Contacts of the strand formed by residues 303 - 309 (chain A) 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 LEU 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TYR* 2.6 35.8 + - - -
153A LEU* 3.6 26.0 - - + +
240A PHE* 3.7 24.2 - - + -
241A GLU 3.7 8.1 - - - +
243A LEU* 4.7 0.2 - - - -
270A LEU* 3.7 29.8 - - + -
287A VAL* 2.9 27.8 + - + +
289A VAL* 3.7 10.8 - - + +
300A VAL* 4.2 10.5 - - + +
301A LYS 3.2 2.9 + - - -
302A TRP* 1.3 74.4 - - - +
304A ARG* 1.3 59.1 + - - +
305A ARG 3.7 20.6 - - - +
306A VAL* 3.7 7.9 - - + -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 5.2 0.2 - - - -
152A ARG* 2.5 49.0 + - - +
153A LEU* 3.7 5.4 - - - +
154A ARG* 3.0 47.6 + - - +
164A SER* 5.5 0.4 + - - -
241A GLU* 2.8 19.1 + - + +
242A GLY 4.0 9.4 - - - +
243A LEU* 3.7 31.2 - - + -
302A TRP 3.3 0.6 + - - -
303A LEU* 1.3 75.3 - - - +
305A ARG* 1.3 65.1 + - + +
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.5 0.2 - - - -
154A ARG* 3.2 26.3 - - + +
156A ASP* 3.0 39.6 + - - +
239A CYS 3.8 0.4 - - - +
240A PHE* 3.3 6.1 - - - -
241A GLU* 3.1 68.1 + - + +
303A LEU* 3.7 5.3 - - - +
304A ARG* 1.3 87.8 - - + +
306A VAL* 1.3 69.7 + - - +
307A ALA* 3.8 14.9 - - + +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.1 8.5 - - + -
154A ARG 2.8 5.9 + - - +
155A VAL* 3.1 15.7 - - + +
156A ASP 3.0 23.6 + - - +
219A LEU* 4.3 7.4 - - + -
222A VAL* 6.2 0.9 - - + -
223A LEU* 4.0 20.4 - - + -
238A VAL* 3.6 26.9 - - + -
239A CYS 3.4 4.5 - - - +
240A PHE* 4.2 9.9 - - + -
270A LEU* 4.6 12.3 - - + -
303A LEU* 3.7 26.2 - - + -
305A ARG* 1.3 80.1 - - - +
307A ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP* 3.4 25.8 - - - +
157A GLY* 4.9 0.2 - - - -
238A VAL* 3.4 5.2 - - - +
239A CYS* 2.7 48.8 + - + +
305A ARG* 3.8 23.1 - - + +
306A VAL* 1.3 73.7 - - - +
308A VAL* 1.3 68.2 + - - +
309A SER* 5.8 1.3 - - - -
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP 3.5 5.3 + - - -
157A GLY* 3.7 1.5 - - - -
158A PRO* 2.9 25.6 - - + +
223A LEU* 4.1 12.6 - - + -
228A PHE* 3.6 42.0 - - + -
232A LEU* 4.3 3.6 - - + -
236A TRP* 3.8 22.7 - - + -
237A HIS 3.4 7.6 - - - +
238A VAL* 4.3 5.6 - - + -
258A TYR* 3.9 32.3 - - + -
307A ALA* 1.3 80.3 - - - +
309A SER* 1.3 66.6 + - - +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A TRP* 3.5 8.2 - - - -
237A HIS* 2.7 39.3 + - - -
239A CYS* 4.1 14.4 - - - -
307A ALA* 5.3 1.6 - - - -
308A VAL* 1.3 76.3 - - - +
310A PRO* 1.3 75.0 - - - +
311A ASP* 3.0 27.5 + - - +
312A GLU 5.0 0.3 + - - -
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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