Contacts of the helix formed by residues 160 - 169 (chain B) in PDB entry 5IFM
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 SER 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.3 16.2 - - - -
238A GLU* 3.0 47.5 + - - +
241A VAL* 4.2 5.4 - - - -
251A ARG* 3.4 8.0 + - - +
159B VAL* 1.3 74.3 - - - +
161B ASN* 1.3 65.1 + - - +
162B GLU 3.6 0.2 + - - -
163B LEU* 3.0 19.8 + - - +
164B LEU* 3.0 17.8 + - - +
179B VAL* 3.5 9.8 - - - +
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Residues in contact with ASN 161 (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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234A GLU 3.1 24.0 + - - -
235A GLY 3.9 0.7 - - - -
236A LEU 2.8 24.7 + - - -
237A PRO* 3.4 18.8 - - - +
160B SER* 1.3 71.6 - - - +
162B GLU* 1.4 63.8 + - - +
164B LEU* 3.3 6.8 + - - +
165B GLU* 3.0 28.5 + - - +
177B ALA* 3.5 22.8 + - - +
178B VAL* 3.4 4.3 - - - +
179B VAL* 2.8 33.2 + - - +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO* 3.6 13.6 - - - +
238A GLU* 2.9 51.6 + - + +
239A LYS* 5.3 0.9 + - - +
160B SER 3.2 0.2 - - - -
161B ASN* 1.4 76.2 + - - +
163B LEU* 1.3 60.0 + - - +
165B GLU* 3.3 11.1 + - - +
166B GLU* 2.9 43.0 + - - +
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Residues in contact with LEU 163 (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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238A GLU* 5.1 0.2 - - - +
251A ARG* 3.7 42.0 - - - +
255A PRO* 3.9 27.4 - - + -
158B TYR 4.0 0.2 - - - +
159B VAL* 4.0 25.8 - - + -
160B SER* 3.0 24.0 + - - +
162B GLU* 1.3 74.8 - - - +
164B LEU* 1.4 53.3 + - - +
166B GLU* 3.2 19.9 + - + +
167B ALA* 2.8 33.7 + - + +
215B LEU* 3.9 20.4 - - + +
216B THR* 4.1 2.7 - - + -
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Residues in contact with LEU 164 (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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152B VAL* 4.6 2.2 - - + -
155B LEU* 3.9 24.9 - - + -
159B VAL* 4.3 7.0 - - + +
160B SER 3.0 12.4 + - - +
161B ASN* 3.4 9.9 - - - +
163B LEU* 1.4 75.2 - - - +
165B GLU* 1.3 61.3 + - - +
167B ALA* 3.5 2.9 + - - -
168B PHE* 3.1 55.2 + - + +
177B ALA* 4.0 2.0 - - + +
178B VAL 3.5 33.7 - - - +
179B VAL* 4.3 6.3 - - + -
191B GLY* 4.3 6.1 - - - -
192B ILE 3.8 18.4 - - - +
193B VAL* 3.8 12.1 - - + -
215B LEU* 3.9 8.5 - - + -
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Residues in contact with GLU 165 (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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68B LYS* 2.7 39.3 + - - -
161B ASN 3.0 14.4 + - - +
162B GLU* 3.5 13.6 - - - +
164B LEU* 1.3 73.7 - - - +
166B GLU* 1.3 59.8 + - + +
168B PHE 3.5 0.3 + - - -
169B SER* 2.9 34.6 + - - -
174B VAL* 3.7 26.8 - - + +
176B ARG* 4.9 0.7 - - - -
177B ALA* 3.6 19.9 + - + +
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Residues in contact with GLU 166 (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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238A GLU* 5.9 0.5 - - - +
255A PRO* 5.2 2.7 - - + -
162B GLU* 2.9 36.1 + - - +
163B LEU* 3.5 21.2 + - + +
165B GLU* 1.3 72.8 - - + +
167B ALA* 1.3 62.4 + - - +
169B SER* 2.7 24.4 + - - -
170B VAL* 4.1 6.6 - - - +
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Residues in contact with ALA 167 (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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255A PRO* 3.6 32.4 - - + +
163B LEU 2.8 20.2 + - - +
164B LEU* 3.6 7.2 - - - +
166B GLU* 1.3 72.3 - - - +
168B PHE* 1.3 61.8 + - + +
170B VAL* 3.3 22.6 + - - +
171B PHE* 4.2 0.2 - - - -
213B PHE* 3.3 15.4 - - + -
215B LEU* 3.6 24.2 - - + -
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Residues in contact with PHE 168 (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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150B LEU* 5.2 0.4 - - + -
152B VAL* 3.9 18.4 - - + -
164B LEU* 3.1 39.5 + - + +
167B ALA* 1.3 77.2 - - + +
169B SER* 1.3 55.2 + - - +
170B VAL 3.1 5.6 - - - -
171B PHE* 3.1 45.0 + + - -
174B VAL* 3.7 6.1 - - + -
193B VAL* 3.7 32.5 - - + -
195B PHE* 3.3 24.5 - + + -
204B ALA* 4.2 4.3 - - + -
208B CYS* 4.3 2.7 - - - -
213B PHE* 3.9 18.6 - + - -
215B LEU* 4.4 7.2 - - + -
222B VAL* 4.3 0.9 - - + -
224B VAL* 3.7 38.8 - - + -
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Residues in contact with SER 169 (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 GLU* 2.9 19.7 + - - -
166B GLU* 2.7 21.0 + - - -
167B ALA 3.3 0.2 - - - -
168B PHE* 1.3 77.3 - - - +
170B VAL* 1.3 59.8 + - - +
171B PHE 3.2 0.7 - - - -
172B GLY* 3.2 24.6 + - - +
174B VAL* 3.8 7.9 - - - -
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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