Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 1B5X
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 LEU 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ALA 3.4 19.5 - - - +
12A LEU* 3.4 40.2 - - + -
13A LYS* 4.1 13.5 - - + +
17A MET* 4.7 7.6 - - + -
18A ASP* 3.2 29.5 + - + +
23A ILE 3.7 0.6 + - - -
24A SER* 1.3 74.0 - - - +
26A ALA* 1.3 56.7 + - - +
28A TRP* 3.0 11.4 + - + +
29A MET* 2.9 29.8 + - + +
125A VAL* 4.0 11.0 - - + -
130A VAL* 3.7 35.2 - - + -
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Residues in contact with ALA 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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24A SER* 3.9 7.2 - - - +
25A LEU* 1.3 79.1 - - - +
27A ASN* 1.3 56.4 + - - +
29A MET* 3.4 4.4 + - - +
30A CYS* 2.9 28.4 + - - +
121A VAL* 3.2 40.7 - - + +
122A ARG* 4.3 3.4 - - - +
124A TYR* 4.2 0.3 - - - +
125A VAL* 3.8 26.7 - - + +
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Residues in contact with ASN 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 ILE* 3.6 18.0 - - + +
24A SER* 2.9 36.1 + - - +
26A ALA* 1.3 75.1 - - - +
28A TRP* 1.3 59.6 + - - +
30A CYS* 3.2 5.9 + - - +
31A LEU* 2.9 29.5 + - - +
106A ILE* 5.0 1.3 - - + -
112A TRP* 2.8 43.3 + - - +
116A CYS* 4.5 2.1 - - - +
121A VAL* 4.2 20.0 - - - +
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Residues in contact with TRP 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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12A LEU* 4.1 18.6 - - + -
17A MET* 3.0 68.3 + - + +
20A TYR* 4.6 9.5 - + - +
23A ILE* 3.4 31.5 + - + +
24A SER 3.3 21.0 + - - -
25A LEU* 3.0 10.2 + - - +
27A ASN* 1.3 77.2 - - - +
29A MET* 1.3 57.6 + - - +
31A LEU* 3.3 19.3 + - + +
32A ALA* 3.0 30.1 + - - +
57A PHE* 4.1 9.1 - + + -
96A ALA* 4.0 21.1 - - + -
100A VAL* 3.6 31.0 - - + -
106A ILE* 3.9 16.6 - - + -
109A TRP* 4.3 1.3 - + - -
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Residues in contact with MET 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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5A ARG* 3.3 35.2 - - + +
8A LEU* 3.7 17.3 - - + -
9A ALA* 3.6 24.2 - - + +
12A LEU* 3.8 6.3 - - + -
25A LEU* 2.9 20.9 + - + +
26A ALA 3.5 9.2 - - - +
28A TRP* 1.3 78.1 - - - +
30A CYS* 1.3 56.5 + - - +
32A ALA* 3.5 1.9 + - - -
33A LYS* 3.1 29.3 + - - +
38A TYR* 3.5 32.5 - - + +
124A TYR* 3.7 20.2 - - + +
125A VAL* 4.0 17.0 - - + -
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Residues in contact with CYS 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 ALA 2.9 16.5 + - - +
27A ASN 3.6 3.8 - - - +
29A MET* 1.3 73.8 - - - +
31A LEU* 1.3 64.4 + - - +
33A LYS 3.5 0.2 + - - -
34A TRP* 3.2 40.5 + - - +
115A ARG 3.8 4.9 - - - -
116A CYS* 2.0 50.4 - - - -
121A VAL* 3.8 9.6 - - + -
124A TYR* 3.7 34.0 - - + -
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Residues in contact with LEU 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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27A ASN 2.9 13.2 + - - +
28A TRP* 3.3 22.2 + - + +
30A CYS* 1.3 77.1 - - - +
32A ALA* 1.3 57.7 + - - +
34A TRP* 3.2 4.6 + - - +
35A GLU* 2.9 48.3 + - + +
57A PHE* 3.7 23.6 - - + -
106A ILE* 4.1 3.6 - - + -
109A TRP* 3.5 62.8 - - + -
111A ALA* 5.2 0.9 - - + -
112A TRP* 4.0 21.5 - - + +
116A CYS* 3.8 5.5 - - - -
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Residues in contact with ALA 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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8A LEU* 4.1 9.2 - - + -
12A LEU* 5.6 0.4 - - + -
28A TRP 3.0 16.5 + - - +
29A MET 3.9 4.0 - - - +
30A CYS 3.5 0.2 - - - -
31A LEU* 1.3 74.8 - - - +
33A LYS* 1.3 62.4 + - - +
36A SER* 3.0 25.3 + - - -
37A GLY 3.1 5.7 + - - -
38A TYR* 3.4 13.3 + - + -
56A ILE* 3.6 33.2 - - + -
57A PHE* 3.9 13.9 - - + -
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Residues in contact with LYS 33 (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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29A MET 3.1 18.8 + - - +
30A CYS 3.6 5.6 - - - +
31A LEU 3.2 0.2 - - - -
32A ALA* 1.3 75.2 - - - +
34A TRP* 1.3 77.8 + - + +
37A GLY* 2.9 32.2 + - - +
38A TYR* 3.5 41.9 + - + +
124A TYR* 3.9 18.4 - - + -
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Residues in contact with TRP 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 CYS* 3.2 34.1 + - - +
31A LEU* 4.1 2.0 - - - +
33A LYS* 1.3 92.9 - - + +
35A GLU* 1.3 63.4 + - - +
111A ALA* 4.5 15.4 - - + +
115A ARG* 3.3 76.1 + - + +
116A CYS* 4.4 0.9 - - - -
119A ARG* 6.3 0.4 - - - -
124A TYR* 3.1 23.2 + - - -
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Residues in contact with GLU 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 LEU* 2.9 34.3 + - + +
34A TRP* 1.3 79.9 - - - +
36A SER* 1.3 59.1 + - - +
42A ALA* 5.2 0.5 - - - +
56A ILE 3.7 13.9 - - - +
57A PHE 3.8 9.6 - - - +
58A GLN* 3.1 41.3 - - + +
109A TRP* 3.2 28.8 - - - +
110A VAL 5.0 0.3 + - - -
111A ALA* 3.2 27.2 + - + +
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Residues in contact with SER 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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32A ALA 3.0 7.0 + - - -
35A GLU* 1.3 76.6 - - - +
37A GLY* 1.3 64.2 + - - +
38A TYR 3.3 1.0 + - - -
39A ASN* 3.2 42.3 + - - +
42A ALA* 3.7 17.1 - - - +
55A GLY 3.7 5.4 - - - -
56A ILE* 2.7 31.6 + - - +
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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