Contacts of the strand formed by residues 258 - 266 (chain U) in PDB entry 3U74
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 MET 258 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47U CYS* 4.6 2.0 - - - -
49U GLU 4.3 4.5 - - - +
50U LYS* 5.2 2.8 + - - -
225U ALA* 4.7 12.3 - - + +
226U THR 4.3 3.6 - - - -
227U GLY* 3.8 22.7 - - - -
228U THR 3.4 13.2 - - - +
229U HIS* 4.3 0.9 - - - +
230U GLU* 5.0 0.4 - - - -
236U TYR* 4.0 30.5 - - + -
238U VAL* 4.6 12.6 - - + -
252U LEU* 4.4 7.4 - - + +
253U GLY* 3.1 22.5 + - - +
256U PHE* 3.1 45.1 - - + +
257U SER* 1.3 78.7 - - - +
259U CYS* 1.3 67.2 + - - +
261U ILE* 3.8 17.2 - - + +
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Residues in contact with CYS 259 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U CYS* 2.0 53.8 - - + -
48U SER 3.4 14.1 - - - +
228U THR* 2.7 58.5 + - - +
230U GLU* 4.0 9.6 - - - -
258U MET* 1.3 75.3 - - - +
260U HIS* 1.3 76.4 + - + +
261U ILE* 3.5 6.7 - - - -
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Residues in contact with HIS 260 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U GLY* 2.6 37.5 + - - -
22U ASP* 3.8 18.8 - - - -
47U CYS* 3.9 6.0 - - + +
48U SER* 4.1 15.6 + - - -
49U GLU* 2.9 15.4 + - - -
226U THR 3.9 0.7 - - - +
227U GLY* 3.6 9.9 - - - -
228U THR* 4.4 14.3 + - + +
259U CYS* 1.3 91.6 - - + +
261U ILE* 1.3 61.8 + - - +
262U ASP 4.1 0.3 + - - -
282U SER* 5.9 1.8 - - - -
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Residues in contact with ILE 261 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U GLU* 2.9 19.9 + - + +
225U ALA* 4.6 8.1 - - + -
226U THR 3.1 9.6 - - - +
227U GLY* 4.4 1.8 - - - -
249U HIS* 3.1 56.6 + - + +
252U LEU* 4.4 7.2 - - + -
253U GLY* 3.7 13.5 - - - +
258U MET* 3.8 31.6 - - + +
259U CYS* 4.0 7.4 - - - -
260U HIS* 1.3 76.8 - - - +
262U ASP* 1.3 78.1 + - - +
263U VAL* 3.7 10.1 - - + -
282U SER* 5.0 4.8 + - - -
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Residues in contact with ASP 262 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224U VAL* 4.0 0.3 - - - +
225U ALA* 3.1 3.8 - - - +
226U THR* 2.7 47.0 + - - +
249U HIS* 4.8 2.0 + - - -
260U HIS 4.1 0.8 + - - -
261U ILE* 1.3 77.7 - - - +
263U VAL* 1.3 65.1 + - - +
264U SER* 4.6 3.6 + - - -
278U VAL 4.2 4.5 - - - +
279U GLN* 4.0 9.2 - - + -
280U TYR* 3.4 48.8 + - - +
282U SER* 4.6 15.6 + - - +
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Residues in contact with VAL 263 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223U LEU* 4.2 15.9 - - + -
224U VAL 3.4 9.9 - - - +
225U ALA* 4.3 2.5 - - + +
247U CYS* 4.2 13.9 - - + +
248U GLN 4.5 5.6 - - - +
249U HIS* 3.8 27.0 + - + +
252U LEU* 3.6 29.4 - - + -
261U ILE* 3.7 18.6 - - + -
262U ASP* 1.3 81.3 + - - +
264U SER* 1.3 72.2 + - - +
265U CYS* 4.4 0.4 - - - -
280U TYR* 5.2 4.7 - - - +
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Residues in contact with SER 264 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222U CYS 3.6 0.7 - - - +
223U LEU* 3.4 4.3 - - - -
224U VAL* 3.0 47.5 + - - +
262U ASP* 4.6 5.0 + - - -
263U VAL* 1.3 77.4 + - - +
265U CYS* 1.3 68.7 + - - +
266U CYS* 5.5 4.4 - - - -
278U VAL* 4.3 16.8 + - - +
280U TYR* 5.6 2.3 - - - +
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Residues in contact with CYS 265 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221U GLN* 4.0 15.5 - - + +
222U CYS 3.1 7.2 - - - +
223U LEU* 3.6 24.2 - - - -
247U CYS* 2.0 52.7 - - + +
263U VAL* 4.4 1.8 - - - -
264U SER* 1.3 83.8 - - - +
266U CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 266 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221U GLN* 3.6 2.9 + - - -
222U CYS* 2.8 36.1 + - - +
264U SER* 5.5 4.0 - - - -
265U CYS* 1.3 79.4 - - - +
267U THR* 1.3 63.2 + - - +
268U LYS 3.8 0.8 + - - +
271U CYS* 2.0 67.8 - - + -
272U ASN* 3.9 2.9 - - - -
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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