Contacts of the strand formed by residues 194 - 198 (chain A) in PDB entry 3SJN
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 GLU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ARG* 3.3 26.7 + - - -
162A SER 3.2 9.9 + - - +
163A SER* 2.8 29.2 + - - +
164A ILE* 2.9 27.0 + - - +
186A ARG* 4.8 0.9 - - - +
192A GLU 3.6 3.7 + - - +
193A MET* 1.3 73.1 - - - +
195A VAL* 1.3 62.2 + - - +
196A GLN* 3.9 1.8 - - - +
222A ASN* 3.3 25.0 + - - +
324A LEU* 5.0 0.3 - - - +
375A UNL 3.2 23.8 - - - -
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Residues in contact with VAL 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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164A ILE* 3.5 24.2 - - + +
166A PHE* 3.8 27.8 - - + -
185A VAL* 4.4 8.5 - - + +
186A ARG* 3.6 38.6 - - + +
189A ALA* 4.4 8.3 - - + -
193A MET* 3.6 11.3 + - + +
194A GLU* 1.3 79.0 - - - +
196A GLN* 1.3 60.3 + - - +
220A ASN 5.1 0.2 + - - -
221A LEU* 3.3 19.8 - - + +
222A ASN* 2.7 30.7 + - - +
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Residues in contact with GLN 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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137A TYR* 3.6 19.1 - - - +
163A SER* 2.9 24.8 + - - -
164A ILE 2.9 20.7 + - - +
165A LYS* 3.2 33.7 - - + -
166A PHE* 3.2 9.0 + - - -
194A GLU 3.9 0.2 - - - -
195A VAL* 1.3 78.5 - - - +
197A ILE* 1.3 66.1 + - - +
221A LEU* 4.5 0.7 - - - -
222A ASN* 3.1 31.5 + - - +
223A TRP* 3.5 52.9 - - + +
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Residues in contact with ILE 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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165A LYS* 4.4 2.0 - - - -
166A PHE* 3.5 38.1 - - + +
171A MET* 5.1 5.6 - - + -
182A VAL* 4.2 7.0 - - + -
196A GLN* 1.3 75.3 - - - +
198A ASP* 1.3 55.3 + - - +
199A LEU* 4.0 15.3 - - + -
203A TRP* 3.9 29.6 - - + -
216A LEU* 4.2 7.0 - - + -
221A LEU* 3.9 30.7 - - + -
223A TRP* 3.0 17.0 + - - +
224A ILE* 3.6 14.8 - - + -
225A GLU* 2.7 36.0 + - - +
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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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165A LYS* 3.8 22.3 + - - -
166A PHE 2.9 15.7 + - - +
167A GLY* 3.0 26.4 - - - -
168A GLY 3.7 2.6 + - - -
171A MET* 4.2 2.8 - - - +
197A ILE* 1.3 75.5 - - - +
199A LEU* 1.3 66.7 + - - +
200A ALA* 3.1 16.7 + - - +
225A GLU* 3.0 21.5 - - + +
226A GLU* 4.2 1.2 - - - +
374A MG 2.2 32.4 - - - -
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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