Contacts of the strand formed by residues 19 - 23 (chain X) in PDB entry 2QW0
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 CYS 19 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17X ASP 3.9 0.8 + - - -
18X HIS* 1.3 79.7 + - + +
20X ALA* 1.3 58.7 + - - +
21X LEU 3.5 30.1 - - - -
22X ALA* 4.1 0.7 - - - -
29X ARG* 3.8 36.1 - - + +
30X LEU 3.7 6.7 - - - -
31X THR* 4.0 5.1 - - + +
32X HIS* 4.2 0.2 - - - -
223X GLY 3.3 7.8 - - - +
224X THR* 2.6 38.9 + - - +
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Residues in contact with ALA 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X HIS 3.3 2.4 + - - -
19X CYS* 1.3 72.8 - - - +
21X LEU* 1.3 53.8 + - - +
30X LEU 2.6 13.2 + - - +
31X THR 3.6 4.0 - - - +
32X HIS* 3.6 35.9 - - + +
35X LEU* 3.9 14.6 - - + -
219X LEU* 3.4 22.4 - - + +
223X GLY 3.8 2.9 - - - -
224X THR* 3.2 2.6 - - - -
225X TYR* 2.7 32.1 + - - +
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Residues in contact with LEU 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X CYS* 3.5 4.4 - - - -
20X ALA* 1.3 84.1 - - + +
22X ALA* 1.3 59.7 + - - +
23X VAL* 4.2 1.9 - - + +
28X LEU* 4.0 0.5 - - - +
29X ARG* 3.2 3.8 - - - -
30X LEU* 2.8 54.9 + - + -
35X LEU* 3.9 33.2 - - + -
65X ALA* 4.3 22.0 - - + +
68X VAL* 4.2 21.5 - - + -
69X ILE* 4.7 0.7 - - + -
215X LEU* 4.6 3.6 - - + -
219X LEU* 4.7 1.1 - - + -
225X TYR* 3.5 28.3 - - + -
227X VAL* 4.3 13.5 - - + -
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Residues in contact with ALA 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X CYS* 4.1 5.6 - - - -
21X LEU* 1.3 74.1 - - - +
23X VAL* 1.3 60.9 + - - +
24X PRO* 3.4 6.9 - - + +
28X LEU 3.5 3.6 - - - -
29X ARG* 3.4 36.3 - - - +
224X THR* 4.1 10.5 - - + +
225X TYR 3.0 8.8 + - - +
226X VAL* 3.4 5.8 - - + -
227X VAL* 2.8 29.5 + - - +
243X GLU* 4.1 8.5 - - - +
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Residues in contact with VAL 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X LEU* 5.2 2.9 - - + +
22X ALA* 1.3 78.8 - - - +
24X PRO* 1.3 67.8 - - + +
25X ALA* 3.1 8.1 - - + -
26X ARG* 3.1 27.2 + - + +
27X GLY 3.1 3.1 + - - -
28X LEU* 2.6 53.7 + - + +
29X ARG* 5.7 0.4 - - - -
65X ALA* 3.7 30.3 - - + +
227X VAL* 4.0 21.8 - - + +
229X GLU* 3.9 13.9 - - - +
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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