Contacts of the strand formed by residues 241 - 249 (chain R) 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 SER 241 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206Q ILE* 4.4 1.8 - - - -
177R ILE 3.4 10.5 - - - -
178R HIS* 3.3 9.8 + - - -
179R ALA 3.0 18.7 + - - -
240R GLY* 1.3 69.9 - - - -
242R LEU* 1.3 61.6 + - - +
283R VAL* 4.7 1.6 - - - +
313R TRP* 3.4 14.2 - - - -
314R TYR* 2.8 60.7 + - - -
316R ASN* 2.9 20.2 + - - -
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Residues in contact with LEU 242 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206Q ILE* 5.0 3.1 - - + -
233Q GLN* 3.2 39.9 - - - +
176R THR* 3.1 4.1 + - - -
177R ILE* 2.7 49.0 + - + +
241R SER* 1.3 75.0 - - - +
243R THR* 1.3 64.3 + - - +
244R GLU* 4.3 8.1 - - + +
296R GLN* 3.9 12.3 - - - +
311R ALA* 4.0 15.7 - - + -
312R ALA 3.7 20.4 - - - -
313R TRP* 3.4 44.0 - - + +
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Residues in contact with THR 243 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R THR* 4.1 1.6 - - + +
155R SER* 2.7 28.7 + - - +
156R LEU* 4.5 20.0 - - + -
174R MET* 4.0 27.8 - - + -
175R THR 3.8 3.1 - - - -
176R THR* 3.7 7.4 + - - +
242R LEU* 1.3 70.7 - - - +
244R GLU* 1.3 65.6 + - - +
245R LEU* 4.9 2.4 - - + +
310R VAL 3.8 0.2 - - - +
311R ALA* 2.9 6.6 - - - +
312R ALA* 2.9 39.4 + - + +
314R TYR* 3.2 12.6 - - - -
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Residues in contact with GLU 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175Q THR* 2.5 37.3 + - - +
233Q GLN* 2.8 28.0 + - - +
173R LEU 4.0 0.3 - - - +
174R MET* 3.3 5.5 - - - +
175R THR* 2.8 42.7 + - - +
177R ILE* 4.0 19.2 - - + +
242R LEU* 4.4 3.1 - - + -
243R THR* 1.3 76.4 - - - +
245R LEU* 1.3 60.4 + - - +
246R THR* 5.3 0.9 - - - +
296R GLN* 4.0 5.5 + - - -
309R LYS* 4.2 18.4 + - + +
310R VAL 3.3 6.7 - - - +
311R ALA* 4.2 10.8 - - + -
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Residues in contact with LEU 245 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R LEU* 3.6 32.5 - - + -
159R VAL* 4.2 9.9 - - + -
160R ALA* 4.7 8.3 - - + -
163R LEU* 3.7 28.0 - - + -
169R LEU* 6.1 0.4 - - + -
173R LEU 3.5 19.1 - - - +
174R MET* 4.1 8.5 - - + -
228R LEU* 3.9 24.7 - - + -
243R THR* 4.1 3.1 - - + -
244R GLU* 1.3 73.7 - - - +
246R THR* 1.3 62.3 + - - +
247R VAL* 3.5 13.2 - - + +
308R VAL 3.6 1.6 - - - +
309R LYS* 3.1 5.6 - - - +
310R VAL* 2.9 40.6 + - + +
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Residues in contact with THR 246 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173Q LEU* 4.1 27.0 - - + +
246Q THR* 4.4 28.7 + - + -
307Q LEU* 4.0 3.5 - - + +
172R GLY* 3.1 1.9 - - - -
173R LEU 2.7 41.2 + - - -
244R GLU* 5.3 1.4 - - - +
245R LEU* 1.3 74.2 + - - +
247R VAL* 1.3 62.3 + - - +
307R LEU* 4.4 19.1 - - + -
308R VAL 3.3 4.0 - - - +
309R LYS* 3.6 23.0 - - - +
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Residues in contact with VAL 247 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307Q LEU* 5.0 0.7 - - - -
163R LEU* 4.2 13.7 - - + -
169R LEU* 3.8 21.1 - - + -
171R GLU 3.3 7.2 - - - +
172R GLY* 4.0 6.5 - - - -
228R LEU* 4.5 0.4 - - + -
245R LEU* 3.5 32.5 - - + +
246R THR* 1.3 81.1 - - - +
248R VAL* 1.3 63.1 + - - +
249R LEU* 3.8 22.3 + - + -
306R GLN 4.2 0.2 - - - +
307R LEU* 3.5 9.7 - - - +
308R VAL* 2.8 52.8 + - + +
310R VAL* 6.2 0.2 - - + -
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Residues in contact with VAL 248 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248Q VAL* 4.6 6.1 - - + -
305Q ARG* 3.4 35.4 - - - +
307Q LEU* 4.0 16.2 - - + -
169R LEU* 4.0 1.0 - - - +
170R VAL* 2.9 29.9 + - + +
171R GLU* 2.8 32.0 + - + +
247R VAL* 1.3 72.1 - - - +
249R LEU* 1.3 72.0 + - - +
306R GLN 4.3 11.2 - - - +
307R LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 249 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Q ARG* 5.0 2.9 + - - -
163R LEU* 4.3 16.2 - - + +
167R PHE* 3.6 37.0 - - + +
168R GLY 3.2 13.2 - - - +
169R LEU* 4.1 12.1 - - + -
170R VAL* 3.7 7.3 - - - +
247R VAL* 3.8 20.2 + - + -
248R VAL* 1.3 86.2 - - - +
250R GLU* 1.3 63.9 + - - +
251R LYS 3.7 13.1 - - - +
252R GLN* 3.7 7.4 - - - +
254R VAL* 4.2 11.4 - - + -
306R GLN 4.9 2.6 + - - -
308R VAL* 3.8 31.6 - - + +
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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