Contacts of the helix formed by residues 183 - 192 (chain B) in PDB entry 4IVR
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 THR 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY 5.4 0.7 + - - -
118B ALA* 4.2 18.5 - - + +
122B THR* 5.5 0.4 + - - -
177B TYR* 4.3 0.4 - - - -
182B MET* 1.3 91.1 - - - +
184B PRO* 1.3 69.5 - - + +
185B GLN* 3.4 17.8 + - - +
186B ALA* 3.1 28.1 + - - +
187B VAL* 3.3 4.0 + - - +
296B GLU* 6.2 0.2 - - - -
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Residues in contact with PRO 184 (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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177B TYR* 3.7 32.8 - - + -
182B MET 3.8 0.4 - - - -
183B THR* 1.3 86.5 - - - +
185B GLN* 1.3 72.6 + - - +
187B VAL* 3.3 7.7 + - + +
188B LEU* 3.0 27.9 + - - +
292B PHE* 4.6 7.2 - - + -
294B ALA* 4.1 14.8 - - + -
296B GLU* 3.8 35.4 - - + +
297B LEU* 4.2 13.7 - - + -
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Residues in contact with GLN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.0 14.4 + - - +
91A LEU 3.0 25.5 + - - +
92A GLY* 3.4 26.5 + - - +
93A ALA* 4.7 1.6 - - - +
127A THR* 5.4 4.3 - - - +
183B THR* 3.4 20.6 - - - +
184B PRO* 1.3 76.0 - - - +
186B ALA* 1.3 55.4 + - - +
188B LEU* 3.1 4.2 + - - +
189B ALA* 2.7 34.5 + - - +
296B GLU* 3.6 30.5 + - - +
297B LEU* 4.1 6.3 - - + -
308B PHE* 3.8 21.1 - - + -
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 5.2 3.6 - - + -
127A THR* 5.2 8.5 + - - +
122B THR* 3.9 18.6 - - + +
182B MET* 3.8 20.9 - - + -
183B THR* 3.1 21.7 + - - +
185B GLN* 1.3 78.5 - - - +
187B VAL* 1.3 64.2 + - - +
189B ALA* 3.1 9.7 + - - +
190B PHE* 3.0 28.0 + - + -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.5 4.7 - - + +
173B PRO* 3.8 24.9 - - + +
174B ALA* 4.3 18.2 - - + +
177B TYR* 4.1 12.8 - - + -
182B MET* 3.6 17.5 - - + -
183B THR 3.3 14.5 + - - +
184B PRO* 3.6 9.4 - - + +
185B GLN 3.2 0.4 - - - -
186B ALA* 1.3 76.0 - - - +
188B LEU* 1.3 59.1 + - - +
190B PHE* 3.1 8.5 + - - +
191B VAL* 2.9 31.7 + - + +
292B PHE* 4.0 26.5 - - + -
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Residues in contact with LEU 188 (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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130A MET* 4.3 9.4 - - + +
184B PRO 3.0 12.6 + - - +
185B GLN 3.6 7.2 - - - +
187B VAL* 1.3 77.7 - - - +
189B ALA* 1.3 55.6 + - - +
191B VAL* 3.2 14.6 + - + +
192B ALA* 3.0 28.4 + - - +
292B PHE* 3.6 32.8 - - + -
297B LEU* 3.8 20.9 - - + -
304B LEU* 5.8 0.2 - - + -
308B PHE* 3.7 43.5 - - + +
311B ALA* 4.0 22.6 - - + +
312B LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 189 (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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87A TYR* 5.0 0.9 - - - +
126A ILE* 3.6 27.1 - - + +
127A THR* 5.0 2.7 - - - +
130A MET* 3.6 32.0 - - + +
185B GLN 2.7 17.7 + - - +
186B ALA* 3.1 11.2 + - - +
188B LEU* 1.3 75.1 - - - +
190B PHE* 1.3 61.9 + - - +
192B ALA* 3.7 6.1 + - - +
193B LEU* 3.6 22.4 + - - +
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Residues in contact with PHE 190 (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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126A ILE* 3.9 25.4 - - + -
122B THR* 3.6 32.5 - - + -
125B GLN* 4.1 16.6 - - + -
126B ILE* 3.7 26.9 - - + -
168B ALA 4.0 7.6 - - - -
169B LEU* 3.0 36.3 - - + +
173B PRO* 3.5 34.5 - - + -
182B MET* 4.7 7.9 - - - -
186B ALA 3.0 16.1 + - - -
187B VAL* 3.1 6.7 + - - +
189B ALA* 1.3 77.3 - - - +
191B VAL* 1.3 67.1 + - - +
193B LEU* 3.0 18.0 + - + +
194B ILE* 3.4 7.8 + - - +
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Residues in contact with VAL 191 (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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169B LEU 4.1 5.8 - - - +
170B LEU* 3.7 31.2 - - + -
187B VAL* 2.9 22.2 + - + +
188B LEU* 3.2 23.5 + - + +
190B PHE* 1.3 77.4 - - - +
192B ALA* 1.3 62.7 + - - +
194B ILE* 3.1 30.3 + - + +
292B PHE* 5.0 1.8 - - + -
311B ALA* 3.5 27.8 - - + +
314B VAL* 3.8 6.7 - - + +
315B LEU* 4.0 22.9 - - + +
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Residues in contact with ALA 192 (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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130A MET* 4.5 3.4 - - + +
133A ALA* 4.1 18.7 - - + +
134A VAL* 3.4 41.7 - - + +
137A ALA* 4.4 9.5 - - - +
188B LEU 3.0 13.7 + - - +
189B ALA* 3.8 10.1 - - - +
190B PHE 3.2 0.4 - - - -
191B VAL* 1.3 77.9 - - - +
193B LEU* 1.3 59.7 + - - +
194B ILE 3.4 3.8 + - - +
311B ALA* 5.1 0.4 - - + -
314B VAL* 4.5 9.8 - - - +
318B ARG* 5.2 0.7 + - - -
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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