Contacts of the strand formed by residues 305 - 314 (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 ARG 305 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170O VAL* 3.8 31.8 - - + +
171O GLU* 2.5 35.5 - - - +
248O VAL* 3.4 26.1 - - - +
249O LEU 4.9 3.8 + - - -
250O GLU* 5.6 1.6 - - - +
252O GLN* 6.0 0.6 + - - -
305O ARG* 4.6 20.2 - - - +
301P SER* 3.5 1.2 - - - -
302P VAL 2.8 29.3 + - - +
303P GLY 3.3 1.2 + - - -
304P ASP* 1.3 84.8 - - + +
306P GLN* 1.3 57.7 + - - +
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Residues in contact with GLN 306 (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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171O GLU* 3.3 8.7 + - - +
247P VAL 4.2 3.8 - - - +
248P VAL* 4.4 13.2 - - - +
249P LEU 5.0 1.9 + - - -
251P LYS 4.2 1.7 - - - +
252P GLN* 3.9 5.7 + - - +
253P ASP* 3.3 19.2 + - - +
254P VAL* 3.0 56.7 + - - +
299P VAL* 3.6 7.2 - - + +
300P MET 3.0 5.8 - - - +
301P SER* 2.9 29.2 + - - +
303P GLY 5.6 0.7 - - - +
304P ASP 4.1 7.0 + - - +
305P ARG* 1.3 79.2 - - - +
307P LEU* 1.3 68.6 + - - +
308P VAL* 4.8 4.8 - - + +
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Residues in contact with LEU 307 (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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171O GLU* 3.8 18.1 + - + +
172O GLY* 3.8 33.7 - - - -
173O LEU* 3.9 17.5 - - + +
246O THR 3.9 11.0 - - - +
248O VAL* 3.7 10.3 - - + -
307O LEU* 3.7 27.4 - - + -
246P THR* 4.4 11.4 - - + -
247P VAL 3.4 6.1 - - - +
248P VAL* 3.7 17.5 - - + -
298P ARG 3.8 0.9 - - - +
299P VAL* 3.5 3.5 - - - +
300P MET* 2.9 35.8 + - + +
306P GLN* 1.3 77.0 - - - +
308P VAL* 1.3 63.7 + - - +
309P LYS 4.2 0.2 - - - -
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Residues in contact with VAL 308 (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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173O LEU* 4.7 0.4 - - - -
163P LEU* 4.8 2.7 - - + -
245P LEU 3.6 1.0 - - - +
246P THR* 3.3 1.8 - - - -
247P VAL* 2.7 55.8 + - + +
249P LEU* 3.8 23.6 - - + +
254P VAL* 4.4 11.7 - - + -
259P VAL* 3.9 25.4 - - + -
297P THR* 5.2 0.9 - - + -
298P ARG 3.6 6.3 - - - +
299P VAL* 4.1 20.2 - - + -
306P GLN* 4.8 7.2 - - + -
307P LEU* 1.3 80.1 - - - +
309P LYS* 1.3 67.0 + - - +
310P VAL* 4.4 8.4 + - + +
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Residues in contact with LYS 309 (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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173O LEU* 3.7 27.1 - - + +
174O MET 2.7 37.0 + - - +
175O THR* 2.8 19.8 + - - +
230O GLY* 4.5 5.1 - - - -
231O GLY 4.6 2.0 - - - +
244P GLU* 4.0 18.2 - - + +
245P LEU 3.2 13.0 - - - +
246P THR* 3.6 17.5 - - - +
296P GLN 4.5 8.5 - - - +
297P THR* 3.3 6.4 - - - +
298P ARG* 2.9 42.1 + - + +
307P LEU 4.2 0.6 - - - -
308P VAL* 1.3 72.8 - - - +
310P VAL* 1.3 73.2 + - - +
311P ALA* 6.3 0.4 - - + -
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Residues in contact with VAL 310 (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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159P VAL* 3.6 30.1 - - + -
163P LEU* 4.4 11.0 - - + -
244P GLU* 3.3 2.3 - - - -
245P LEU* 2.9 44.1 + - + +
259P VAL* 3.6 31.0 - - + -
263P MET* 4.9 2.5 - - + -
292P PHE* 3.5 19.3 - - + -
296P GLN 4.5 5.8 - - - -
297P THR* 4.1 5.2 - - + +
308P VAL* 4.6 6.7 - - + +
309P LYS* 1.3 84.5 - - - +
311P ALA* 1.3 65.7 + - - +
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Residues in contact with ALA 311 (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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159P VAL* 5.8 0.4 - - - -
242P LEU* 4.0 6.5 - - + -
243P THR 2.9 12.3 - - - +
244P GLU* 4.2 13.7 - - + +
292P PHE* 4.0 6.6 - - - -
293P ASP* 3.0 29.0 + - - +
296P GLN* 2.9 40.2 - - + +
309P LYS* 6.3 0.4 - - + -
310P VAL* 1.3 81.3 - - - +
312P ALA* 1.3 61.1 - - - +
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Residues in contact with ALA 312 (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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155P SER* 4.1 6.7 - - - +
159P VAL* 3.9 18.6 - - + -
242P LEU* 3.5 4.8 - - - -
243P THR* 2.8 42.5 + - + +
290P SER* 3.5 25.4 - - - +
291P LEU 3.3 13.0 - - - +
292P PHE* 4.1 2.5 - - - -
293P ASP 4.4 0.2 - - - +
311P ALA* 1.3 75.0 - - - +
313P TRP* 1.3 61.6 + - - +
314P TYR* 3.9 2.6 - - - -
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Residues in contact with TRP 313 (chain P).
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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206O ILE* 3.4 29.6 - - + -
208O PRO* 3.6 28.5 - - + -
155P SER* 4.9 0.2 - - - -
241P SER 3.3 22.9 - - - -
242P LEU* 3.5 24.7 - - + +
278P ILE* 3.5 35.8 - - + +
279P VAL* 4.1 1.1 - - - -
280P SER* 3.5 35.9 - - - -
283P VAL* 3.7 25.1 - - + -
286P MET* 3.5 1.9 - - - +
290P SER* 3.5 2.3 - - - -
291P LEU* 2.7 46.5 + - + +
293P ASP* 2.9 35.2 + - + +
312P ALA* 1.3 73.5 - - - +
314P TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 314 (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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151P GLY* 3.4 15.3 - - - -
152P THR* 2.7 42.6 + - - -
155P SER* 3.2 15.7 - - - -
176P THR* 2.7 21.4 + - - -
178P HIS* 3.2 7.8 - - - -
241P SER* 2.7 61.5 + - - +
242P LEU 3.8 4.7 - - - -
243P THR* 3.1 19.5 - - - -
283P VAL* 4.0 5.2 - - - -
286P MET* 3.5 8.3 - - - -
289P GLY 3.6 19.1 - - - +
312P ALA 3.9 2.2 - - - -
313P TRP* 1.3 76.7 - - - +
315P ASP* 1.3 57.1 + - - +
316P ASN* 3.3 19.4 + - + -
319P SER* 4.0 5.6 - - - -
337P GOL 3.7 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