Contacts of the strand formed by residues 212 - 217 (chain A) in PDB entry 6JKG
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 VAL 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A PHE* 4.6 0.7 - - - -
201A HIS* 3.7 20.2 - - + +
209A PRO 5.6 2.2 - - - +
211A LEU* 1.3 74.1 - - - +
213A PRO* 1.3 76.3 - - + +
214A ILE* 3.5 18.2 + - + +
228B ILE* 3.5 4.6 - - - -
229B GLY 2.9 33.9 + - - +
231B GLY* 3.3 36.6 - - - +
269B GLU 4.6 1.1 - - - +
270B HIS* 3.6 30.5 - - + -
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Residues in contact with PRO 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ALA* 4.1 30.3 - - + +
147A SER* 5.4 0.9 - - - +
149A ILE* 4.2 11.2 - - + -
150A PHE* 4.4 9.4 - - + -
201A HIS* 5.0 3.1 - - + -
211A LEU 4.5 0.2 - - - +
212A VAL* 1.3 93.6 - - + +
214A ILE* 1.3 60.8 + - - +
215A LEU 3.6 0.7 - - - -
266A HIS* 4.4 5.4 - - + -
226B PHE* 4.2 23.6 - - + -
227B VAL 3.5 6.3 - - - +
228B ILE* 4.5 2.0 - - + -
268B LEU* 3.2 38.9 - - + +
269B GLU 4.3 3.4 - - - +
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 3.7 27.8 - - + -
213A PRO* 1.3 74.1 - - - +
215A LEU* 1.3 72.5 + - + +
227B VAL* 2.8 10.0 + - + +
229B GLY* 3.6 26.7 - - - +
234B LEU* 4.6 9.4 - - + -
242B ASN 5.1 2.2 - - - +
245B HIS* 4.6 9.9 - - + -
246B GLY* 4.5 17.3 - - - +
249B LEU* 4.0 11.9 - - + -
267B ILE* 3.4 7.8 - - + +
268B LEU* 2.8 29.9 + - - +
270B HIS* 3.7 31.4 - - + +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 1.3 94.1 + - + +
216A ILE* 1.3 61.8 + - - +
198B ILE* 4.5 15.5 - - + -
226B PHE* 3.1 8.2 - - - +
227B VAL* 2.7 54.4 + - + +
246B GLY* 3.5 35.9 - - - +
249B LEU* 5.1 0.2 - - + -
250B ALA* 3.7 21.8 - - + -
265B PHE* 4.0 13.2 - - + -
266B HIS 3.2 14.6 - - - +
267B ILE* 3.8 20.9 - - + -
268B LEU* 4.5 3.4 - - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 5.1 7.0 - - + -
215A LEU* 1.3 76.0 - - - +
217A GLU* 1.3 72.2 + - - +
218A ALA* 3.3 0.3 + - - -
266A HIS* 4.9 10.1 - - + -
216B ILE* 3.0 48.2 - - + -
217B GLU 4.2 9.9 - - - +
218B ALA* 4.2 19.5 - - + -
224B MET* 4.5 10.3 - - + -
225B LYS 4.0 6.7 - - - +
226B PHE* 4.2 5.8 - - + -
265B PHE* 3.7 2.9 - - - -
266B HIS* 2.9 36.4 + - + +
268B LEU* 3.8 26.2 - - + -
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE* 1.3 77.8 - - - +
218A ALA* 1.3 75.1 + - - +
219A ALA* 4.4 5.8 - - - +
220A ARG* 5.4 3.3 + - - +
224A MET* 2.9 18.4 - - - +
223B LYS 4.7 1.9 - - - +
224B MET* 4.1 13.5 - - + +
225B LYS* 3.0 42.8 + - - +
263B LYS* 3.8 35.0 - - + +
264B ALA 3.7 4.0 - - - +
265B PHE* 3.6 21.1 - - + -
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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