Contacts of the strand formed by residues 19 - 27 (chain A) in PDB entry 2XOA
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 GLU 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ASP 3.6 1.7 + - - +
18A ASP* 1.3 75.3 - - - +
20A VAL* 1.3 57.9 + - - +
66A CYS* 3.4 34.3 - - + +
67A PHE 3.2 17.0 - - - +
68A THR* 4.2 11.7 + - - +
112A ALA* 4.6 8.8 - - - +
204A PRO* 3.5 1.7 - - - +
205A ILE* 2.6 41.1 + - + +
206A CYS* 3.0 36.7 + - - +
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Residues in contact with VAL 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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14A LEU* 4.3 15.9 - - + -
18A ASP* 4.6 2.5 - - + +
19A GLU* 1.3 81.1 - - - +
21A VAL* 1.3 66.7 + - - +
22A LEU* 5.2 2.2 - - + -
65A CYS 3.7 0.5 - - - +
66A CYS* 3.7 3.8 - - - -
67A PHE* 2.6 45.1 + - + +
69A LEU* 3.8 27.1 - - + -
109A LEU* 3.9 22.9 - - + -
202A MET* 3.7 31.0 - - + -
203A ASN 3.2 12.1 - - - +
204A PRO* 4.3 0.9 - - + -
205A ILE* 4.0 3.4 - - - +
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Residues in contact with VAL 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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20A VAL* 1.3 75.9 - - - +
22A LEU* 1.3 63.3 + - - +
23A GLN* 5.0 1.8 - - + -
36A CYS* 4.1 24.9 - - + -
62A LEU* 5.0 5.2 - - + -
65A CYS* 3.6 35.4 - - + +
66A CYS* 4.5 3.6 - - - +
67A PHE* 5.4 0.2 - - - -
201A ASN 3.4 0.5 - - - +
202A MET* 3.3 5.4 - - - -
203A ASN* 2.9 53.5 + - + +
205A ILE* 3.7 25.4 - - + -
267A ILE* 4.4 9.2 - - + -
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Residues in contact with LEU 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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20A VAL* 5.2 3.4 - - + -
21A VAL* 1.3 72.1 - - - +
23A GLN* 1.3 60.0 + - - +
36A CYS* 3.1 3.1 - - - -
37A LEU* 2.7 65.0 + - + +
65A CYS 4.8 2.2 + - - -
67A PHE* 5.4 6.8 - - + -
109A LEU* 3.9 23.1 - - + -
118A LEU* 4.2 1.8 - - + -
171A LEU* 3.9 25.6 - - + -
180A LEU* 4.0 6.7 - - + -
200A TRP* 3.6 16.3 - - + -
201A ASN 4.2 2.2 - - - +
202A MET* 3.3 45.5 - - + +
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Residues in contact with GLN 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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21A VAL* 5.0 2.1 - - + +
22A LEU* 1.3 73.2 - - - +
24A CYS* 1.3 71.3 + - - +
34A LYS* 3.1 39.5 + - + +
35A LEU 3.2 15.3 - - - +
36A CYS* 4.2 12.4 - - - -
52A THR* 4.1 10.2 + - - -
200A TRP* 3.2 10.8 - - - -
201A ASN* 2.7 56.9 + - + +
203A ASN* 3.6 26.5 + - - +
267A ILE* 4.8 9.5 - - - +
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Residues in contact with CYS 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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23A GLN* 1.3 77.7 - - - +
25A SER* 1.3 65.7 + - - +
34A LYS* 3.6 2.3 - - - -
35A LEU* 2.9 41.9 + - - +
49A LEU* 4.2 11.7 - - - -
182A LEU* 4.1 21.5 - - - -
198A THR* 4.1 9.0 - - + -
199A LEU 3.8 14.8 - - - +
200A TRP* 3.5 35.6 - - + -
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Residues in contact with SER 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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24A CYS* 1.3 77.5 - - - +
26A ALA* 1.3 61.8 + - - +
32A GLN* 4.1 23.4 + - - -
33A LEU 3.2 15.7 - - - -
34A LYS* 4.5 9.2 - - - -
35A LEU* 4.8 0.9 - - - -
182A LEU* 3.4 16.0 - - - +
199A LEU 4.9 1.4 + - - -
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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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25A SER* 1.3 75.8 - - - +
27A THR* 1.3 63.2 - - - +
28A VAL* 5.2 3.1 - - + -
32A GLN* 3.6 5.2 - - - -
33A LEU* 2.7 36.3 + - + +
35A LEU* 4.0 19.5 - - + -
182A LEU* 4.1 12.6 - - + -
189A LEU* 4.2 20.4 - - + -
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Residues in contact with THR 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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26A ALA* 1.3 72.8 - - - +
28A VAL* 1.3 69.5 + - - +
30A LYS* 4.3 14.2 + - - -
31A GLU 3.4 7.0 + - - -
32A GLN* 3.0 22.6 + - - +
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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