Contacts of the strand formed by residues 305 - 314 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301O SER* 3.3 1.2 - - - -
302O VAL 2.8 31.1 + - - +
303O GLY 3.3 0.8 - - - -
304O ASP* 1.3 85.0 - - + +
306O GLN* 1.3 57.6 + - - +
170P VAL* 3.8 32.7 - - + +
171P GLU* 2.7 33.6 - - - +
248P VAL* 3.5 25.9 - - - +
249P LEU 5.0 3.2 + - - -
250P GLU* 5.8 1.2 - - - +
305P ARG* 4.6 19.6 - - - +
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Residues in contact with GLN 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247O VAL 4.2 4.0 - - - +
248O VAL* 4.5 12.8 - - - +
249O LEU 5.0 2.1 + - - -
251O LYS 4.0 4.2 - - - +
252O GLN* 3.7 5.2 + - - +
253O ASP* 3.1 18.9 + - - +
254O VAL* 2.9 56.8 + - - +
299O VAL* 3.6 7.0 - - + +
300O MET 2.9 7.6 - - - +
301O SER* 3.2 26.0 + - - +
304O ASP* 4.0 8.0 + - - +
305O ARG* 1.3 80.3 - - - +
307O LEU* 1.3 66.2 + - - +
308O VAL* 4.9 5.5 - - + +
171P GLU* 3.2 8.6 + - - +
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Residues in contact with LEU 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O THR* 4.4 12.6 - - + -
247O VAL 3.5 5.6 - - - +
248O VAL* 3.6 29.6 - - + -
298O ARG 4.0 0.5 - - - +
299O VAL* 3.5 3.6 - - - +
300O MET* 2.9 34.7 + - + +
306O GLN* 1.3 75.6 - - - +
308O VAL* 1.3 62.8 + - - +
171P GLU* 3.8 18.9 + - + +
172P GLY* 3.7 31.9 - - - -
173P LEU* 3.8 23.9 - - + +
246P THR 3.9 7.9 - - - +
247P VAL* 4.9 0.2 - - - -
248P VAL* 3.7 17.0 - - + -
307P LEU* 3.7 8.7 - - + -
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Residues in contact with VAL 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163O LEU* 4.9 2.2 - - + -
245O LEU 3.6 0.9 - - - +
246O THR* 3.3 2.2 - - - -
247O VAL* 2.8 52.5 + - + +
249O LEU* 3.7 26.2 - - + +
254O VAL* 4.4 11.9 - - + -
259O VAL* 4.0 24.0 - - + -
297O THR* 5.3 0.9 - - + -
298O ARG 3.5 7.9 - - - +
299O VAL* 4.3 17.3 - - + -
306O GLN* 4.9 7.0 - - + -
307O LEU* 1.3 77.7 - - - +
309O LYS* 1.3 67.1 + - - +
310O VAL* 4.6 8.7 - - + +
173P LEU* 4.7 0.9 - - - -
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Residues in contact with LYS 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O GLU* 4.0 16.6 - - + +
245O LEU 3.2 13.0 - - - +
246O THR* 3.8 16.8 - - - +
296O GLN 3.8 10.3 - - - +
297O THR* 3.2 5.4 - - - +
298O ARG* 2.8 47.1 + - + +
307O LEU 4.2 0.4 - - - -
308O VAL* 1.3 73.6 - - - +
310O VAL* 1.3 74.6 + - - +
311O ALA* 6.4 0.7 - - + -
173P LEU* 3.8 27.1 - - + +
174P MET 2.8 37.4 + - - +
175P THR* 2.9 20.0 + - - +
230P GLY* 4.3 5.9 - - - -
231P GLY 4.6 2.0 - - - +
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Residues in contact with VAL 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 3.5 29.6 - - + -
163O LEU* 4.1 11.0 - - + -
243O THR 3.7 0.3 - - - +
244O GLU* 3.4 2.4 - - - +
245O LEU* 3.0 43.8 + - + +
259O VAL* 3.6 30.7 - - + -
263O MET* 4.9 2.5 - - + -
292O PHE* 3.5 18.4 - - + -
296O GLN 4.5 4.5 - - - -
297O THR* 4.2 6.5 - - + +
308O VAL* 4.6 7.4 - - + +
309O LYS* 1.3 83.3 - - - +
311O ALA* 1.3 65.0 + - - +
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Residues in contact with ALA 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 5.7 0.4 - - - -
242O LEU* 4.0 10.1 - - + -
243O THR 3.0 11.2 - - - +
244O GLU* 4.3 10.5 - - + +
292O PHE* 3.9 7.1 - - - -
293O ASP* 3.1 30.0 + - - +
296O GLN* 3.7 37.6 - - + +
309O LYS* 6.4 0.7 - - + -
310O VAL* 1.3 81.5 - - - +
312O ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O SER 4.0 6.7 - - - +
159O VAL* 3.8 19.7 - - + -
242O LEU* 3.6 4.7 - - - -
243O THR* 2.8 36.4 + - + +
290O SER* 3.4 25.4 - - - +
291O LEU 3.1 13.2 - - - +
292O PHE* 4.2 1.8 - - - -
311O ALA* 1.3 74.2 - - - +
313O TRP* 1.3 61.5 + - - +
314O TYR* 4.0 2.8 - - - -
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Residues in contact with TRP 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241O SER 3.3 23.1 - - - -
242O LEU* 3.4 23.1 - - + -
278O ILE* 3.5 42.1 - - + +
279O VAL* 3.8 2.0 - - - -
280O SER* 3.4 43.1 - - - -
283O VAL* 3.8 25.4 - - + -
286O MET* 3.6 1.5 - - - +
290O SER* 3.5 2.1 - - - -
291O LEU* 2.6 47.2 + - + +
293O ASP* 2.9 36.1 + - + +
296O GLN* 3.8 3.7 + - - -
312O ALA* 1.3 73.9 - - - +
314O TYR* 1.3 62.7 + - - +
206P ILE* 3.6 20.9 - - + -
208P PRO* 3.7 21.8 - - + -
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Residues in contact with TYR 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151O GLY* 3.4 32.3 - - - -
152O THR* 2.7 24.6 + - - -
155O SER* 3.2 14.4 - - - -
176O THR* 2.6 22.5 + - - -
178O HIS* 3.2 8.6 - - - -
241O SER* 2.8 55.8 + - - +
242O LEU 3.8 1.6 - - - -
243O THR* 3.2 19.1 - - - -
283O VAL* 4.1 5.4 - - - -
286O MET* 3.6 9.0 - - - -
289O GLY 3.7 20.2 - - - +
312O ALA 4.0 1.8 - - - -
313O TRP* 1.3 77.1 - - - +
315O ASP* 1.3 59.1 + - - +
316O ASN* 3.2 29.1 + - + -
319O SER* 4.1 5.2 - - - -
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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