Contacts of the strand formed by residues 205 - 209 (chain B) in PDB entry 3KQG
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 ASN 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TYR* 3.2 9.1 - - - -
202B PHE 3.0 27.1 + - - +
203B LYS 3.2 12.5 + - - -
204B GLY* 1.3 84.0 + - - +
206B PHE* 1.3 60.3 + - - +
207B TYR* 3.4 27.6 + - + +
238B GLU* 5.8 1.0 - - - -
320B LYS* 3.9 25.8 - - + +
321B ARG 3.7 4.5 - - - +
322B PRO* 3.3 27.0 - - - +
323B TYR 4.0 0.9 - - - +
169D THR* 5.5 9.2 - - - +
172D ARG* 5.8 1.0 - - - -
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 4.1 2.0 - - - -
191B ILE* 4.0 22.2 - - + -
194B VAL* 3.6 43.1 - - + -
195B VAL* 5.0 1.1 - - + -
199B TRP* 3.9 17.4 - - + -
200B LYS 3.4 11.9 - - - +
201B TYR* 3.7 23.1 - + + -
205B ASN* 1.3 73.8 - - - +
207B TYR* 1.3 60.8 + - - +
320B LYS* 3.3 5.4 - - - +
321B ARG* 2.7 63.8 + - + +
322B PRO 4.2 0.7 - - - -
323B TYR* 3.6 47.8 - + + -
324B VAL 4.9 0.4 - - - -
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Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.4 8.6 - - - -
200B LYS* 2.8 37.9 + - + +
202B PHE* 3.7 19.3 + - + -
205B ASN* 3.4 39.5 + - + +
206B PHE* 1.3 74.2 - - - +
208B TYR* 1.3 61.3 + - - +
209B PHE* 3.9 18.4 - - + -
231B THR* 3.5 23.1 - - - -
238B GLU* 2.7 28.0 + - - +
241B PHE* 3.6 24.9 - + - -
242B LEU* 3.9 20.9 - - + -
318B ILE* 4.2 2.7 - - + -
319B CYS 3.1 13.0 - - - +
320B LYS* 3.6 12.9 - - + -
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLN 5.1 2.9 - - - -
198B GLY* 3.9 17.0 - - - -
199B TRP* 3.6 48.4 - + + +
207B TYR* 1.3 75.8 - - - +
209B PHE* 1.3 64.4 + - - +
210B SER* 3.5 30.5 - - - -
211B LEU* 4.4 11.2 + - + +
222B PHE* 3.7 32.4 - + - -
226B ARG* 5.5 2.0 - - - -
317B PHE 3.3 2.8 - - - +
318B ILE* 3.1 7.3 - - - -
319B CYS* 2.8 45.3 + - + -
244C LYS 4.7 5.1 + - - -
245C THR* 4.4 8.7 + - - -
247C GLY* 4.1 21.5 + - - -
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Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY 5.3 2.0 + - - +
200B LYS* 3.5 40.4 + - + +
207B TYR* 3.9 17.7 - - + -
208B TYR* 1.3 84.1 - - - +
210B SER* 1.3 67.7 + - - +
211B LEU* 3.8 7.1 + - - +
241B PHE* 4.2 4.7 - + - -
242B LEU* 4.1 22.0 - - + -
245B THR* 3.4 41.1 - - + -
246B ALA* 3.8 13.2 - - - -
251B TYR* 3.9 25.4 - + + +
317B PHE 3.7 4.0 - - - -
318B ILE* 3.6 28.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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