Contacts of the strand formed by residues 213 - 218 (chain B) in PDB entry 3IKH
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 GLN 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B LEU 3.5 1.9 - - - +
209B VAL* 3.5 4.5 - - - -
210B GLN* 2.9 31.2 + - + +
211B GLU* 3.0 29.5 + - - +
212B GLY* 1.3 84.3 + - - +
214B ARG* 1.3 61.2 + - - +
215B GLN* 5.4 5.8 - - + +
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Residues in contact with ARG 214 (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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207B TRP* 3.8 27.6 - - + -
208B LEU 3.5 4.9 - - - +
209B VAL* 4.8 21.6 - - + +
212B GLY* 3.6 14.0 + - - +
213B GLN* 1.3 77.9 - - - +
215B GLN* 1.3 67.8 + - - +
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Residues in contact with GLN 215 (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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206B ALA 3.9 0.2 - - - +
207B TRP* 3.3 6.7 - - - -
208B LEU* 2.7 66.7 + - + +
210B GLN* 5.0 3.1 - - - +
213B GLN* 5.4 6.0 - - + +
214B ARG* 1.3 82.1 - - - +
216B PHE* 1.3 62.8 + - - +
250B ASP* 5.3 0.5 - - - +
251B ALA* 3.9 27.3 + - + +
254B LEU* 5.0 0.9 - - - +
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Residues in contact with PHE 216 (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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201B GLN* 5.1 3.6 - - - -
204B ALA* 3.8 25.1 - - + -
205B GLY* 4.0 4.7 - - - -
206B ALA* 3.4 27.6 - - - -
207B TRP* 3.7 45.6 - + + -
215B GLN* 1.3 75.0 - - - +
217B CYS* 1.3 62.9 + - - +
218B PRO* 3.8 29.0 - - + +
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Residues in contact with CYS 217 (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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205B GLY* 3.2 0.3 - - - -
206B ALA* 2.7 42.5 + - + +
215B GLN 4.1 0.2 + - - -
216B PHE* 1.3 75.9 - - - +
218B PRO* 1.3 75.8 - - - +
251B ALA* 4.7 4.3 - - - +
254B LEU* 3.7 37.5 - - + -
255B ALA* 3.7 13.0 - - - -
258B SER* 3.5 23.9 + - - +
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Residues in contact with PRO 218 (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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204B ALA 3.9 4.5 - - - +
216B PHE* 3.8 30.5 - - + +
217B CYS* 1.3 99.8 - - + +
219B ALA* 1.3 69.4 + - - +
220B VAL* 3.9 1.6 + - - +
258B SER* 3.7 5.9 + - - -
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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