Contacts of the strand formed by residues 134 - 140 (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 LEU 134 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74Q CYS* 5.0 2.7 - - + -
75Q SER 3.2 4.7 - - - +
76Q VAL* 3.1 52.0 - - + -
86Q LEU* 3.9 15.7 - - + -
90Q LEU* 4.2 13.2 - - + -
114Q LEU* 3.4 31.9 - - + -
118Q LYS* 4.5 3.8 - - - +
132Q VAL* 4.0 9.0 - - + +
133Q SER* 1.3 78.7 - - - +
135Q LEU* 1.3 66.7 + - - +
136Q TYR* 3.9 9.6 - - + +
149Q GLN* 3.3 10.2 - - - +
150Q SER* 2.8 38.5 + - - -
164Q ILE* 5.5 0.9 - - - -
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Residues in contact with LEU 135 (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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34Q CYS* 4.2 5.2 - - - -
35Q LEU* 4.2 1.8 - - - -
36Q GLY* 3.7 20.0 - - - +
45Q LEU* 3.6 27.6 - - + -
74Q CYS* 3.2 11.1 - - - +
75Q SER* 3.0 35.7 + - - +
134Q LEU* 1.3 83.1 - - - +
136Q TYR* 1.3 66.0 + - - +
137Q ILE* 4.0 1.1 - - + +
147Q LEU* 4.2 8.3 - - + -
148Q TYR 3.0 8.7 - - - +
149Q GLN* 3.7 17.7 - - + -
162Q THR* 3.4 29.2 - - + -
164Q ILE* 4.1 26.0 - - + -
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Residues in contact with TYR 136 (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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68Q LEU* 4.2 15.9 - - + -
73Q ALA 3.5 4.9 - - - +
74Q CYS* 4.3 2.5 - - + -
90Q LEU* 3.9 28.3 - - + -
107Q CYS* 4.4 13.6 - - - -
110Q LEU* 5.4 1.6 - - + -
111Q VAL* 2.9 53.1 + - + +
114Q LEU* 3.3 30.8 - - - +
115Q CYS* 4.4 0.5 - - - -
134Q LEU* 3.9 6.3 - - + +
135Q LEU* 1.3 81.5 - - - +
137Q ILE* 1.3 63.4 + - - +
146Q GLN 3.7 0.3 - - - +
147Q LEU* 2.8 8.9 - - - +
148Q TYR* 2.5 51.9 + - + +
150Q SER* 3.8 27.1 + - - -
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Residues in contact with ILE 137 (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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43Q VAL* 3.7 28.9 - - + +
44Q LEU 3.9 11.0 - - - +
45Q LEU* 3.8 27.4 - - + -
65Q ILE* 4.3 3.4 - - + -
72Q MET* 3.6 1.0 - - - -
73Q ALA* 2.9 54.9 + - + +
74Q CYS* 5.0 0.4 - - - +
75Q SER 6.2 0.2 - - - +
107Q CYS* 4.1 4.3 - - - -
135Q LEU* 4.0 1.1 - - + -
136Q TYR* 1.3 77.7 - - - +
138Q GLY* 1.3 57.7 + - - +
146Q GLN 3.7 3.8 - - - -
147Q LEU* 4.0 11.9 - - + -
214Q ALA* 3.8 24.9 - - + +
216Q LEU* 3.9 17.7 - - + -
225Q ILE* 5.3 1.1 - - + -
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Residues in contact with GLY 138 (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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43Q VAL* 3.8 0.6 - - - +
71Q ASP 3.5 7.4 - - - -
72Q MET* 3.9 3.1 - - - -
107Q CYS* 3.9 11.0 - - - -
137Q ILE* 1.3 74.9 - - - +
139Q TRP* 1.3 60.3 + - - -
140Q ASP 4.0 1.8 - - - -
145Q PHE* 3.3 10.4 - - - -
146Q GLN* 2.9 33.0 + - - +
216Q LEU* 3.2 16.5 - - - +
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Residues in contact with TRP 139 (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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71Q ASP* 3.1 43.5 + - - +
72Q MET* 4.4 2.6 - - - +
138Q GLY* 1.3 74.3 - - - -
140Q ASP* 1.3 63.6 + - - +
141Q LYS* 3.5 19.6 + - + -
144Q GLY* 2.9 23.2 - - - -
145Q PHE* 2.8 60.7 - + + +
216Q LEU* 4.5 0.2 - - + -
218Q ARG* 2.9 50.2 - - - +
223Q THR* 3.5 12.3 - - + -
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Residues in contact with ASP 140 (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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72Q MET* 4.1 10.0 - - - +
106Q PRO* 3.7 18.4 - - + +
107Q CYS* 3.4 25.2 + - - +
108Q GLU* 4.5 2.1 + - - +
138Q GLY 4.0 1.0 - - - -
139Q TRP* 1.3 81.0 - - - +
141Q LYS* 1.3 62.5 + - - +
142Q HIS* 4.0 3.5 - - - +
143Q TYR* 3.0 36.2 + - - +
144Q GLY* 3.0 20.1 + - - +
146Q GLN* 2.7 36.7 + - - +
73Y TYR* 4.2 4.2 + - - -
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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