Contacts of the strand formed by residues 232 - 239 (chain F) in PDB entry 3IKM
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 GLY 232 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133E HIS* 4.6 0.4 - - - -
93F SER 4.0 10.5 - - - -
94F GLY 3.8 18.2 - - - -
215F PHE* 3.4 8.7 - - - +
216F HIS* 2.3 52.2 + - - +
217F PRO* 4.2 1.6 - - - +
218F VAL* 4.9 3.7 - - - +
231F ILE* 1.3 70.4 - - - +
233F GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E LEU* 3.0 14.3 - - + +
132E HIS* 2.7 34.7 + - - +
133E HIS* 2.7 41.9 + - + +
93F SER 4.4 1.4 - - - +
94F GLY* 4.2 7.4 + - - +
96F HIS* 4.3 17.1 - - + -
213F VAL* 3.7 6.9 - - + +
214F CYS 3.6 6.7 - - - +
215F PHE* 3.0 33.4 - - + +
216F HIS* 4.3 0.7 - - - +
232F GLY* 1.3 74.6 - - - -
234F LYS* 1.3 78.3 + - - +
343F ASP* 4.4 2.4 - - - +
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Residues in contact with LYS 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU 5.6 1.3 - - - -
92F LEU* 3.0 29.3 + - - +
93F SER 4.4 6.5 - - - +
94F GLY* 6.0 0.4 - - - -
96F HIS* 6.3 0.9 - - - -
213F VAL* 4.2 1.8 - - - +
214F CYS* 2.8 38.3 + - - +
216F HIS* 3.3 34.3 - - + +
233F GLU* 1.3 90.5 - - - +
235F THR* 1.3 62.0 + - - +
236F GLU* 3.4 1.2 + - - +
341F ASP* 3.6 11.3 - - - +
342F LEU* 4.2 3.6 - - - +
343F ASP* 3.7 19.5 - - - +
344F ARG* 2.6 48.9 - - - +
347F LEU* 4.8 3.0 - - - +
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Residues in contact with THR 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E HIS* 5.1 0.3 - - - -
107F ARG* 4.8 23.5 + - - +
211F ILE* 3.8 24.7 - - + +
212F GLY* 3.5 15.7 - - - +
213F VAL* 2.6 26.5 - - - +
234F LYS* 1.3 65.7 - - - +
236F GLU* 1.3 55.7 + - - +
341F ASP* 2.3 29.9 + - - +
342F LEU 4.1 1.2 - - - +
343F ASP* 4.0 17.2 + - - -
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Residues in contact with GLU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU 5.7 2.8 - - - +
185F LEU* 3.1 18.3 + - + +
211F ILE* 2.8 36.4 - - - +
212F GLY 2.7 14.8 + - - -
214F CYS* 2.6 37.5 - - - +
216F HIS* 3.5 28.1 + - - -
234F LYS 3.7 1.0 - - - +
235F THR* 1.3 71.9 - - - +
237F ALA* 1.3 59.9 + - - +
238F SER* 5.6 0.4 - - - -
340F GLY* 3.3 22.8 - - - +
341F ASP* 2.7 27.3 - - + +
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Residues in contact with ALA 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TRP* 3.8 35.9 - - + -
210F GLN 4.0 5.6 - - - -
211F ILE* 4.1 7.4 - - + -
236F GLU* 1.3 77.2 - - - +
238F SER* 1.3 56.3 + - - +
338F VAL* 2.9 3.1 - - - +
339F ASN* 2.2 38.8 - - + +
340F GLY* 3.6 1.4 - - - -
341F ASP* 3.3 10.6 - - + +
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Residues in contact with SER 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TRP* 5.2 2.6 - - - -
127F PRO* 5.1 2.6 - - - +
185F LEU* 3.7 27.7 + - - +
186F LEU* 3.8 21.5 + - - -
189F ALA* 4.7 2.4 - - - +
209F ALA* 2.4 30.8 - - - +
210F GLN 3.5 12.9 + - - +
236F GLU* 4.0 1.5 - - - -
237F ALA* 1.3 74.3 - - - +
239F LEU* 1.3 51.7 + - - +
240F VAL* 4.2 5.5 - - - +
338F VAL* 3.0 14.8 - - - -
340F GLY* 5.7 2.2 - - - -
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Residues in contact with LEU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TRP* 5.2 4.0 - - + -
118F VAL* 4.6 21.8 - - + -
207F GLY* 3.1 30.5 - - - +
209F ALA* 3.1 8.1 - - + -
238F SER* 1.3 67.4 - - - +
240F VAL* 1.3 73.7 + - - +
255F TRP* 3.7 39.5 - - + -
336F LEU* 2.5 35.8 - - + +
337F SER 5.0 0.7 - - - +
338F VAL* 2.4 50.0 - - + +
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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