Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 1GWP
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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PRO* 5.1 5.8 - - - +
15A ILE* 1.3 84.1 - - - +
17A PRO* 1.4 70.4 - - - +
18A ARG* 3.1 9.9 + - - +
19A THR* 3.1 27.7 + - - +
20A LEU* 3.0 32.2 + - - +
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Residues in contact with PRO 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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15A ILE 4.6 1.3 - - - +
16A SER* 1.4 90.7 - - - +
18A ARG* 1.3 58.4 + - + +
19A THR 3.2 0.2 - - - -
20A LEU* 4.1 5.1 - - + +
21A ASN* 2.7 37.7 + - - +
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Residues in contact with ARG 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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16A SER* 3.1 7.2 + - - +
17A PRO* 1.3 82.2 - - + +
19A THR* 1.3 59.1 + - - +
21A ASN* 3.7 9.4 + - + +
22A ALA* 3.0 35.1 + - - +
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Residues in contact with THR 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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15A ILE* 4.4 15.7 - - + -
16A SER* 3.1 24.6 + - - +
18A ARG* 1.3 76.6 - - - +
20A LEU* 1.3 60.4 + - - +
22A ALA* 3.4 4.5 + - - +
23A TRP* 2.8 34.8 + - - +
43A LEU* 3.4 32.0 - - + +
55A MET* 4.4 11.9 - - - -
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Residues in contact with LEU 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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15A ILE* 3.1 40.2 - - + -
16A SER 3.0 14.3 + - - +
17A PRO* 4.1 4.5 - - + +
19A THR* 1.3 77.2 - - + +
21A ASN* 1.3 54.7 + - - +
23A TRP* 3.4 3.5 - - - +
24A VAL* 2.8 42.3 + - + +
54A THR* 3.1 22.0 - - + -
55A MET* 3.5 30.7 - - + -
58A THR* 3.6 27.1 - - + +
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Residues in contact with ASN 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 PRO 2.7 25.7 + - - +
18A ARG* 3.7 10.1 + - - +
20A LEU* 1.3 71.0 - - - +
22A ALA* 1.3 69.0 + - - +
24A VAL* 3.1 11.3 + - - +
25A LYS* 2.8 23.6 + - - +
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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 ARG* 3.0 23.2 + - - +
19A THR* 3.8 4.5 - - - +
21A ASN* 1.3 81.8 - - - +
23A TRP* 1.3 51.3 - - - +
25A LYS* 2.9 12.3 + - - +
26A VAL* 2.7 42.5 + - + +
39A MET* 6.2 0.9 - - + -
43A LEU* 6.2 1.6 - - + -
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Residues in contact with TRP 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 THR 2.8 22.4 + - - +
20A LEU* 3.4 5.8 - - - +
21A ASN 3.1 0.2 - - - -
22A ALA* 1.3 72.2 - - - +
24A VAL* 1.3 54.7 + - - +
26A VAL* 2.6 27.0 + - - +
27A VAL* 2.7 38.2 + - + +
36A VAL* 3.3 37.5 - - + -
39A MET* 3.5 24.5 - - + -
40A PHE* 2.8 58.8 - + + -
43A LEU* 4.6 3.1 - - + +
55A MET* 3.5 37.6 + - + -
58A THR* 3.3 28.9 - - + +
59A VAL* 4.5 12.8 - - + +
138A LEU* 5.5 4.7 - - + -
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Residues in contact with VAL 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 LEU* 2.8 31.6 + - + +
21A ASN* 3.4 9.2 - - - +
23A TRP* 1.3 74.4 - - - +
25A LYS* 1.3 57.9 - - - +
27A VAL* 3.5 6.0 + - - +
28A GLU* 2.9 42.1 + - + +
58A THR* 3.3 31.6 - - + +
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Residues in contact with LYS 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 ASN* 2.8 14.6 + - - +
22A ALA* 3.1 15.5 - - - +
24A VAL* 1.3 79.3 - - - +
26A VAL* 1.3 56.6 + - + +
28A GLU* 3.2 13.7 - - + +
29A GLU* 2.9 39.7 + - - +
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Residues in contact with VAL 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* 2.7 22.2 + - + +
23A TRP* 2.6 12.6 + - + +
25A LYS* 1.3 67.8 - - + +
27A VAL* 1.3 53.1 + - - +
28A GLU 2.9 1.1 - - - -
29A GLU* 2.6 12.2 + - - +
30A LYS* 2.5 57.1 + - + +
35A GLU 5.1 0.4 - - - +
36A VAL* 3.5 18.4 - - + -
39A MET* 3.3 41.1 - - + -
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Residues in contact with VAL 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 TRP* 2.7 67.4 + - + +
24A VAL* 3.9 6.3 - - - +
26A VAL* 1.3 71.4 - - - +
28A GLU* 1.3 59.3 - - - +
30A LYS* 3.9 7.9 - - - -
31A ALA* 2.5 39.1 + - - +
32A PHE* 4.8 7.4 - - + +
36A VAL* 4.3 3.1 - - + -
58A THR* 5.7 0.4 - - + -
59A VAL* 4.2 22.0 - - + -
60A GLY* 4.5 10.8 - - - +
62A HIS* 6.3 0.9 - - + -
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Residues in contact with GLU 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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24A VAL* 2.9 29.2 + - + +
25A LYS* 3.2 13.9 - - + +
26A VAL 2.8 1.2 + - - -
27A VAL* 1.3 80.0 - - - +
29A GLU* 1.3 58.2 + - + +
30A LYS 3.3 3.1 + - - -
31A ALA* 4.9 3.8 - - - +
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Residues in contact with GLU 29 (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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25A LYS* 2.9 25.2 + - - +
26A VAL* 2.6 12.1 + - - +
28A GLU* 1.3 73.9 - - + +
30A LYS* 1.3 81.5 + - + +
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Residues in contact with LYS 30 (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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26A VAL* 2.5 42.1 + - + +
27A VAL* 3.8 3.6 - - - +
28A GLU 3.1 0.6 - - - -
29A GLU* 1.3 105.4 + - + +
31A ALA* 1.3 75.2 + - - +
33A SER* 3.5 33.2 + - - -
35A GLU* 3.4 34.3 - - + -
36A VAL* 3.9 14.8 - - + +
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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