Contacts of the helix formed by residues 20 - 32 (chain A) in PDB entry 2CRX
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 1.3 76.4 + - - +
21A ASP* 1.3 68.3 + - - +
22A GLU 3.1 0.7 - - - -
23A VAL* 3.6 14.4 + - - +
24A ARG* 3.0 36.4 + - - +
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Residues in contact with ASP 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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19A THR* 4.2 7.3 + - - +
20A SER* 1.3 88.7 + - - +
22A GLU* 1.3 59.8 + - + +
23A VAL 3.4 0.2 - - - -
24A ARG* 3.5 14.6 - - - +
25A LYS* 2.9 31.0 + - - +
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Residues in contact with GLU 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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19A THR* 2.8 45.5 + - - +
21A ASP* 1.3 82.6 - - + +
23A VAL* 1.3 62.1 + - + +
25A LYS* 3.6 5.6 + - - +
26A ASN* 3.0 27.0 + - - +
103A GLY* 6.1 2.9 - - - +
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Residues in contact with VAL 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* 3.7 15.9 - - - +
20A SER* 3.6 11.8 + - - +
21A ASP 3.4 0.4 - - - -
22A GLU* 1.3 75.2 - - + +
24A ARG* 1.3 72.3 + - + +
26A ASN* 3.0 19.8 + - - +
27A LEU* 3.0 27.8 + - + +
64A PHE* 5.4 5.8 - - + -
102A SER* 4.3 14.6 - - - -
103A GLY* 4.6 7.4 - - - +
104A LEU* 4.2 28.0 - - + -
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Residues in contact with ARG 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 SER* 3.0 26.6 + - - +
21A ASP* 3.5 15.3 - - - +
22A GLU 3.3 0.2 - - - -
23A VAL* 1.3 84.8 - - + +
25A LYS* 1.3 63.5 + - - +
27A LEU* 3.1 10.1 + - - +
28A MET* 3.1 44.9 + - + +
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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 ASP 2.9 17.5 + - - +
22A GLU* 3.6 8.3 - - - +
24A ARG* 1.3 76.8 - - - +
26A ASN* 1.3 60.6 + - - +
28A MET* 3.3 16.0 + - + +
29A ASP* 2.9 52.2 + - - +
32A ARG* 5.1 0.7 - - - +
69B GLU* 3.0 29.8 + - - +
112B ALA* 4.9 2.0 - - - +
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Residues in contact with ASN 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 GLU* 3.0 19.5 + - - +
23A VAL* 3.0 10.0 + - - +
25A LYS* 1.3 78.0 - - - +
27A LEU* 1.3 59.4 + - - +
28A MET 3.1 2.0 - - - -
29A ASP* 3.3 15.2 - - - +
30A MET* 2.9 34.2 + - - +
101A ARG 3.4 15.9 - - - +
102A SER* 3.5 4.0 - - - +
103A GLY* 3.5 26.5 - - - +
111B ASN* 3.1 23.3 + - - +
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Residues in contact with LEU 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 VAL* 3.0 25.1 + - + +
24A ARG* 3.1 9.2 + - + +
26A ASN* 1.3 75.1 - - - +
28A MET* 1.3 64.9 + - + +
30A MET* 3.4 30.4 - - + +
31A PHE* 3.1 24.1 + - - +
64A PHE* 4.6 22.0 - - + -
98A LEU* 5.6 5.4 - - + -
102A SER* 3.9 13.7 - - - +
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Residues in contact with MET 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 ARG* 3.1 37.4 + - + +
25A LYS* 3.4 19.7 - - + +
26A ASN 3.1 0.2 - - - -
27A LEU* 1.3 78.8 - - + +
29A ASP* 1.3 55.7 + - - +
31A PHE* 3.2 5.5 + - - +
32A ARG* 2.8 37.6 + - - +
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Residues in contact with ASP 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 45.7 + - - +
26A ASN* 3.3 19.8 - - - +
28A MET* 1.3 77.5 - - - +
30A MET* 1.3 61.4 + - - +
32A ARG* 3.1 28.3 + - - +
33A ASP* 3.2 22.2 + - - +
111B ASN* 3.3 31.9 + - + +
112B ALA* 3.8 7.9 + - - +
115B LEU* 3.6 10.1 - - + +
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Residues in contact with MET 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 ASN 2.9 19.6 + - - +
27A LEU* 3.4 29.6 - - + +
29A ASP* 1.3 77.8 - - - +
31A PHE* 1.3 60.5 + - - +
33A ASP 3.7 1.9 - - - +
34A ARG* 3.4 22.3 + - - +
37A PHE* 5.7 1.1 - - + -
42A TRP* 4.0 22.6 - - + -
97A MET* 4.5 11.9 - - + +
98A LEU* 4.8 10.8 - - - -
101A ARG* 2.6 56.1 - - + +
102A SER* 4.2 0.9 - - - +
111B ASN* 5.0 0.7 - - - +
115B LEU* 3.7 16.7 - - + +
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Residues in contact with PHE 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 LEU 3.1 19.7 + - - +
28A MET* 3.2 5.8 + - - +
30A MET* 1.3 75.1 - - - +
32A ARG* 1.3 57.2 + - - +
34A ARG* 2.7 66.7 + - - -
42A TRP* 5.5 1.8 - - - -
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Residues in contact with ARG 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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25A LYS* 5.8 0.9 - - - +
28A MET 2.8 16.3 + - - +
29A ASP* 3.1 25.2 + - - +
31A PHE* 1.3 80.0 - - - +
33A ASP* 1.3 57.2 + - - +
34A ARG* 3.4 14.6 + - - +
35A GLN* 5.2 1.2 + - - +
69B GLU* 2.7 42.8 + - - -
72B ARG* 3.0 42.9 - - - +
112B ALA* 3.4 15.8 - - - +
119B ARG* 3.2 15.2 + - - +
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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