Contacts of the strand formed by residues 228 - 235 (chain P) in PDB entry 3K9Q
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 LEU 228 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300O MET* 3.4 6.1 - - - +
156P LEU* 4.4 11.0 - - + -
160P ALA* 4.0 28.0 - - + -
169P LEU* 3.8 21.1 - - + -
172P GLY* 3.4 26.0 - - - +
214P ALA* 3.2 32.4 + - + +
215P LYS* 3.6 8.1 - - - +
217P ILE* 4.1 10.9 - - + +
224P ILE* 4.1 12.7 + - + -
226P GLY* 4.5 5.2 - - - +
227P LYS* 1.3 87.4 - - + +
229P ASP* 1.3 63.6 + - - +
245P LEU* 4.0 23.1 - - + -
247P VAL* 4.6 1.3 - - + -
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Residues in contact with ASP 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298O ARG* 5.5 10.6 - - - +
299O VAL 5.8 0.2 - - - +
300O MET* 3.2 24.7 - - + +
172P GLY 3.3 2.4 + - - -
173P LEU* 3.3 15.2 - - + -
174P MET* 2.9 21.0 + - - +
211P THR 5.1 1.0 - - - +
214P ALA* 3.5 15.1 - - - +
215P LYS* 3.3 44.3 + - - +
228P LEU* 1.3 71.3 - - - +
230P GLY* 1.3 80.7 + - - +
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Residues in contact with GLY 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298O ARG* 6.0 7.4 - - - -
309O LYS* 4.3 6.3 - - - -
173P LEU* 4.3 3.3 - - - +
174P MET* 3.0 22.4 - - - -
210P SER* 5.5 0.5 - - - -
211P THR 3.8 15.1 + - - +
214P ALA* 4.0 1.5 - - - +
229P ASP* 1.3 95.7 + - - +
231P GLY* 1.3 58.8 + - - -
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Residues in contact with GLY 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309O LYS* 4.6 2.4 - - - +
174P MET* 3.0 14.9 + - - +
175P THR* 3.4 6.5 - - - -
176P THR* 3.0 22.2 + - - +
209P ASN 3.9 6.5 - - - -
210P SER* 4.9 1.3 - - - -
211P THR* 3.7 13.5 - - - -
230P GLY* 1.3 74.2 - - - -
232P ALA* 1.3 59.2 + - - -
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Residues in contact with ALA 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175P THR* 4.9 0.4 - - - -
176P THR* 3.2 25.1 - - + +
178P HIS* 4.8 7.6 - - + -
208P PRO* 3.3 4.2 - - - +
209P ASN* 2.8 45.9 + - + +
210P SER 4.8 1.1 - - - +
211P THR* 4.3 9.6 - - + -
231P GLY* 1.3 75.0 - - - -
233P GLN* 1.3 70.2 + - - +
234P ARG* 4.1 9.6 - - - +
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Residues in contact with GLN 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O ILE* 4.1 20.4 - - + -
242O LEU* 3.3 13.9 - - - +
244O GLU* 2.9 29.1 + - - +
296O GLN* 3.2 22.8 - - - +
175P THR* 4.2 8.0 - - + +
176P THR 2.8 9.7 + - - +
177P ILE* 3.4 6.3 - - - -
178P HIS* 2.7 27.5 + - - -
206P ILE* 3.8 15.5 - - + +
207P ILE 3.5 1.7 - - - -
208P PRO* 3.1 31.9 - - - +
232P ALA* 1.3 79.0 + - - +
234P ARG* 1.3 61.5 + - - +
235P VAL* 3.6 7.3 + - + +
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Residues in contact with ARG 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P HIS* 3.3 26.1 + - - +
179P ALA 3.6 16.2 - - - -
180P TYR* 4.8 1.6 - - - -
181P THR* 3.1 24.5 + - - +
183P ASP* 3.7 15.4 + - - -
184P GLN* 2.6 57.1 + - - +
198P ARG* 4.8 3.0 - - + +
202P ALA 5.7 0.4 - - - -
205P ASN 3.4 5.6 - - - +
207P ILE* 2.7 44.3 + - + +
209P ASN* 4.4 21.9 + - + +
232P ALA* 4.9 7.7 - - + +
233P GLN* 1.3 72.3 - - - +
235P VAL* 1.3 59.7 + - - +
337P GOL 4.4 13.7 + - - -
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Residues in contact with VAL 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O ILE* 4.0 9.9 - - + -
206O ILE* 4.0 21.1 - - + -
235O VAL* 4.0 24.9 - - + -
236O PRO* 4.9 0.7 - - + -
177P ILE* 3.9 30.7 - - + -
178P HIS 2.8 16.6 + - - +
180P TYR* 3.5 21.5 + - - +
202P ALA 4.6 2.0 - - - -
205P ASN 4.3 0.9 - - - -
206P ILE* 4.2 9.4 - - + -
233P GLN 3.9 5.4 - - - +
234P ARG* 1.3 79.9 - - - +
236P PRO* 1.4 71.5 - - + +
237P VAL* 2.8 14.7 + - + +
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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
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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