Contacts of the strand formed by residues 32 - 36 (chain R) in PDB entry 5A0Q
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 ALA 32 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R SER 2.9 6.7 + - - +
31R THR* 1.3 67.1 - - - +
33R VAL* 1.3 61.5 + - - +
44R GLY 3.3 8.7 - - - +
45R VAL* 3.9 17.3 - - + -
72R ALA* 3.8 12.3 - - + +
73R PHE 4.3 1.1 - - - +
74R ALA* 3.9 11.9 - - + -
132R LEU* 3.4 24.1 - - + +
160R ALA* 3.3 3.7 - - - -
161R ILE 2.9 32.3 + - - +
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Residues in contact with VAL 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R THR 3.0 10.4 + - - +
32R ALA* 1.3 72.6 - - - +
34R GLY* 1.3 64.4 + - - +
43R LEU* 3.7 2.8 - - - +
44R GLY 2.9 34.1 + - - +
72R ALA* 5.2 1.0 - - - +
132R LEU* 4.1 3.1 - - - +
160R ALA* 3.8 9.0 - - + -
168R VAL* 4.1 21.5 - - + -
172R LEU* 4.1 17.0 - - + -
190R LEU* 5.1 1.6 - - + -
191R VAL* 3.9 36.8 - - + +
194R ALA* 4.5 9.2 - - + -
195R LEU* 4.0 24.5 - - + -
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Residues in contact with GLY 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R VAL* 1.3 79.9 - - - +
35R VAL* 1.3 74.9 + - - +
42R VAL 3.7 9.9 - - - -
43R LEU* 4.0 5.2 - - - -
132R LEU* 3.9 6.5 - - - +
144R LEU* 3.4 13.2 - - - -
159R ASN 3.0 26.7 + - - +
172R LEU* 4.5 0.2 - - - +
191R VAL* 5.0 1.3 - - - -
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Residues in contact with VAL 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R VAL* 5.2 0.2 - - + -
34R GLY* 1.3 86.4 - - - +
36R ARG* 1.3 60.0 + - - +
37R GLY* 3.2 3.5 + - - +
41R VAL* 3.9 0.9 - - - -
42R VAL* 2.9 40.7 + - + +
144R LEU* 3.0 10.9 - - - +
157R LYS 3.6 5.8 - - - +
158R ALA* 3.7 19.7 - - + -
172R LEU* 4.2 4.0 - - + -
176R TYR* 4.2 9.9 - - + -
187R THR* 3.3 24.7 - - - +
190R LEU* 3.3 36.8 - - + -
191R VAL* 4.0 4.0 - - + +
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Residues in contact with ARG 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R VAL* 1.3 69.3 - - - +
37R GLY* 1.3 64.9 + - - +
38R ARG* 3.5 9.8 + - - +
41R VAL* 4.7 2.9 - - + -
141R THR* 4.5 8.3 - - - +
142R PRO* 2.9 69.9 + - + +
143R ARG* 3.9 8.7 - - - +
144R LEU* 3.4 18.7 - - + +
156R TRP 4.8 4.2 + - - -
157R LYS* 3.0 53.2 + - - +
176R TYR* 3.6 16.0 + - - -
60S GLU* 4.6 11.1 + - - -
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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