Contacts of the strand formed by residues 212 - 217 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ILE* 3.6 2.1 - - - -
229A GLY* 2.9 32.1 + - - +
231A GLY* 3.7 30.1 - - - +
234A LEU* 5.2 6.1 - - + -
268A LEU* 5.7 0.7 - - + -
269A GLU 5.7 0.2 - - - +
270A HIS* 5.1 7.6 - - + -
150B PHE* 4.5 3.4 - - - -
201B HIS* 2.6 55.9 - - + +
210B GLN 5.5 0.2 - - - -
211B LEU* 1.3 72.9 - - - +
213B PRO* 1.3 83.4 - - + +
214B ILE* 3.5 4.6 + - + +
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Residues in contact with PRO 213 (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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226A PHE* 4.6 17.3 - - + -
227A VAL 3.7 7.0 - - - +
228A ILE* 4.5 4.0 - - + -
268A LEU* 3.2 37.3 - - + +
270A HIS* 6.1 0.5 - - - +
146B ALA* 4.1 30.5 - - + +
147B SER 5.2 0.2 - - - +
149B ILE* 4.2 16.4 - - + -
150B PHE* 3.9 17.0 - - + -
201B HIS* 4.6 0.7 - - - +
211B LEU 4.6 0.2 - - - +
212B VAL* 1.3 100.3 - - + +
214B ILE* 1.3 59.5 + - - +
215B LEU 4.8 0.4 - - - +
216B ILE* 5.3 1.6 - - + -
266B HIS* 4.9 2.0 - - + -
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Residues in contact with ILE 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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227A VAL* 2.8 18.5 + - + +
228A ILE 4.0 1.6 - - - -
229A GLY* 3.4 33.0 - - - +
234A LEU* 4.9 8.3 - - + -
242A ASN* 5.3 7.6 - - + +
245A HIS* 4.5 12.1 - - + +
246A GLY* 4.6 11.4 - - - +
249A LEU* 3.5 23.8 - - + -
267A ILE* 3.5 14.7 - - + -
268A LEU* 2.9 28.9 + - - +
270A HIS* 6.3 3.8 - - + -
212B VAL* 3.8 6.5 - - + +
213B PRO* 1.3 75.6 - - - +
215B LEU* 1.3 70.6 + - + +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A ILE* 3.4 35.9 - - + -
226A PHE* 3.1 28.9 - - - +
227A VAL* 3.3 29.4 + - + -
246A GLY* 3.6 33.2 - - - +
250A ALA* 4.9 5.2 - - + -
265A PHE* 3.5 24.2 - - + -
266A HIS 3.0 16.8 - - - +
267A ILE* 4.0 9.2 - - + -
268A LEU 4.8 0.2 - - - +
213B PRO* 3.7 0.7 - - - +
214B ILE* 1.3 88.8 + - + +
216B ILE* 1.3 66.5 + - - +
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Residues in contact with ILE 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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216A ILE* 3.0 50.9 - - + +
224A MET* 4.4 16.8 - - + -
225A LYS 3.5 6.3 - - - +
226A PHE* 4.9 4.7 - - + -
265A PHE* 3.3 5.6 - - - -
266A HIS* 3.0 33.5 + - + +
268A LEU* 3.5 32.8 - - + -
149B ILE* 5.3 1.3 - - + -
213B PRO* 5.3 0.9 - - + -
215B LEU* 1.3 79.0 - - - +
217B GLU* 1.3 70.9 + - - +
218B ALA* 4.5 0.2 - - - -
266B HIS* 4.3 22.4 - - + +
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Residues in contact with GLU 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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216A ILE* 4.2 0.3 - - - +
223A LYS 4.2 13.6 - - - +
224A MET* 3.8 9.2 + - - +
225A LYS* 2.7 48.1 + - - +
263A LYS* 2.9 45.0 + - + +
264A ALA 3.2 15.5 - - - +
265A PHE* 3.4 8.7 - - + -
216B ILE* 1.3 81.7 - - - +
218B ALA* 1.3 69.0 + - - +
219B ALA* 4.0 10.1 - - - +
224B MET* 3.6 16.0 - - + +
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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