Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 2GDZ
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 3.4 7.1 - - - +
13A ALA 3.2 0.6 - - - -
14A ALA* 1.3 79.4 - - - +
16A GLY* 1.3 70.1 + - - +
17A ILE 3.5 0.3 + - - -
18A GLY 3.4 5.4 + - - -
19A ARG* 3.1 20.2 + - - +
38A ASN* 4.6 14.0 + - - +
41A ALA* 4.6 8.3 - - + +
189A ALA* 3.6 17.2 - - - +
300A NAD 3.2 56.3 + - - +
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Residues in contact with GLY 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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15A GLN* 1.3 75.5 - - - +
17A ILE* 1.3 63.7 + - - -
19A ARG* 3.2 4.9 + - - +
20A ALA* 3.1 19.6 + - - +
188A THR* 3.9 13.9 - - - -
222A PRO* 4.3 7.9 - - - +
300A NAD 3.5 17.3 - - - -
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Residues in contact with ILE 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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16A GLY* 1.3 71.0 - - - -
18A GLY* 1.3 50.7 + - - +
20A ALA* 3.1 9.8 + - - +
21A PHE* 2.8 69.0 + - + -
91A ASN* 3.6 8.5 - - - +
136A MET* 4.4 7.2 - - + -
183A PRO* 4.8 1.1 - - + -
186A VAL* 4.0 35.7 - - + -
188A THR* 4.2 2.7 - - + -
222A PRO* 4.4 4.0 - - + +
225A ILE* 4.0 16.4 - - + -
300A NAD 2.8 56.7 + - + +
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Residues in contact with GLY 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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10A VAL* 3.8 10.3 - - - +
12A GLY 3.4 8.7 - - - -
13A ALA* 3.8 10.3 - - - -
15A GLN 3.4 2.4 + - - -
16A GLY 3.3 0.8 - - - -
17A ILE* 1.3 76.1 - - - +
19A ARG* 1.3 57.8 + - - +
21A PHE* 3.1 7.2 + - - +
22A ALA* 2.9 27.2 + - - +
91A ASN* 3.3 29.2 - - - +
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Residues in contact with ARG 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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13A ALA 3.2 15.1 + - - +
14A ALA 3.8 11.9 + - - -
15A GLN* 3.1 23.5 + - - +
16A GLY 3.7 2.5 - - - +
18A GLY* 1.3 77.1 - - - +
20A ALA* 1.3 55.9 + - - +
22A ALA* 3.2 4.3 + - + +
23A GLU* 2.9 61.3 + - + +
44A GLN 5.3 0.6 - - - -
45A CYS* 3.8 41.7 + - - +
48A ALA* 3.5 28.3 - - - +
49A LEU* 4.6 7.2 - - + +
52A GLN* 5.3 3.6 - - - +
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Residues in contact with ALA 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 GLY 3.1 7.5 + - - +
17A ILE 3.3 8.3 - - - +
19A ARG* 1.3 77.0 - - - +
21A PHE* 1.3 56.1 + - - +
23A GLU* 3.4 14.0 + - - +
24A ALA* 2.9 31.2 + - - +
222A PRO* 3.7 43.5 - - + +
223A PRO* 4.1 7.2 - - + -
226A ALA* 3.6 8.0 - - + +
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Residues in contact with PHE 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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10A VAL* 4.2 10.3 - - + -
17A ILE* 2.8 46.1 + - + -
18A GLY* 3.1 14.8 + - - +
20A ALA* 1.3 68.8 - - + +
22A ALA* 1.3 58.1 + - - +
24A ALA* 3.2 2.3 + - - +
25A LEU* 2.8 41.5 + - - +
89A VAL* 3.7 28.3 - - + -
91A ASN* 3.8 6.1 - - + -
136A MET* 3.6 26.7 - - - -
181A ILE* 4.3 7.4 - - + -
225A ILE* 3.6 15.3 - - + -
226A ALA* 3.6 29.4 - - + -
229A LEU* 3.6 26.2 - - + -
