Contacts of the strand formed by residues 34 - 38 (chain Q) 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 CYS 34 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q GLY 4.5 3.1 - - - +
33Q THR* 1.3 78.8 - - - +
35Q LEU* 1.4 64.7 + - - +
45Q LEU* 3.7 10.1 - - - -
46Q ALA 3.3 15.9 - - - -
47Q ALA* 4.1 10.8 - - + +
64Q LYS* 5.8 2.7 - - - -
75Q SER* 3.1 30.5 - - - -
77Q ALA* 5.1 6.5 - - + -
135Q LEU* 4.2 6.7 - - - -
163Q CYS* 2.9 20.3 - - - -
164Q ILE* 2.9 31.3 + - + +
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Residues in contact with LEU 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q THR* 5.1 3.4 - - + -
34Q CYS* 1.4 75.2 - - - +
36Q GLY* 1.4 58.6 - - - +
37Q ILE* 4.2 8.5 - - + -
44Q LEU* 3.9 13.9 - - + -
45Q LEU* 3.5 5.7 - - - -
46Q ALA* 2.8 56.8 + - + +
135Q LEU* 4.4 1.6 - - - -
162Q THR 3.4 14.6 - - - +
163Q CYS* 3.9 13.2 - - + +
175Q LEU* 5.1 5.6 - - + -
193Q ALA* 4.0 17.5 - - + +
196Q VAL* 3.6 37.5 - - + -
197Q LEU* 3.9 17.0 - - + +
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Residues in contact with GLY 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q LEU* 1.4 72.2 - - - +
37Q ILE* 1.4 65.3 + - - +
44Q LEU* 3.2 13.9 - - - -
45Q LEU* 4.0 9.9 - - - -
135Q LEU* 3.7 9.9 - - - +
137Q ILE* 5.1 0.2 - - - -
147Q LEU* 3.8 14.4 - - - +
161Q ALA* 3.5 1.2 - - - -
162Q THR 3.0 31.4 + - - +
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Residues in contact with ILE 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q LEU* 4.2 12.6 - - + -
36Q GLY* 1.4 78.1 - - - +
38Q LEU* 1.3 74.7 + - - +
39Q ALA 4.0 0.2 + - - -
42Q GLY 4.3 0.3 - - - +
43Q VAL* 3.6 2.3 - - - +
44Q LEU* 3.0 42.1 + - + +
147Q LEU* 4.5 0.2 - - - +
160Q LYS 3.9 2.7 - - - +
161Q ALA* 4.1 7.2 - - + -
175Q LEU* 3.9 28.5 - - + -
179Q TYR* 3.6 21.1 - - + -
184Q MET* 5.8 0.2 - - + -
189Q ALA* 4.3 20.7 - - + +
192Q LEU* 4.0 7.0 - - + -
193Q ALA* 3.9 31.2 - - - +
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Residues in contact with LEU 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q ILE* 1.3 85.8 - - - +
39Q ALA* 1.3 80.9 + - - +
40Q ASN* 5.3 4.3 - - - +
42Q GLY 4.0 0.2 - - - -
43Q VAL* 4.0 14.6 - - + +
145Q PHE* 3.6 28.5 - - + +
146Q GLN* 3.7 21.8 - - - +
147Q LEU* 4.1 4.1 - - + +
159Q TRP 4.4 9.4 - - - +
160Q LYS* 3.0 36.1 + - + +
179Q TYR* 3.1 29.0 + - - +
184Q MET* 4.7 1.0 - - - +
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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