Contacts of the helix formed by residues 28 - 37 (chain A) in PDB entry 1P9B
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASP 3.2 2.8 + - - -
27A GLU* 1.3 80.9 - - - +
29A LYS* 1.3 64.6 + - - +
30A GLY 3.5 2.2 - - - -
31A LYS* 3.4 8.8 + - - +
32A ILE* 3.4 20.6 + - - +
273A VAL* 4.1 6.3 - - - +
336A ASN* 4.3 3.3 + - - -
338A THR* 4.7 3.0 - - - +
1603A GDP 2.8 34.7 + - - -
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Residues in contact with LYS 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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19A ILE* 4.4 10.1 - - + +
21A GLY* 3.7 22.2 - - - +
26A ASP 3.4 0.4 - - - +
27A GLU* 2.9 21.7 + - - +
28A GLY* 1.3 70.1 - - - +
30A GLY* 1.3 64.3 + - - +
31A LYS 3.2 0.3 + - - -
32A ILE* 3.3 9.7 - - - +
33A ILE* 2.9 31.7 + - + +
54A HIS* 3.5 16.8 - - + -
229A GLU* 5.4 0.9 - - + -
230A GLY 3.4 28.5 - - - +
232A ASN 3.3 16.6 + - - +
273A VAL* 4.0 20.2 - - + -
1601A IMO 2.8 22.8 + - - -
1603A GDP 2.6 30.7 + - - +
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Residues in contact with GLY 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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29A LYS* 1.3 76.4 - - - +
31A LYS* 1.3 57.3 + - - +
33A ILE* 3.7 2.6 - - - +
34A ASP* 3.0 30.8 + - - +
54A HIS* 3.8 7.5 - - - +
55A THR 3.8 9.6 - - - -
56A ILE* 4.0 1.6 - - - +
70A CYS* 3.7 28.9 - - - +
1603A GDP 2.9 16.9 + - - -
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Residues in contact with LYS 31 (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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28A GLY* 3.4 12.8 + - - +
29A LYS 3.1 0.6 - - - -
30A GLY* 1.3 77.9 - - - +
32A ILE* 1.3 59.3 + - - +
34A ASP* 3.4 6.3 + - - +
35A MET* 3.0 25.9 + - + +
55A THR 3.5 13.3 + - - +
56A ILE* 5.1 2.2 - - - +
57A SER 5.9 0.9 - - - +
336A ASN* 6.2 0.2 - - - +
338A THR* 6.0 2.4 - - + +
425A GLY* 3.7 8.7 - - - -
427A GLY 2.5 24.8 + - - +
428A PRO 3.9 11.7 - - - +
429A ASN 3.3 22.4 - - - +
430A ARG* 4.8 7.0 - - - +
432A ASN 2.8 22.1 + - - -
433A MET* 3.8 21.0 - - + +
1603A GDP 3.2 39.3 + - + +
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Residues in contact with ILE 32 (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 ILE* 3.4 27.6 - - + -
28A GLY 3.4 7.2 + - - +
29A LYS* 3.3 11.9 + - - +
31A LYS* 1.3 75.8 - - - +
33A ILE* 1.3 62.6 + - - +
35A MET* 4.1 13.2 - - + -
36A LEU* 2.8 50.8 + - + +
271A VAL* 4.2 9.6 - - + -
273A VAL* 4.5 0.7 - - + -
336A ASN* 3.5 42.0 - - + +
423A TRP* 3.9 25.8 - - + -
433A MET* 4.3 5.4 - - + -
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Residues in contact with ILE 33 (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 ILE* 3.2 29.6 - - + -
29A LYS 2.9 21.9 + - - +
30A GLY 3.7 4.0 - - - +
32A ILE* 1.3 77.2 - - - +
34A ASP* 1.3 51.9 + - - +
36A LEU 3.4 0.5 + - - -
37A SER* 2.7 42.1 + - - +
43A THR* 3.7 15.0 - - + -
70A CYS* 3.4 21.8 - - + -
227A LEU* 3.7 11.4 - - + +
228A ILE 4.4 2.0 - - - +
229A GLU* 3.4 59.7 - - + +
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Residues in contact with ASP 34 (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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30A GLY 3.0 17.6 + - - +
31A LYS* 3.7 5.5 - - - +
33A ILE* 1.3 78.3 - - - +
35A MET* 1.3 57.9 + - - +
37A SER* 3.3 2.7 + - - -
56A ILE* 3.5 24.2 - - + +
70A CYS 3.3 16.2 - - - +
73A LEU* 3.6 12.0 - - - +
74A TYR* 2.7 40.2 + - - -
430A ARG* 2.6 55.6 + - - +
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Residues in contact with MET 35 (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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31A LYS* 3.0 17.9 + - + +
32A ILE* 3.5 9.0 - - + +
33A ILE 3.2 0.2 - - - -
34A ASP* 1.3 80.2 - - - +
36A LEU* 1.3 79.4 + - + +
37A SER 3.3 0.3 + - - -
38A GLU* 3.3 19.1 + - - +
39A TYR* 4.9 2.9 - - - -
74A TYR* 3.9 0.6 + - - -
423A TRP* 3.4 38.4 - - + +
430A ARG* 4.2 30.6 - - + +
433A MET* 3.7 38.8 - - + -
435A VAL* 5.6 2.5 - - + -
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Residues in contact with LEU 36 (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 VAL* 5.0 8.7 - - + -
19A ILE* 3.9 17.3 - - + -
32A ILE* 2.8 43.4 + - + +
35A MET* 1.3 86.7 - - + +
37A SER* 1.3 57.6 + - - +
38A GLU 3.0 10.5 + - - -
39A TYR* 3.1 16.9 + - + +
40A SER* 3.1 14.7 + - - +
227A LEU* 3.5 23.6 - - + -
271A VAL* 5.3 0.9 - - + -
423A TRP* 4.3 23.8 - - + +
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Residues in contact with SER 37 (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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33A ILE* 2.7 28.4 + - - +
34A ASP 3.6 7.4 - - - -
35A MET 3.2 1.0 - - - -
36A LEU* 1.3 69.7 - - - +
38A GLU* 1.3 64.3 + - - +
39A TYR 3.1 1.0 + - - -
40A SER* 3.4 19.6 + - - +
43A THR* 3.1 21.8 + - - -
71A GLY* 3.3 25.1 - - - -
74A TYR* 3.8 17.6 - - - +
77A ASN* 4.2 4.5 + - - +
227A LEU* 3.5 9.2 - - - +
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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