Contacts of the strand formed by residues 290 - 298 (chain C) in PDB entry 5U0A
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 HIS 290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C PHE* 4.3 3.1 - - - -
175C PRO* 3.5 33.6 + - + -
176C LEU 2.9 13.2 + - - +
177C ASP* 2.9 34.7 + - + -
178C SER* 3.1 5.9 + - - +
284C PRO* 3.8 2.3 - - - +
285C SER* 2.7 36.9 + - - +
289C SER* 1.3 101.2 + - - +
291C VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 4.5 7.2 - - + -
148C VAL* 3.7 14.9 - - + +
151C LEU* 5.6 3.1 - - + -
175C PRO* 3.0 24.6 - - - +
176C LEU* 3.1 11.5 + - + +
178C SER* 5.0 0.9 - - - -
181C ALA* 3.3 33.0 - - + -
282C LEU* 3.6 36.1 - - + -
283C HIS 3.3 8.7 - - - +
290C HIS* 1.3 76.7 - - - +
292C VAL* 1.3 65.0 + - - +
293C ASP 3.3 22.7 - - - +
294C ALA* 5.0 2.5 - - + -
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL* 3.3 19.6 + - - +
173C PRO* 5.1 6.5 - - + +
175C PRO* 4.6 13.0 - - + +
283C HIS* 3.1 17.5 + - + +
284C PRO 4.5 1.1 - - - +
285C SER* 4.0 29.2 - - - +
286C PRO* 5.5 1.8 - - + -
291C VAL* 1.3 77.9 - - - +
293C ASP* 1.3 79.8 + - - +
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 4.0 32.2 + - + +
147C GLY* 4.7 4.0 - - - -
148C VAL* 4.3 3.4 - - - +
173C PRO* 5.9 1.7 - - - +
283C HIS* 2.8 46.1 + - + +
291C VAL* 3.3 10.0 - - - +
292C VAL* 1.3 96.7 - - - +
294C ALA* 1.3 61.3 + - - +
295C TRP* 4.8 2.2 - - + -
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C THR* 3.5 2.4 - - - -
146C SER* 2.7 31.7 + - - -
147C GLY 2.7 30.5 + - - +
148C VAL* 4.1 4.5 - - + +
151C LEU* 3.9 30.3 - - + -
280C VAL* 5.3 1.3 - - + -
281C LEU 3.5 8.7 - - - +
282C LEU* 4.8 3.1 - - - -
291C VAL* 5.0 1.1 - - + -
293C ASP* 1.3 77.6 - - - +
295C TRP* 1.3 59.8 + - - +
296C VAL* 5.1 0.9 - - + -
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Residues in contact with TRP 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 3.3 22.3 - - + +
139C ARG* 4.1 30.2 + - + -
142C CYS* 4.1 27.0 + - + -
144C LYS 3.9 7.2 - - - -
145C THR* 3.2 46.4 - - + +
146C SER* 3.6 3.6 - - - -
198C THR* 5.5 1.1 - - - -
279C ALA 3.4 2.4 - - - +
280C VAL* 3.2 6.7 - - - -
281C LEU* 2.8 74.6 + - + +
283C HIS* 3.4 50.9 - + + -
293C ASP* 4.7 1.6 - - + -
294C ALA* 1.3 74.9 - - - +
296C VAL* 1.3 61.5 + - - +
297C THR* 4.0 1.6 - - - +
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C SER* 2.9 26.7 + - - +
150C LYS* 4.6 14.4 - - + +
151C LEU* 4.0 42.2 - - + +
188C THR* 5.3 6.1 - - + -
193C PRO* 5.9 1.6 - - + -
197C CYS* 3.1 17.4 - - + +
198C THR* 3.9 0.9 + - - -
278C HIS* 3.2 35.7 - - + +
279C ALA 3.6 2.0 - - - -
280C VAL* 4.4 12.3 - - + +
294C ALA* 5.1 0.2 - - + -
295C TRP* 1.3 74.9 - - - +
297C THR* 1.3 68.5 + - - +
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Residues in contact with THR 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 4.4 8.0 - - - +
142C CYS* 4.1 8.5 - - - -
197C CYS* 3.4 7.2 - - - -
198C THR* 3.0 31.3 + - - +
200C ARG* 3.2 33.4 - - - +
210C VAL* 4.4 1.8 - - - -
278C HIS* 4.9 3.4 - - - -
279C ALA* 2.7 48.0 + - - +
295C TRP* 4.0 0.9 + - - +
296C VAL* 1.3 86.3 + - - +
298C TRP* 1.3 80.5 + - + +
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Residues in contact with TRP 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C CYS* 4.8 0.9 - - - -
199C ALA* 4.8 0.2 - - - +
200C ARG* 3.1 70.3 + - - +
202C VAL* 4.5 2.2 - - + -
205C ARG* 4.4 18.2 - - + -
207C GLU* 3.3 29.0 + - - +
208C ARG* 5.0 0.4 - - - -
209C ASN 3.7 9.2 - - - +
210C VAL* 3.5 24.2 - - + +
211C THR* 5.6 0.7 - - + +
257C PRO* 3.2 31.2 - - + -
258C LEU* 4.7 0.4 - - + -
277C ARG 3.9 11.4 - - - +
278C HIS* 5.0 0.2 - - - +
279C ALA* 4.1 0.7 - - - +
297C THR* 1.3 92.6 - - + +
299C ALA* 1.3 58.6 + - - +
300C TRP 3.5 21.5 - - - +
301C ARG* 3.4 43.7 - - + -
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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