Contacts of the strand formed by residues 214 - 218 (chain B) in PDB entry 1QK0
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 THR 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B MET* 4.4 8.3 - - + -
149B LEU* 4.3 13.6 - - + +
164B GLY 3.6 2.5 - - - +
166B PHE* 3.8 22.9 - - + -
206B VAL* 4.7 9.8 - - + +
209B TYR 4.8 0.9 + - - -
212B ILE* 3.1 13.5 + - - +
213B ARG* 1.3 72.5 + - - +
215B LEU* 1.3 63.6 + - - +
216B LEU* 3.7 26.2 + - + -
257B ASN* 2.8 18.7 + - - -
258B VAL* 3.4 14.6 - - - +
259B ALA 3.1 23.2 + - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 3.7 39.9 - - + +
93B PHE* 3.6 40.8 - - + -
96B VAL* 5.1 2.9 - - + -
98B PRO* 5.2 2.5 - - + -
133B PHE* 3.8 8.0 - - + -
163B ALA* 4.4 16.6 - - + -
164B GLY 2.8 12.8 + - - +
165B GLN* 3.4 21.6 - - + +
166B PHE 3.0 25.1 + - - +
213B ARG* 4.5 7.9 - - + -
214B THR* 1.3 74.8 - - - +
216B LEU* 1.3 61.0 + - - +
259B ALA* 3.5 13.7 - - + +
261B TYR* 5.5 2.9 - - + -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 4.6 0.7 - - - -
136B LEU* 5.5 0.7 - - + -
145B MET* 4.6 6.5 - - + -
166B PHE* 3.3 31.4 - - + +
168B VAL* 4.4 10.1 - - + -
202B ILE* 5.2 3.8 - - + -
206B VAL* 5.4 1.8 - - + -
214B THR* 3.7 27.6 - - + +
215B LEU* 1.3 73.9 - - - +
217B VAL* 1.3 57.6 + - - +
218B ILE* 3.9 6.5 + - + -
253B LEU* 3.7 33.4 - - + -
258B VAL* 4.0 22.0 - - + -
259B ALA 2.8 14.0 + - - +
260B MET* 3.3 11.1 - - + -
261B TYR* 2.8 37.8 + - - +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.5 26.9 - - + -
166B PHE 3.0 6.5 + - - -
167B VAL* 3.5 13.6 - - + +
168B VAL* 2.9 26.5 + - - +
216B LEU* 1.3 72.1 - - - +
218B ILE* 1.3 66.3 + - - +
220B PRO* 4.0 24.5 - - + -
261B TYR 3.3 8.3 - - - +
263B ASP* 4.7 3.1 - - + -
300B ALA* 4.1 13.9 - - + -
303B VAL* 4.2 9.2 - - + -
348B ILE* 3.9 22.9 - - + -
394B VAL* 4.2 12.3 - - + -
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.5 29.4 - - + -
216B LEU* 4.2 3.6 - - + -
217B VAL* 1.3 72.8 - - - +
219B GLU* 1.3 82.7 + - + +
220B PRO* 3.8 1.6 - - - -
246B ILE* 4.7 6.3 - - + -
249B ALA* 4.8 11.7 - - + -
250B VAL* 4.7 13.7 - - + -
253B LEU* 4.4 6.1 - - + -
260B MET* 3.9 45.3 - - + -
261B TYR 2.8 16.2 + - - +
262B LEU* 4.0 24.3 - - + +
263B ASP* 3.0 22.2 + - - +
296B LEU* 5.4 0.4 - - + -
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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
------------------------------------------------------------
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