Contacts of the helix formed by residues 158 - 167 (chain Q) in PDB entry 5XS0
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 PHE 158 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76P ASN* 3.5 16.4 + - - +
81P TYR* 3.6 24.7 - - + +
43Q LEU* 3.3 27.1 - - + +
79Q PHE* 4.3 6.1 - + + -
113Q VAL* 3.6 33.0 - - + -
115Q LEU* 3.5 40.4 - - + -
119Q SER* 4.1 6.3 - - - -
120Q TYR 4.7 1.3 - - - -
121Q HIS* 3.3 35.7 - + + -
154Q ALA 4.3 3.4 - - - -
155Q LEU* 3.6 24.9 - - + +
156Q ARG 3.0 2.2 + - - -
157Q SER* 1.3 78.0 - - - +
159Q GLY* 1.3 57.1 + - - +
162Q LEU* 3.7 21.3 - - + -
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Residues in contact with GLY 159 (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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73P ASN* 4.6 3.8 - - - -
76P ASN* 3.6 13.9 - - - +
43Q LEU* 4.0 10.3 - - - +
155Q LEU 4.7 0.4 + - - -
156Q ARG 3.3 14.2 + - - +
157Q SER 3.4 1.8 - - - -
158Q PHE* 1.3 79.0 - - - +
160Q ASN* 1.3 67.9 - - - -
161Q ALA 3.3 3.1 - - - -
162Q LEU* 3.3 9.9 + - - -
163Q GLY 3.6 0.3 + - - -
164Q ASN* 3.4 11.8 + - - -
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Residues in contact with ASN 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P ASN* 3.4 34.3 + - - +
43Q LEU 3.1 4.0 + - - +
44Q ARG* 3.5 26.8 + - - +
45Q GLN 3.5 14.1 - - - +
46Q ARG* 4.5 13.3 + - + +
47Q LEU* 3.1 13.3 - - - +
159Q GLY* 1.3 73.2 - - - -
161Q ALA* 1.3 64.1 + - - +
163Q GLY 2.9 12.3 + - - -
164Q ASN* 3.6 1.3 + - - +
165Q CYS* 3.5 41.6 + - + +
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Residues in contact with ALA 161 (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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192P LYS* 4.8 9.2 - - + -
42Q ALA 3.4 26.0 - - - +
43Q LEU* 2.9 23.1 + - + +
45Q GLN* 3.1 15.5 + - + +
47Q LEU* 3.5 21.6 - - - +
74Q LEU* 3.6 16.6 - - - +
78Q MET* 4.6 8.1 - - + -
159Q GLY 3.3 0.2 - - - -
160Q ASN* 1.3 75.3 - - - +
162Q LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 162 (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 LEU* 4.0 12.8 - - + -
47Q LEU* 5.0 0.2 - - - -
66Q ILE* 5.0 3.5 - - - +
71Q VAL* 4.3 20.6 - - + +
74Q LEU* 3.7 33.4 - - + +
75Q ALA* 3.7 18.4 - - + +
78Q MET* 4.5 3.8 - - + -
79Q PHE* 3.6 30.3 - - + -
152Q LYS 4.9 1.6 - - - +
155Q LEU* 3.4 31.3 - - + +
156Q ARG* 3.9 12.5 + - - -
158Q PHE* 3.7 19.3 - - + -
159Q GLY 3.3 7.4 + - - +
160Q ASN 3.1 1.0 - - - -
161Q ALA* 1.3 77.8 - - - +
163Q GLY* 1.3 56.9 + - - +
164Q ASN 3.9 0.7 - - - -
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Residues in contact with GLY 163 (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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47Q LEU* 4.2 2.6 - - - +
66Q ILE* 3.9 23.5 - - - +
156Q ARG* 3.9 12.0 + - - +
160Q ASN 2.9 7.9 + - - -
161Q ALA 3.4 1.2 + - - -
162Q LEU* 1.3 79.7 - - - +
164Q ASN* 1.3 65.3 + - - +
165Q CYS 3.3 2.9 - - - -
166Q ILE* 3.1 26.1 - - - +
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Residues in contact with ASN 164 (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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69P HIS* 3.2 32.8 - - - +
72P ILE* 3.4 29.8 - - - +
73P ASN* 3.6 13.3 + - - +
156Q ARG* 3.3 31.7 - - - +
159Q GLY 3.4 25.1 + - - +
160Q ASN* 3.6 2.6 + - - +
163Q GLY* 1.3 73.3 - - - +
165Q CYS* 1.3 66.0 + - - +
166Q ILE 3.1 2.5 - - - -
167Q LEU* 3.0 29.1 + - - +
168Q ASP 4.4 0.2 + - - -
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Residues in contact with CYS 165 (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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69P HIS* 5.9 0.9 - - - -
73P ASN* 6.0 0.2 - - - +
46Q ARG* 3.9 17.9 - - + +
47Q LEU* 3.4 46.9 - - - -
52Q ILE* 5.8 0.7 - - - -
160Q ASN* 3.5 27.2 + - + +
163Q GLY 4.8 0.7 - - - -
164Q ASN* 1.3 78.4 - - - +
166Q ILE* 1.3 65.5 + - - +
167Q LEU 2.9 2.7 + - - -
168Q ASP* 3.0 20.5 + - + +
171Q TYR* 3.3 30.1 - - + -
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Residues in contact with ILE 166 (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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52Q ILE* 3.7 33.0 - - + -
64Q CYS* 3.7 40.3 - - + +
65Q TYR* 4.4 8.3 - - - +
66Q ILE* 4.9 9.4 - - + -
156Q ARG* 4.8 10.1 - - - +
163Q GLY 3.1 23.5 + - - +
164Q ASN 3.0 1.0 + - - -
165Q CYS* 1.3 81.9 - - - +
167Q LEU* 1.3 76.0 + - + +
168Q ASP 3.4 0.6 + - - -
171Q TYR* 4.3 11.4 - - + -
172Q LEU* 4.0 21.6 - - + +
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Residues in contact with LEU 167 (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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67P GLU* 4.2 4.5 - - - +
68P GLY* 5.4 1.3 - - - -
69P HIS* 3.7 32.3 + - + +
72P ILE* 5.5 1.6 - - + -
156Q ARG* 3.7 32.1 - - - +
164Q ASN* 3.0 33.0 + - - +
165Q CYS 2.9 1.4 - - - -
166Q ILE* 1.3 92.0 - - + +
168Q ASP* 1.3 60.4 + - - +
169Q LYS* 3.5 9.8 + - - +
172Q LEU* 5.6 0.9 - - - -
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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