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Residues in contact with ALA 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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10A VAL* 4.7 2.0 - - + +
13A ALA* 4.7 2.7 - - + -
18A GLY 2.9 12.4 + - - +
19A ARG* 3.2 9.8 + - - +
21A PHE* 1.3 74.9 - - - +
23A GLU* 1.3 57.8 + - - +
25A LEU* 3.3 4.6 + - - +
26A LEU* 2.9 37.5 + - + +
32A VAL* 4.1 22.9 - - + -
34A LEU* 4.0 29.2 - - + -
49A LEU* 4.8 6.5 - - + -
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Residues in contact with GLU 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 ARG* 2.9 53.8 + - + +
20A ALA* 3.8 11.9 + - - +
22A ALA* 1.3 75.9 - - - +
24A ALA* 1.3 56.3 + - - +
26A LEU* 3.3 8.9 + - - +
27A LEU* 2.9 31.2 + - - +
49A LEU* 3.7 22.5 - - + +
52A GLN* 5.2 8.8 + - - +
53A PHE* 4.1 6.5 - - + -
223A PRO* 6.0 1.9 - - - +
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Residues in contact with ALA 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 ALA 2.9 17.9 + - - +
21A PHE* 3.7 3.1 - - - +
23A GLU* 1.3 75.8 - - - +
25A LEU* 1.3 63.5 + - - +
27A LEU* 3.3 9.0 + - - +
28A LYS* 3.1 29.1 + - + +
226A ALA* 3.6 22.4 - - + +
227A ASN* 6.0 0.9 - - - +
229A LEU* 5.9 0.4 - - + -
230A ILE* 4.3 16.4 - - + -
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Residues in contact with LEU 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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3A VAL* 4.2 12.8 - - + -
8A ALA* 3.8 13.5 - - + -
10A VAL* 3.6 29.8 - - + -
21A PHE 2.8 23.5 + - - +
22A ALA 3.6 3.4 - - - +
24A ALA* 1.3 76.7 - - - +
26A LEU* 1.3 61.8 + - - +
28A LYS* 3.1 11.8 + - - +
29A GLY 3.2 0.3 + - - -
30A ALA* 3.0 28.8 + - + +
32A VAL* 3.7 13.5 - - + -
87A ILE* 4.3 9.2 - - + -
89A VAL* 4.9 2.2 - - + -
229A LEU* 4.0 14.1 - - + -
230A ILE* 3.8 14.1 - - + -
233A ILE* 3.7 29.2 - - + -
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Residues in contact with LEU 26 (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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22A ALA* 2.9 24.0 + - + +
23A GLU 3.7 0.9 - - - +
25A LEU* 1.3 76.1 - - - +
27A LEU* 1.3 62.6 + - - +
29A GLY* 3.0 15.1 + - - -
30A ALA 3.5 20.1 - - - +
32A VAL* 3.9 11.7 - - + -
34A LEU* 5.4 0.2 - - + -
49A LEU* 4.0 20.4 - - + -
53A PHE* 3.5 46.4 - - + -
57A LYS* 3.6 35.2 + - + +
58A THR* 3.6 27.4 - - + -
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Residues in contact with LEU 27 (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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23A GLU 2.9 17.2 + - - +
24A ALA* 3.7 9.0 - - - +
25A LEU 3.3 0.2 - - - -
26A LEU* 1.3 77.2 - - - +
28A LYS* 1.3 60.2 + - + +
29A GLY* 3.2 2.6 + - - -
53A PHE* 3.5 21.2 - - + -
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Residues in contact with LYS 28 (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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3A VAL* 3.6 18.3 - - + +
4A ASN* 3.3 26.4 + - - +
24A ALA 3.1 14.1 + - - +
25A LEU* 3.1 10.6 + - - +
27A LEU* 1.3 77.8 - - + +
29A GLY* 1.3 57.4 + - - +
30A ALA 3.5 1.3 - - - -
230A ILE* 3.5 26.6 - - + +
234A GLU* 2.8 32.7 + - - -
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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