Contacts of the strand formed by residues 169 - 179 (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 169 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160P ALA* 5.1 4.5 - - + +
163P LEU* 5.2 4.9 - - + -
164P ASN* 3.0 31.5 + - + +
168P GLY* 1.3 71.3 - - - +
170P VAL* 1.3 62.3 + - - +
171P GLU 3.7 26.2 - - - +
224P ILE* 3.9 35.0 - - + -
227P LYS* 3.2 32.2 + - + -
228P LEU* 3.8 22.0 - - + -
245P LEU* 6.5 0.2 - - + -
247P VAL* 3.9 25.4 - - + -
248P VAL 3.9 2.9 - - - +
249P LEU* 4.2 7.2 - - + -
250P GLU* 4.9 3.9 - - - +
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Residues in contact with VAL 170 (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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302O VAL* 3.9 15.0 - - + +
305O ARG* 3.8 45.8 - - + +
168P GLY 3.4 0.2 + - - -
169P LEU* 1.3 75.5 - - - +
171P GLU* 1.3 72.7 + - + +
227P LYS* 3.7 19.0 - - - +
248P VAL* 2.8 22.2 + - + +
249P LEU 3.7 25.4 - - - +
250P GLU* 3.7 17.3 - - + +
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Residues in contact with GLU 171 (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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300O MET* 3.7 12.6 - - + +
302O VAL* 3.5 21.0 + - + +
305O ARG* 2.7 50.1 + - - +
306O GLN 3.2 10.2 + - - +
307O LEU* 3.9 23.2 - - + +
169P LEU* 3.7 8.6 - - - +
170P VAL* 1.3 85.1 - - + +
172P GLY* 1.3 59.2 + - - +
227P LYS* 3.3 11.7 - - - +
247P VAL* 3.4 3.5 - - - +
248P VAL* 2.8 41.1 + - + +
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Residues in contact with GLY 172 (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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300O MET* 3.9 3.4 - - - +
307O LEU* 3.7 5.8 - - - -
171P GLU* 1.3 78.0 - - - +
173P LEU* 1.3 69.5 + - - +
227P LYS 2.9 8.4 + - - +
228P LEU* 3.4 19.4 - - - +
229P ASP 3.3 21.3 + - - -
245P LEU* 5.0 0.2 - - - -
246P THR 3.2 12.1 - - - -
247P VAL* 4.0 2.9 - - - -
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Residues in contact with LEU 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O THR* 4.1 15.3 - - + +
298O ARG* 5.0 12.1 - - + +
300O MET* 3.7 21.8 - - + +
307O LEU* 3.8 33.1 - - + +
309O LYS* 3.8 39.3 - - + +
172P GLY* 1.3 81.9 - - - +
174P MET* 1.3 62.2 + - - +
229P ASP* 3.3 28.3 - - + +
230P GLY* 4.3 2.9 - - - +
244P GLU 4.0 0.5 - - - +
245P LEU* 3.6 3.8 - - - +
246P THR* 2.8 42.1 + - - +
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Residues in contact with MET 174 (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* 2.8 19.8 + - - -
152P THR* 3.9 24.9 - - + -
156P LEU* 4.1 10.8 - - - -
173P LEU* 1.3 74.5 - - - +
175P THR* 1.3 64.6 + - - +
176P THR* 4.4 1.8 - - + -
211P THR* 3.7 22.4 - - + -
214P ALA* 3.9 28.3 - - + +
229P ASP 2.9 12.5 + - - +
230P GLY* 3.0 1.5 - - - +
231P GLY 3.0 45.4 + - - +
243P THR* 3.8 19.3 - - + -
244P GLU 3.2 11.9 - - - +
245P LEU* 4.0 13.2 - - + -
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Residues in contact with THR 175 (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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175O THR* 6.3 0.2 - - + -
177O ILE* 5.2 1.1 - - + -
244O GLU* 2.6 38.2 + - - +
309O LYS* 2.9 21.2 + - - +
173P LEU 4.4 0.2 + - - -
174P MET* 1.3 73.3 - - - +
176P THR* 1.3 74.7 + - - +
177P ILE* 4.0 13.1 + - + -
231P GLY 3.4 7.2 + - - +
232P ALA* 4.9 0.7 - - - -
233P GLN* 4.2 14.1 - - + +
242P LEU 4.0 0.2 - - - +
243P THR* 3.8 0.2 - - - -
244P GLU* 2.8 45.9 + - - +
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Residues in contact with THR 176 (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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152P THR* 3.9 18.8 - - + +
174P MET* 4.3 2.0 - - + +
175P THR* 1.3 73.6 - - - +
177P ILE* 1.3 60.9 + - - +
178P HIS* 3.4 7.5 + - + -
211P THR* 4.4 6.5 - - + -
231P GLY 3.0 13.6 + - - +
232P ALA* 3.2 23.9 - - + +
233P GLN 2.8 31.2 + - - +
242P LEU 2.9 16.9 + - - -
243P THR* 3.5 12.0 + - - -
314P TYR* 2.7 29.8 + - - +
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Residues in contact with ILE 177 (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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175O THR* 5.0 1.1 - - + -
177O ILE* 4.1 23.6 - - + -
206O ILE* 3.6 15.7 - - + +
233O GLN* 4.0 19.3 - - + -
235O VAL* 4.0 15.0 - - + -
175P THR* 4.2 13.0 - - + +
176P THR* 1.3 70.3 - - - +
178P HIS* 1.3 59.6 + - - +
233P GLN* 3.4 4.9 - - + -
235P VAL* 3.9 31.6 - - + -
241P SER* 3.4 4.0 - - - -
242P LEU* 2.9 45.5 + - + +
244P GLU* 4.0 29.4 - - + +
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Residues in contact with HIS 178 (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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206O ILE* 5.0 0.2 - - - -
152P THR* 3.8 5.2 - - - -
176P THR* 4.0 13.2 - - + +
177P ILE* 1.3 75.5 - - - +
179P ALA* 1.3 89.5 + - - +
181P THR* 4.0 13.0 - - + -
232P ALA* 4.8 2.9 - - + -
233P GLN 2.7 14.2 + - - +
234P ARG* 3.3 22.3 + - - +
235P VAL* 2.8 30.4 + - - +
240P GLY 4.4 0.4 - - - -
241P SER* 3.4 4.9 - - - -
314P TYR* 3.2 23.7 + - - -
316P ASN* 3.6 29.9 - - + +
337P GOL 2.7 32.5 + - - -
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Residues in contact with ALA 179 (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* 1.3 97.6 + - - +
180P TYR* 1.3 62.7 + - - +
181P THR* 3.7 0.3 + - - +
234P ARG* 3.6 5.0 - - - -
235P VAL 4.0 0.7 - - - -
237P VAL* 3.0 26.5 - - + +
238P ALA 3.8 2.5 - - - +
239P THR* 3.4 29.8 - - - +
240P GLY 3.4 14.5 + - - +
241P SER* 3.0 4.9 + - - -
316P ASN* 3.8 8.1 - - - +
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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