Contacts of the strand formed by residues 191 - 198 (chain A) in PDB entry 1SLL
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 ASN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A SER* 3.2 3.9 + - - -
123A TYR* 2.8 65.4 + - + +
180A VAL* 3.5 7.5 - - + +
181A ARG* 2.8 47.6 + - - +
189A VAL* 3.4 13.7 - - - +
190A PHE* 1.3 75.2 + - - +
192A THR* 1.3 64.3 + - - +
193A VAL* 4.2 0.4 - - + -
209A ASN* 3.0 31.0 - - - +
274A THR* 3.8 0.9 - - - -
276A TYR* 4.9 1.6 - - - -
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Residues in contact with THR 192 (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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120A ILE* 4.1 18.6 - - + -
121A LEU 3.4 12.1 - - - +
122A SER* 4.2 11.2 + - - +
191A ASN* 1.3 73.5 + - - +
193A VAL* 1.3 65.1 + - - +
208A ALA* 3.3 2.1 - - - -
209A ASN* 2.9 37.3 + - - +
270A ALA 3.8 8.6 + - - +
271A THR* 3.3 28.0 + - + -
273A VAL* 4.7 3.7 - - + +
274A THR* 2.8 27.1 + - - +
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Residues in contact with VAL 193 (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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120A ILE* 3.3 4.0 - - - +
121A LEU* 2.9 61.3 + - + +
123A TYR* 3.8 22.2 - - + -
134A LEU* 4.1 13.7 - - + -
151A ILE* 4.7 5.8 - - + -
159A ILE* 3.4 33.2 - - + -
180A VAL* 4.1 6.3 - - + -
192A THR* 1.3 80.8 - - - +
194A ALA* 1.3 65.9 + - - +
206A LEU* 6.0 0.2 - - + -
207A PHE 3.2 6.1 - - - +
208A ALA* 4.0 8.5 - - + -
271A THR* 3.8 2.7 - - - -
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Residues in contact with ALA 194 (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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119A ILE 3.0 11.7 - - - +
120A ILE* 4.1 5.2 - - + -
121A LEU* 5.6 0.4 - - - -
151A ILE* 5.5 1.8 - - - -
193A VAL* 1.3 79.4 - - - +
195A LEU* 1.3 60.4 + - - +
205A ARG 3.7 0.7 - - - +
206A LEU* 3.4 9.3 - - - +
207A PHE* 2.9 41.5 + - + +
267A LEU* 3.9 26.2 - - + -
271A THR* 3.8 15.7 - - + -
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Residues in contact with LEU 195 (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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117A GLY 4.0 0.9 - - - +
118A THR* 3.3 7.1 - - - +
119A ILE* 2.8 36.9 + - + +
149A PHE* 3.3 35.2 - - + -
151A ILE* 3.9 19.9 - - + +
161A ILE* 3.6 33.7 - - + -
174A LEU* 5.4 0.7 - - + -
194A ALA* 1.3 74.3 - - - +
196A LYS* 1.3 67.1 + - - +
197A ALA* 4.6 6.5 - - + +
204A CYS* 4.6 5.4 - - + -
205A ARG 3.4 16.4 - - - +
206A LEU* 4.1 13.0 - - + -
223A PHE* 4.1 15.3 - - + -
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Residues in contact with LYS 196 (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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117A GLY 3.7 3.4 - - - -
118A THR* 4.4 4.9 - - - +
195A LEU* 1.3 76.8 - - - +
197A ALA* 1.3 59.5 + - - +
198A ASP* 3.7 30.1 + - + -
203A GLN* 3.6 4.5 - - - +
204A CYS* 3.1 7.1 - - - +
205A ARG* 2.9 43.1 + - + +
207A PHE* 4.4 3.6 - - + -
261A ALA* 4.1 16.8 - - + -
262A LEU 2.9 30.1 + - - +
263A SER* 3.9 2.8 - - - +
264A ASP* 3.0 36.3 + - - +
267A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 197 (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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116A GLN* 3.3 8.8 - - - +
117A GLY 2.8 36.3 + - - +
195A LEU* 4.1 3.0 - - + +
196A LYS* 1.3 72.1 - - - +
198A ASP* 1.3 59.3 + - - +
203A GLN 3.8 3.1 - - - -
204A CYS* 4.3 8.7 - - - -
221A PHE* 3.8 14.1 - - + -
223A PHE* 3.6 39.3 - - + -
261A ALA* 4.0 3.1 - - - +
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Residues in contact with ASP 198 (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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116A GLN* 4.6 1.0 - - - +
196A LYS* 3.7 27.9 + - + -
197A ALA* 1.3 70.2 - - - +
199A ALA* 1.3 58.5 + - - +
200A ALA* 3.3 12.8 + - - +
201A ASN* 2.8 40.6 + - + +
202A LYS* 2.8 24.3 + - - -
203A GLN* 2.8 30.5 + - + +
221A PHE* 3.7 3.1 - - - -
261A ALA* 4.1 16.8 - - + +
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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