* 3.4 25.1 + - - -
359A GLN* 6.2 1.4 - - - +
362A LEU* 3.7 19.3 - - - +
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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