Contacts of the helix formed by residues 8 - 22 (chain A) in PDB entry 2GER
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 ALA 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY* 1.3 77.6 - - - +
9A GLY* 1.3 72.1 + - - +
10A GLN 3.6 0.9 + - - -
11A LEU* 4.3 1.6 + - - +
12A ALA* 3.0 35.1 + - - +
32A ALA* 4.9 4.0 - - + -
33A SER 4.1 6.7 - - - +
34A SER* 5.4 0.9 - - - -
35A PRO* 5.8 0.7 - - + -
38A ASP* 5.4 2.0 - - - +
41A THR* 3.5 13.9 - - + -
42A VAL* 4.7 11.9 - - + -
45A LEU* 4.8 5.8 - - + -
52A LEU* 5.7 2.0 - - + -
69A ALA* 4.0 10.2 + - - +
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Residues in contact with GLY 9 (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 ALA* 1.3 82.9 - - - +
10A GLN* 1.3 70.0 + - - +
13A PHE* 3.5 7.3 + - - +
38A ASP* 4.6 9.1 + - - -
41A THR* 2.9 36.8 + - - +
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Residues in contact with GLN 10 (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 ALA 3.6 0.2 + - - -
9A GLY* 1.3 73.5 - - - +
11A LEU* 1.3 56.7 + - - +
12A ALA 2.5 17.5 + - - -
13A PHE* 2.5 31.3 + - - -
14A ALA* 3.1 8.1 + - - -
40A ALA* 5.7 6.2 - - - +
41A THR* 4.4 9.0 + - - -
124A THR* 4.4 18.6 - - + -
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Residues in contact with LEU 11 (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 ALA 4.6 2.2 - - - +
10A GLN* 1.3 76.9 - - - +
12A ALA* 1.3 63.6 + - - +
14A ALA* 2.9 13.6 + - + +
15A LEU* 2.8 46.6 + - + +
69A ALA* 4.6 18.2 - - + +
95A CYS* 4.6 26.7 - - + +
121A MET* 5.9 3.4 - - + -
122A THR* 4.8 27.4 - - + +
123A ASN 5.7 1.8 - - - -
124A THR* 4.9 6.1 - - + +
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Residues in contact with ALA 12 (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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5A PHE* 3.9 30.3 - - + -
8A ALA* 3.0 42.4 + - - +
9A GLY 3.9 0.2 - - - +
10A GLN 2.5 4.9 + - - -
11A LEU* 1.3 76.4 - - - +
13A PHE* 1.3 54.3 + - - +
15A LEU* 3.0 1.4 + - - +
16A ALA* 2.5 40.5 + - + +
32A ALA* 5.3 2.5 - - + -
41A THR* 5.2 0.7 - - + -
45A LEU* 5.3 4.3 - - + -
69A ALA* 4.6 3.2 - - + +
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Residues in contact with PHE 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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9A GLY 3.5 9.6 + - - +
10A GLN* 2.5 22.1 + - - +
12A ALA* 1.3 75.7 - - - +
14A ALA* 1.3 56.4 + - - +
16A ALA* 3.8 6.1 - - - -
17A LYS* 2.8 66.4 + - + +
41A THR* 4.8 6.7 - - + -
44A ALA* 4.4 22.4 - - + -
45A LEU* 3.7 30.6 - - + +
48A MET* 4.2 9.6 - - + -
127A VAL* 5.1 12.1 - - + -
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Residues in contact with ALA 14 (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 GLN 3.1 5.1 + - - +
11A LEU* 2.9 26.1 + - + +
13A PHE* 1.3 79.8 - - - +
15A LEU* 1.3 64.4 + - - +
17A LYS* 3.6 1.6 - - - +
18A GLY 2.9 19.9 + - - -
123A ASN 4.9 0.2 - - - +
124A THR* 3.8 20.6 - - + +
126A VAL* 3.2 15.5 - - + +
127A VAL* 3.5 28.1 - - + -
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Residues in contact with LEU 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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5A PHE* 3.4 32.8 - - + -
11A LEU* 2.8 34.4 + - + +
