Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 1NMS
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 PHE 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B THR* 3.7 22.2 - - - -
143B PHE* 3.5 30.7 - - + -
144B ARG* 3.7 7.0 - - + -
156B LYS* 3.3 21.3 - - + -
158B PHE* 3.7 31.9 - + - -
189B VAL 3.7 20.6 - - - -
190B ASP* 3.3 23.6 - - + +
191B ALA 3.4 5.5 - - - -
192B ASP* 1.3 82.0 - - - +
194B LEU* 1.3 61.3 + - - +
195B TYR* 4.1 26.5 - + + -
266B VAL 4.2 0.3 - - - +
268B MET* 2.8 35.1 + - + +
269B LEU* 3.4 2.5 + - - -
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Residues in contact with LEU 194 (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 LYS 2.9 6.8 + - - +
157B LEU* 3.4 23.4 - - + -
158B PHE* 2.8 27.5 + - - +
159B ILE* 6.0 0.7 - - + -
193B PHE* 1.3 72.8 - - - +
195B TYR* 1.3 77.4 + - - +
196B ALA* 3.8 7.4 - - + +
232B PHE* 3.8 22.9 - - + -
233B MET* 3.0 42.2 - - + -
236B LEU* 4.0 8.1 - - + -
265B ILE* 4.1 8.3 - - + -
266B VAL 3.5 4.3 - - - +
267B SER* 3.7 17.5 - - - +
269B LEU* 3.9 10.3 - - + -
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.0 11.7 - - + -
137B LYS* 5.5 5.2 + - - +
140B THR* 3.4 42.7 + - + +
158B PHE* 3.2 13.2 - + + +
160B ILE* 3.8 15.9 - - + -
193B PHE* 4.1 23.2 - + + -
194B LEU* 1.3 80.3 - - - +
196B ALA* 1.3 59.8 - - - +
197B TYR* 3.4 38.5 + + + -
264B CYS 3.8 0.3 - - - +
265B ILE* 3.7 1.2 - - - -
266B VAL* 2.8 49.1 + - + -
268B MET* 3.8 27.6 - - + -
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Residues in contact with ALA 196 (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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158B PHE 2.8 8.7 + - - -
159B ILE* 3.5 19.3 - - + -
160B ILE* 2.9 25.5 + - - -
194B LEU* 3.8 14.3 - - + +
195B TYR* 1.3 70.4 - - - +
197B TYR* 1.3 62.9 + - - +
215B PHE* 3.6 19.6 - - + -
219B LEU* 5.6 0.4 - - + -
232B PHE* 5.3 0.7 - - + -
236B LEU* 4.2 20.6 - - + -
264B CYS 4.2 1.8 - - - -
265B ILE* 4.9 4.0 - - + +
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Residues in contact with TYR 197 (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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124B GLU* 5.6 0.2 - - - -
125B GLY* 6.1 3.2 - - - -
136B LEU* 3.7 14.0 - - + +
160B ILE* 3.4 33.0 - - + -
164B ARG* 3.5 41.0 + - + +
195B TYR* 3.4 40.3 - + + -
196B ALA* 1.3 75.6 - - - +
198B SER* 1.3 61.5 + - - +
199B THR 3.7 16.2 - - - +
215B PHE* 3.8 2.8 - - - -
263B PRO* 3.4 6.2 - - - +
264B CYS 2.9 43.1 + - - +
266B VAL* 3.7 21.5 - - + -
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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