Contacts of the helix formed by residues 158 - 167 (chain B) in PDB entry 5XRZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASN* 3.3 15.9 - - - +
81A TYR* 3.9 18.9 - - + +
43B LEU* 3.5 23.0 - - + +
79B PHE* 4.1 7.4 - + - -
113B VAL* 3.9 36.3 - - + -
115B LEU* 3.7 41.5 - - + -
119B SER* 4.4 5.4 - - - -
120B TYR 5.2 0.2 - - - -
121B HIS* 3.2 35.4 - + - -
154B ALA 4.6 1.1 - - - -
155B LEU* 3.6 33.4 - - + +
156B ARG 2.8 8.9 + - - -
157B SER* 1.3 74.3 - - - +
159B GLY* 1.3 55.0 + - - +
162B LEU* 3.6 19.1 - - + -
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN* 4.9 3.8 - - - -
76A ASN* 4.4 9.3 - - - +
43B LEU* 4.0 13.0 - - - -
155B LEU 4.7 0.2 + - - -
156B ARG 3.3 5.1 + - - +
157B SER 3.6 0.8 - - - -
158B PHE* 1.3 81.2 - - - +
160B ASN* 1.3 67.0 + - - -
161B ALA 3.2 2.7 - - - -
162B LEU* 3.1 13.0 + - - +
163B GLY 3.7 0.2 + - - -
164B ASN* 3.2 19.7 + - - +
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN* 2.8 39.5 + - - +
77A GLU* 5.8 1.0 + - - -
43B LEU 3.3 4.3 + - - +
44B ARG* 3.7 21.9 + - - +
45B GLN 3.3 14.8 - - - +
46B ARG* 4.5 18.5 + - + +
47B LEU* 3.2 12.1 - - - +
159B GLY* 1.3 72.3 - - - -
161B ALA* 1.3 64.0 + - - +
163B GLY 3.1 10.9 + - - -
164B ASN* 3.4 13.9 + - - +
165B CYS* 3.3 27.2 + - + +
195K ASP* 5.3 3.6 + - - -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 4.7 10.3 - - + -
42B ALA 3.4 26.2 - - - +
43B LEU* 3.1 21.2 + - + +
45B GLN* 3.0 17.4 + - + +
47B LEU* 3.3 27.4 - - - +
74B LEU* 4.1 12.2 - - + +
78B MET* 5.2 4.7 - - + -
159B GLY 3.2 0.2 - - - -
160B ASN* 1.3 75.8 - - - +
162B LEU* 1.3 59.3 + - + +
163B GLY 3.4 0.4 - - - -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.9 15.0 - - + -
66B ILE* 5.5 1.6 - - - -
71B VAL* 4.2 24.5 - - + +
74B LEU* 3.8 33.9 - - + +
75B ALA* 4.0 14.8 - - + +
78B MET* 4.7 4.3 - - + -
79B PHE* 3.6 31.0 - - + -
152B LYS 4.9 0.5 - - - +
155B LEU* 3.5 23.7 - - + +
156B ARG* 3.9 14.0 + - - +
158B PHE* 3.6 24.9 - - + -
159B GLY 3.1 7.6 + - - +
160B ASN 3.1 1.0 - - - -
161B ALA* 1.3 77.2 - - - +
163B GLY* 1.3 57.0 + - - +
164B ASN 3.7 1.6 - - - -
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.3 3.2 - - - +
66B ILE* 4.2 22.2 - - - +
156B ARG* 3.7 17.6 + - - -
160B ASN 3.1 6.6 + - - -
161B ALA 3.4 2.2 + - - -
162B LEU* 1.3 80.2 - - - +
164B ASN* 1.3 63.7 + - - +
165B CYS 3.2 3.4 - - - -
166B ILE* 3.2 25.5 - - - +
167B LEU* 5.5 0.2 - - - +
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Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS* 3.4 35.0 + - - +
72A ILE* 3.3 32.6 - - - +
73A ASN* 2.8 40.2 + - - +
156B ARG* 3.6 16.4 + - - +
159B GLY* 3.2 25.0 + - - +
160B ASN* 3.6 2.7 + - - +
162B LEU 3.7 0.4 - - - -
163B GLY* 1.3 77.9 - - - +
165B CYS* 1.3 61.1 + - - +
166B ILE 3.4 0.6 + - - -
167B LEU* 3.9 10.8 + - - +
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Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ARG* 4.2 16.8 - - + +
47B LEU* 3.6 23.6 - - - -
160B ASN* 3.3 36.4 + - + +
163B GLY* 4.8 0.9 - - - -
164B ASN* 1.3 76.6 - - - +
166B ILE* 1.3 58.9 + - - +
167B LEU 3.0 6.1 - - - -
168B ASP* 2.9 26.8 + - + +
171B TYR* 3.1 41.8 - - + -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 3.7 42.4 - - + -
64B CYS* 3.9 28.3 - - + +
65B TYR* 4.5 3.6 - - - -
66B ILE* 4.2 16.8 - - + -
156B ARG* 3.6 29.2 - - - +
163B GLY* 3.2 21.0 + - - +
165B CYS* 1.3 79.5 - - - +
167B LEU* 1.3 67.2 + - + +
168B ASP 3.4 0.9 - - - -
171B TYR* 4.4 6.1 - - + -
172B LEU* 3.9 24.6 - - + +
4L T 4.8 7.4 - - + +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU* 4.0 4.3 - - - +
69A HIS* 3.3 39.4 + - + +
72A ILE* 6.6 0.4 - - + -
156B ARG* 3.5 28.3 - - - +
163B GLY 5.5 0.2 - - - +
164B ASN* 3.9 9.1 + - - +
165B CYS 3.0 1.2 - - - -
166B ILE* 1.3 85.4 - - + +
168B ASP* 1.3 61.5 + - - +
169B LYS* 3.4 9.3 + - - +
172B LEU* 5.9 0.7 - - - -
3L T 3.2 53.1 - - + +
4L T 3.9 28.5 - - + +
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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