Contacts of the strand formed by residues 139 - 143 (chain E) in PDB entry 1SSP
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 VAL 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E VAL* 3.6 1.4 - - - +
138E LYS* 1.3 81.5 - - - +
140E VAL* 1.3 73.7 + - - +
141E ILE* 4.5 0.2 - - + -
199E GLY 3.1 3.4 + - - +
200E VAL* 4.1 22.0 - - + -
201E LEU 2.8 25.6 + - - -
241E VAL* 3.2 13.7 - - + +
243E LEU* 4.4 16.6 - - + -
287E THR* 3.5 33.7 - - + -
291E LEU* 3.9 9.6 - - + -
299E ILE* 3.8 22.4 - - + -
301E TRP* 4.5 3.6 - - + -
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E VAL* 3.9 17.0 - - + -
139E VAL* 1.3 79.9 - - - +
141E ILE* 1.3 66.3 + - - +
142E LEU* 3.9 9.8 + - + +
201E LEU* 3.5 23.6 - - + +
203E LEU* 4.7 9.0 - - + -
230E VAL* 5.5 2.2 - - + -
233E LEU* 3.9 12.1 - - + -
240E LEU* 4.7 6.1 - - + -
241E VAL 2.8 10.6 + - - +
242E PHE* 3.5 38.4 - - + -
243E LEU* 2.7 34.0 + - - +
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Residues in contact with ILE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E VAL* 4.2 1.1 - - + -
140E VAL* 1.3 73.0 - - - +
142E LEU* 1.3 61.2 + - - +
157E CYS* 3.6 15.7 - - - -
158E PHE* 4.3 2.2 - - + -
195E TRP* 4.2 15.5 - - + -
200E VAL* 3.8 17.5 - - + -
201E LEU 2.8 9.9 + - - +
202E LEU* 3.8 21.1 - - + -
203E LEU* 3.0 28.4 + - - +
243E LEU* 3.4 24.2 - - + -
245E TRP* 3.8 47.1 - - + -
284E PHE* 4.8 0.4 - - + -
301E TRP* 4.2 9.9 - - + -
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 3.9 8.5 + - + -
141E ILE* 1.3 75.9 - - - +
143E GLY* 1.3 61.1 + - - +
203E LEU* 3.3 32.8 - - + +
204E ASN 3.4 26.2 - - - +
205E ALA* 3.4 7.2 - - - +
230E VAL* 4.6 6.1 - - + -
242E PHE* 6.1 0.7 - - + -
243E LEU 2.7 14.1 + - - +
244E LEU* 3.9 11.7 - - + -
245E TRP* 3.0 27.9 + - - +
249E ALA* 3.1 21.2 - - + +
252E LYS* 3.5 42.4 - - + -
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Residues in contact with GLY 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E URA 3.7 4.9 - - - -
141E ILE 4.1 0.4 + - - -
142E LEU* 1.3 76.3 - - - +
144E GLN* 1.3 57.6 + - - -
158E PHE* 4.0 18.4 - - - -
203E LEU 2.8 12.1 + - - -
204E ASN* 3.2 16.6 - - - -
205E ALA* 2.8 20.6 + - - +
245E TRP 4.2 3.6 - - - -
249E ALA* 3.7 12.7 - - - +
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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
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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