Contacts of the strand formed by residues 274 - 283 (chain A) in PDB entry 1UHG
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 GLU 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ARG* 4.0 3.1 - - - +
219A VAL* 3.0 29.6 + - - +
271A ASN 3.6 16.0 - - - +
272A VAL* 4.0 8.2 - - - +
273A MET* 1.3 83.1 - - - +
275A GLU* 1.3 67.6 + - - +
276A ARG* 3.0 34.3 + - + +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 3.2 39.0 - - + +
217A PHE* 3.4 35.0 + - - -
218A ARG* 3.6 16.7 + - + +
274A GLU* 1.3 72.4 - - - +
276A ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 3.7 7.5 - - - +
217A PHE 2.9 30.4 + - - +
219A VAL* 3.8 30.3 + - + +
221A SER* 4.1 21.4 - - - +
228A LYS* 6.1 0.6 - - - +
274A GLU* 3.0 38.0 + - + +
275A GLU* 1.3 79.3 - - - +
277A LYS* 1.3 64.8 + - - +
278A ILE* 3.2 6.1 + - + +
356A GLU* 2.6 47.1 + - - +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 4.5 5.8 - - + -
215A GLY* 3.5 17.5 - - - +
216A LEU* 3.8 17.0 - - + +
276A ARG* 1.3 71.7 - - - +
278A ILE* 1.3 61.1 + - - +
350A ASP* 2.6 37.7 + - - -
354A VAL* 3.7 30.8 - - + +
356A GLU* 4.3 10.0 - - - +
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN 3.7 0.3 - - - +
214A ILE* 3.4 4.1 - - - -
215A GLY 2.9 35.8 + - - +
217A PHE* 3.9 13.5 - - + -
219A VAL* 4.0 19.1 - - + -
228A LYS* 6.0 1.1 - - + -
230A LEU* 4.7 0.7 - - + -
276A ARG 3.7 12.6 - - - +
277A LYS* 1.3 77.4 - - - +
279A LYS* 1.3 73.7 + - - +
280A VAL* 3.5 17.6 + - + +
354A VAL* 4.1 3.4 - - - -
356A GLU* 3.3 36.6 - - + +
357A GLU* 3.5 9.4 - - - +
358A PHE* 3.5 26.7 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 3.6 30.1 - - + +
213A GLN 3.7 4.0 - - - -
214A ILE* 3.6 21.1 - - + -
278A ILE* 1.3 72.6 - - - +
280A VAL* 1.3 56.6 + - - +
281A TYR* 4.1 12.6 + - + +
351A ALA 2.7 29.6 + - - -
352A ALA* 5.1 0.2 - - - +
354A VAL* 3.3 29.6 + - + +
355A SER* 5.4 2.2 - - - +
356A GLU 2.9 10.1 + - - +
357A GLU* 3.1 19.2 - - + +
358A PHE 2.7 32.9 + - - +
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PHE* 4.1 18.9 - - + -
211A MET 3.6 0.3 - - - +
212A TYR* 3.2 8.2 - - - -
213A GLN* 2.8 41.3 + - + +
217A PHE* 3.8 32.3 - - + -
230A LEU* 3.7 32.5 - - + -
232A LEU* 4.7 3.1 - - + -
278A ILE* 3.9 12.3 - - + +
279A LYS* 1.3 75.5 - - - +
281A TYR* 1.3 72.9 + - - +
282A LEU* 4.5 4.9 - - + -
358A PHE* 3.6 7.4 - - + +
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A MET* 3.9 22.4 - - - -
210A MET* 3.7 14.6 - - + -
211A MET 3.3 4.9 - - - -
212A TYR* 3.3 44.9 - + + -
279A LYS* 4.2 17.2 + - + +
280A VAL* 1.3 76.3 - - - +
282A LEU* 1.3 62.7 + - - +
357A GLU* 3.8 8.7 + - - -
358A PHE* 2.9 11.7 + - - +
359A ARG* 3.5 67.4 + - + -
360A ALA* 3.0 24.9 + - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 4.2 6.1 - - + -
188A PHE* 4.3 10.1 - - + -
210A MET* 3.4 4.0 - - - -
211A MET* 2.8 52.1 + - + +
230A LEU* 5.7 0.4 - - + -
232A LEU* 3.8 25.6 - - + -
241A MET* 5.0 5.2 - - - -
243A VAL* 4.1 25.8 - - + -
280A VAL* 4.1 6.5 - - + -
281A TYR* 1.3 73.7 - - - +
283A PRO* 1.3 82.6 - - + +
285A MET* 5.1 2.9 - - - -
334A ILE* 4.2 15.9 - - + -
358A PHE* 5.4 2.7 - - + -
360A ALA* 4.2 13.2 - - + -
364A PHE* 4.6 7.6 - - + -
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Residues in contact with PRO 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 4.2 0.7 - - + -
208A VAL* 4.3 4.7 - - + -
209A GLN 3.5 11.2 - - - +
210A MET* 3.4 13.6 - - + -
211A MET* 4.0 7.5 - - - +
282A LEU* 1.3 99.2 - - + +
284A ARG* 1.3 68.6 + - - +
285A MET* 3.4 19.6 + - + +
334A ILE* 4.4 1.6 - - - +
360A ALA 3.5 20.4 - - - +
364A PHE* 4.1 14.6 - - + -
385A PRO* 3.7 30.1 - - + -
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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