Contacts of the strand formed by residues 193 - 200 (chain B) in PDB entry 4IRX
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
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Residue Dist Surf HB Arom Phob DC
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153B VAL* 4.0 18.4 - - + -
154B VAL* 3.6 40.4 - - + -
157B TYR* 3.1 28.3 - - + -
158B PRO* 4.1 9.4 - - + -
160B GLY* 3.8 14.8 - - - -
161B ALA* 3.5 11.9 - - + -
163B VAL* 5.3 2.5 - - + -
186B LEU* 4.1 28.9 - - + +
189B GLY* 3.5 38.4 - - - -
190B GLY 3.0 14.0 + - - +
191B PRO* 4.2 1.8 - - - +
192B ALA* 1.3 81.2 - - + +
194B LYS* 1.3 61.8 + - - +
195B ILE* 3.8 2.3 + - - +
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Residues in contact with LYS 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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161B ALA 2.9 14.1 + - - +
162B ARG* 3.7 15.0 - - + +
163B VAL* 2.8 31.6 + - - +
191B PRO* 2.7 36.5 + - - +
192B ALA* 4.2 10.3 - - - +
193B PHE* 1.3 72.3 - - - +
195B ILE* 1.3 62.5 + - - +
196B VAL* 3.3 15.2 + - + -
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Residues in contact with ILE 195 (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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163B VAL* 3.5 4.0 - - + +
165B VAL* 4.1 17.7 - - + -
182B VAL* 5.0 0.2 - - + -
183B HIS* 3.7 32.3 - - + +
186B LEU* 3.6 36.8 - - + -
193B PHE 3.8 2.1 + - - +
194B LYS* 1.3 68.5 - - - +
196B VAL* 1.3 63.4 + - - +
197B THR* 3.9 22.8 - - - +
198B GLU* 4.2 11.0 - - + +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 3.6 43.5 - - + +
163B VAL 2.9 23.5 + - - +
164B VAL* 3.6 20.2 - - + -
194B LYS* 4.0 17.5 - - + +
195B ILE* 1.3 73.6 - - - +
197B THR* 1.3 65.1 + - - +
219B MSE 3.7 25.2 - - + +
224B PRO* 4.9 0.9 - - + -
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Residues in contact with THR 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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164B VAL* 3.5 5.7 - - + -
165B VAL 3.0 23.7 + - - +
195B ILE* 3.3 8.0 - - - +
196B VAL* 1.3 83.3 - - - +
198B GLU* 1.3 64.2 + - - +
199B GLN* 3.0 23.1 + - - +
215B ILE* 3.6 46.7 - - + -
219B MSE 4.2 7.4 - - + -
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Residues in contact with GLU 198 (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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165B VAL* 3.3 31.8 - - + +
167B THR* 4.1 10.2 - - + +
179B VAL* 3.5 17.8 - - - +
183B HIS* 2.7 37.8 + - - -
195B ILE* 4.2 11.0 - - + +
197B THR* 1.3 77.6 + - - +
199B GLN* 1.3 67.0 + - - +
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Residues in contact with GLN 199 (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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165B VAL 3.0 5.3 + - - -
166B ILE* 3.2 10.2 - - + +
167B THR* 2.8 24.9 + - - -
197B THR* 3.0 21.9 + - - +
198B GLU* 1.3 80.1 - - - +
200B THR* 1.3 63.1 + - - +
211B VAL* 3.6 27.7 - - + +
215B ILE* 3.6 26.6 - - + +
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Residues in contact with THR 200 (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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166B ILE* 4.6 0.7 - - - -
167B THR* 3.0 25.3 + - - -
170B PRO* 3.3 24.4 - - + +
199B GLN* 1.3 77.9 - - - +
201B ALA* 1.3 58.7 + - - +
202B ASN* 3.0 39.6 + - - +
207B GLN* 5.1 0.3 - - - +
211B VAL* 4.0 15.7 - - - +
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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