12A ALA 3.6 0.4 - - - +
14A ALA* 1.3 67.7 - - - +
16A ALA* 1.3 69.4 + - - +
18A GLY* 3.0 2.4 + - - -
19A PHE* 2.9 51.4 + - + -
67A PHE* 4.8 14.6 - - + -
69A ALA* 6.1 1.3 - - + -
95A CYS* 5.1 7.6 - - - -
120A CYS* 5.9 0.7 - - - -
122A THR* 4.2 11.4 - - + -
126A VAL* 3.5 30.5 - - + -
153A LEU* 4.5 10.3 - - + -
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Residues in contact with ALA 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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5A PHE* 3.8 18.4 - - + -
12A ALA* 2.5 26.1 + - + +
13A PHE* 3.8 7.6 - - - +
15A LEU* 1.3 73.9 - - - +
17A LYS* 1.3 59.0 + - - +
19A PHE* 3.5 4.9 + - - +
20A THR* 3.1 24.3 + - - +
30A ILE* 4.8 5.9 - - + +
45A LEU* 4.1 10.5 - - + -
48A MET* 3.1 20.4 - - + +
50A VAL* 4.7 6.7 - - + -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 2.8 42.4 + - + +
16A ALA* 1.3 71.8 - - - +
18A GLY* 1.3 63.3 + - - +
20A THR* 2.5 21.9 + - - +
21A ALA* 3.1 19.7 + - + +
48A MET* 3.5 30.7 - - - +
127A VAL* 3.4 31.4 - - + +
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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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14A ALA 2.9 15.0 + - - -
15A LEU 3.6 1.8 - - - -
17A LYS* 1.3 74.8 - - - +
19A PHE* 1.3 51.6 + - - +
21A ALA* 3.7 2.9 - - - +
22A ALA* 2.8 35.9 + - - +
126A VAL 3.8 21.3 - - - -
127A VAL* 4.2 6.7 - - - +
128A VAL 4.4 6.0 - - - +
156A VAL* 3.3 14.1 - - - +
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Residues in contact with PHE 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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3A VAL* 6.0 3.1 - - + -
5A PHE* 4.1 8.5 - + - -
15A LEU* 2.9 42.6 + - + +
16A ALA* 3.6 5.2 - - - +
18A GLY* 1.3 73.6 - - - +
20A THR* 1.3 69.3 + - - +
22A ALA* 3.1 14.6 + - - +
24A VAL* 3.4 17.3 + - + +
25A LEU* 4.0 20.6 + - + -
30A ILE* 5.4 4.5 - - + -
67A PHE* 3.9 23.8 - + - -
152A LEU* 3.2 50.5 - - + -
153A LEU* 4.1 20.0 - - + -
155A SER* 4.2 3.6 - - - -
156A VAL* 3.5 18.2 - - + -
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Residues in contact with THR 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 ALA 3.1 7.2 + - - +
17A LYS* 2.5 36.2 + - - +
19A PHE* 1.3 76.4 - - - +
21A ALA* 1.3 51.1 + - - +
23A GLY* 2.7 30.5 + - - -
24A VAL 4.1 0.3 + - - -
25A LEU 5.4 1.5 - - - +
26A ALA* 5.4 5.6 - - - +
27A ALA* 3.7 35.4 - - + +
30A ILE* 4.4 5.6 - - + -
48A MET* 3.0 31.2 - - + +
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Residues in contact with ALA 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 LYS* 3.1 20.3 + - + +
18A GLY* 4.0 4.7 - - - +
20A THR* 1.3 79.3 + - - +
22A ALA* 1.3 60.5 + - - +
23A GLY* 3.0 2.2 + - - -
127A VAL 5.5 3.8 - - - +
128A VAL 5.4 4.5 - - - +
129A ARG* 5.9 0.2 + - - -
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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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18A GLY 2.8 23.0 + - - +
19A PHE* 3.3 9.4 - - - +
20A THR 2.9 0.8 + - - -
21A ALA* 1.3 73.6 - - - +
23A GLY* 1.3 58.9 + - - +
24A VAL* 3.1 10.0 + - + +
129A ARG* 5.1 12.9 + - - +
155A SER* 3.1 39.5 - - - +
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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