Contacts of the strand formed by residues 152 - 157 (chain B) in PDB entry 1SOX
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 ARG 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PRO 4.8 0.6 + - - -
149B SER 2.5 31.5 + - - -
150B SER* 3.4 13.1 + - - +
151B TYR* 1.3 102.0 + - - +
153B LEU* 1.3 61.7 + - - +
154B ARG* 3.9 1.7 + - - +
164B SER* 3.9 26.9 - - - +
165B LEU 3.3 10.3 - - - -
166B SER* 3.2 33.1 - - - +
169B GLU* 5.4 0.2 - - - -
304B ARG* 4.0 8.5 - - - +
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Residues in contact with LEU 153 (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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151B TYR* 3.4 24.2 - - + +
152B ARG* 1.3 72.8 - - - +
154B ARG* 1.3 72.0 + - - +
155B VAL* 3.8 9.3 + - + +
163B LEU 3.6 1.2 - - - +
164B SER* 3.5 4.2 - - - -
165B LEU* 2.7 52.5 + - + +
170B LEU* 4.3 21.8 - - + -
270B LEU* 3.9 28.3 - - + -
287B VAL* 4.9 1.3 - - + -
303B LEU* 3.7 28.9 - - + -
304B ARG 3.7 13.0 - - - +
305B ARG* 4.0 1.6 - - - +
306B VAL* 4.3 2.5 - - + -
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG 3.9 1.8 + - - +
153B LEU* 1.3 74.6 - - - +
155B VAL* 1.3 66.5 + - - +
156B ASP* 2.8 36.3 + - - +
162B THR* 3.4 27.3 + - - +
163B LEU 3.5 7.1 + - - +
164B SER* 4.8 2.9 - - - +
304B ARG 3.0 16.0 + - - +
305B ARG* 3.3 20.6 - - + +
306B VAL* 2.8 26.5 + - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.3 17.9 - - + +
154B ARG* 1.3 78.8 - - - +
156B ASP* 1.3 67.5 + - - +
161B GLY 5.1 0.2 - - - -
162B THR* 3.3 3.5 - - - +
163B LEU* 2.8 59.0 + - + +
165B LEU* 4.4 2.7 - - + -
222B VAL* 4.0 23.6 - - + -
223B LEU* 4.2 23.6 - - + -
226B ALA* 4.4 11.9 - - + -
228B PHE* 4.6 2.9 - - + -
306B VAL* 3.3 17.3 - - + +
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ARG* 2.8 37.4 + - - +
155B VAL* 1.3 77.0 - - - +
157B GLY* 1.3 63.0 + - - +
161B GLY 5.4 1.1 - - - -
162B THR* 4.0 14.4 - - - +
228B PHE* 3.8 11.5 - - - -
305B ARG* 2.7 48.0 + - - +
306B VAL 3.0 8.8 + - - +
307B ALA* 3.2 5.4 - - - +
308B VAL 3.0 21.8 + - - +
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Residues in contact with GLY 157 (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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156B ASP* 1.3 82.8 + - - +
158B PRO* 1.3 77.7 - - - +
159B GLY 3.3 0.5 + - - -
160B GLY 3.1 22.2 + - - +
162B THR* 5.3 0.6 + - - -
228B PHE* 3.5 11.1 - - - -
308B VAL 3.9 6.7 - - - -
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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
------------------------------------------------------------
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