Contacts of the helix formed by residues 154 - 163 (chain J) in PDB entry 4XLN
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 THR 154 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130J ASN 5.4 1.0 + - - -
131J LYS* 4.8 15.9 - - - +
132J TYR* 3.5 15.6 - - - +
153J LEU* 1.3 75.3 - - - +
155J ASP* 1.3 92.1 + - - +
156J GLU* 3.5 17.0 - - - +
157J GLU* 3.1 33.4 + - + +
158J TYR* 3.3 14.9 + - - +
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Residues in contact with ASP 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ASN 5.2 5.5 + - - +
132J TYR* 4.1 13.1 + - + -
154J THR* 1.3 90.9 + - - +
156J GLU* 1.3 89.5 + - - +
158J TYR* 3.6 6.4 + - - +
159J ARG* 3.4 24.6 + - - +
568J ARG* 6.0 3.1 - - - +
105L GLN* 3.9 24.8 - - + +
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Residues in contact with GLU 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J THR* 3.5 17.9 - - - +
155J ASP* 1.3 92.4 + - - +
157J GLU* 1.3 61.4 + - + +
158J TYR 3.1 0.5 + - - -
159J ARG* 3.2 13.8 - - - +
160J GLU* 2.9 38.6 + - - +
165J LYS* 6.1 2.2 - - - +
105L GLN* 6.1 3.4 - - + -
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Residues in contact with GLU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 4.1 29.5 - - + +
143J ASP* 5.7 0.2 - - - +
152J LEU 4.5 2.1 - - - +
153J LEU* 3.4 19.6 - - + +
154J THR* 3.1 39.3 + - + +
155J ASP 3.4 0.8 - - - -
156J GLU* 1.3 83.4 - - + +
158J TYR* 1.3 57.5 + - - +
160J GLU* 3.4 12.7 + - - +
161J LEU* 3.0 36.1 + - + +
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Residues in contact with TYR 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J TYR* 3.4 46.9 - + + -
153J LEU* 4.6 8.3 - - + +
154J THR 3.3 14.4 + - - +
155J ASP 4.0 1.6 - - - +
156J GLU 3.2 1.0 - - - -
157J GLU* 1.3 74.3 - - - +
159J ARG* 1.3 60.1 + - + +
160J GLU 3.0 3.4 - - - -
161J LEU* 2.8 7.3 + - - +
162J ARG* 2.8 57.5 + - + -
163J TYR* 6.2 3.6 - + - -
452J ILE* 3.7 24.8 + - + -
453J ASP* 4.4 6.8 + - - -
454J ALA* 3.4 36.4 + - + -
455J ARG* 5.0 3.5 + - - +
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Residues in contact with ARG 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ASP* 3.4 21.4 - - - +
156J GLU* 3.2 17.7 - - - +
158J TYR* 1.3 78.8 - - + +
160J GLU* 1.3 56.6 + - - +
162J ARG* 4.8 1.1 - - - -
163J TYR* 2.8 54.7 + - + +
164J GLY 2.9 10.7 + - - +
105L GLN* 5.7 8.1 - - - +
106L VAL* 5.4 12.7 - - - +
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Residues in contact with GLU 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 6.0 2.5 - - - +
143J ASP* 5.7 1.2 - - - +
156J GLU* 2.9 29.0 + - - +
157J GLU* 3.4 13.7 - - - +
158J TYR 3.0 0.2 - - - -
159J ARG* 1.3 79.4 - - - +
161J LEU* 1.3 69.7 + - + +
164J GLY* 3.3 25.5 - - - +
165J LYS* 3.7 46.9 + - + +
397J LYS* 4.0 5.9 + - - -
448J GLU 4.8 0.2 - - - +
449J SER* 4.7 0.5 - - - -
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Residues in contact with LEU 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ALA* 4.1 22.9 - - + -
141J VAL 4.3 15.0 - - - +
142J LEU* 4.4 21.3 - - + -
147J VAL* 4.1 15.0 - - + -
153J LEU* 5.0 8.3 - - + -
157J GLU* 3.0 21.4 + - + +
158J TYR* 2.8 6.3 + - - +
160J GLU* 1.3 89.8 - - + +
162J ARG* 1.3 53.0 + - - +
449J SER* 3.1 7.2 - - - +
450J TYR* 2.5 51.8 + - + -
452J ILE* 3.9 19.7 - - + -
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Residues in contact with ARG 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J TYR* 2.8 52.9 + - + +
159J ARG* 4.8 0.4 - - - -
161J LEU* 1.3 74.6 - - - +
163J TYR* 1.3 106.3 + - + +
164J GLY 3.5 0.2 - - - -
412J GLY 5.0 8.7 + - - -
414J ARG* 2.7 56.6 + - - +
434J ARG* 4.3 0.6 - - - +
449J SER* 3.0 3.5 + - - -
450J TYR 3.2 10.5 - - - +
451J ASP* 4.2 9.7 + - - -
452J ILE* 4.3 10.1 - - + +
150L ILE 5.4 4.2 + - - -
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Residues in contact with TYR 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J TYR* 6.2 3.6 - + - -
159J ARG* 2.8 39.5 + - + +
162J ARG* 1.3 125.1 + - + +
164J GLY* 1.3 59.8 + - - +
412J GLY 5.8 0.9 - - - -
434J ARG* 3.8 38.8 + - - +
436J GLU* 4.8 3.5 - - - +
447J VAL* 3.4 23.1 - - - +
449J SER* 4.2 0.4 - - - -
150L ILE 5.3 4.3 + - - -
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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