Contacts of the strand formed by residues 274 - 283 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B ARG* 3.9 2.9 - - - -
219B VAL* 2.9 39.3 + - - +
272B VAL 4.5 4.0 - - - +
273B MET* 1.3 76.7 - - - +
275B GLU* 1.3 73.3 + - - +
276B ARG* 2.6 45.1 + - + -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LYS* 5.8 0.5 + - - -
216B LEU* 4.0 37.2 - - + +
217B PHE* 3.4 5.7 - - - -
218B ARG* 3.6 29.6 + - + +
274B GLU* 1.3 79.2 - - - +
276B ARG* 1.3 68.3 + - - +
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LEU* 3.6 9.0 - - - +
217B PHE 2.9 28.6 + - - +
219B VAL* 3.9 14.8 - - + -
274B GLU* 2.6 37.6 + - - +
275B GLU* 1.3 85.4 - - - +
277B LYS* 1.3 64.2 + - - +
278B ILE* 3.3 17.9 + - + +
356B GLU* 3.5 30.7 + - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ILE* 4.4 0.7 - - - -
215B GLY* 3.3 25.1 - - - +
216B LEU* 3.5 34.5 - - + +
276B ARG* 1.3 69.6 - - - +
278B ILE* 1.3 64.9 + - - +
346B GLU* 3.2 21.3 + - - +
350B ASP* 2.8 32.9 + - - -
354B VAL* 3.5 29.4 - - + +
356B GLU* 4.5 5.0 - - - +
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Residues in contact with ILE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLN 3.8 0.2 - - - +
214B ILE* 3.3 4.0 - - - +
215B GLY 3.0 29.0 + - - +
217B PHE* 4.2 8.1 - - + -
219B VAL* 4.4 15.5 - - + -
230B LEU* 3.6 30.5 - - + -
276B ARG* 3.7 17.9 - - + +
277B LYS* 1.3 81.5 - - - +
279B LYS* 1.3 62.6 + - - +
280B VAL* 3.6 15.7 + - + +
354B VAL* 3.8 6.5 - - - -
356B GLU* 3.6 42.6 - - + +
357B GLU* 4.7 2.2 - - - -
358B PHE* 4.4 10.3 - - + -
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B TYR* 3.7 23.1 + - + +
213B GLN 3.6 5.4 - - - -
214B ILE* 3.6 24.0 - - + -
278B ILE* 1.3 72.1 - - - +
280B VAL* 1.3 61.5 + - - +
281B TYR* 4.1 18.8 + - + +
351B ALA* 6.5 0.2 - - - +
354B VAL* 3.7 23.2 + - + -
355B SER* 4.7 7.5 + - - +
356B GLU 2.9 18.9 + - - +
357B GLU* 3.6 19.7 + - + +
358B PHE* 2.8 27.5 + - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PHE* 4.1 19.3 - - + -
211B MET 3.6 0.3 - - - +
212B TYR* 3.2 6.9 - - - -
213B GLN* 2.8 40.8 + - + +
217B PHE* 3.8 31.9 - - + -
230B LEU* 3.6 27.6 - - + -
232B LEU* 4.6 4.0 - - + -
278B ILE* 3.9 18.6 - - + +
279B LYS* 1.3 78.5 - - - +
281B TYR* 1.3 69.6 + - - +
282B LEU* 4.5 5.4 - - + +
358B PHE* 3.5 6.3 - - + +
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Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLN* 6.2 1.3 - - - -
196B MET* 3.8 24.2 - - + -
210B MET* 3.8 14.6 - - + -
211B MET 3.2 4.9 - - - -
212B TYR* 3.4 46.3 - + + -
279B LYS* 4.1 25.1 + - + +
280B VAL* 1.3 76.8 - - - +
282B LEU* 1.3 59.4 + - - +
357B GLU* 4.2 7.0 - - + -
358B PHE* 3.0 11.8 + - - +
359B ARG* 3.6 68.2 + - + -
360B ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TRP* 4.2 13.5 - - + -
188B PHE* 4.3 9.4 - - + -
210B MET* 3.5 3.6 - - - -
211B MET* 2.8 50.1 + - + +
230B LEU* 5.7 0.9 - - + -
232B LEU* 3.7 27.1 - - + -
241B MET* 4.9 6.5 - - - -
243B VAL* 4.2 24.5 - - + -
280B VAL* 4.0 7.0 - - + -
281B TYR* 1.3 74.2 - - - +
283B PRO* 1.3 82.7 - - + +
285B MET* 5.1 2.9 - - - -
334B ILE* 4.2 8.3 - - + -
358B PHE* 5.5 2.2 - - + -
360B ALA* 4.1 13.9 - - + -
364B PHE* 4.5 8.3 - - + -
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Residues in contact with PRO 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PHE* 4.3 0.4 - - + -
208B VAL* 4.2 8.1 - - + -
209B GLN 3.5 10.5 - - - +
210B MET* 3.5 9.8 - - + -
211B MET* 3.9 7.7 - - - +
282B LEU* 1.3 99.3 - - + +
284B ARG* 1.3 70.2 + - - +
285B MET* 3.2 21.9 + - + +
334B ILE* 4.3 1.4 - - - +
360B ALA* 3.5 23.1 - - + +
364B PHE* 4.1 13.2 - - + -
385B PRO* 3.7 31.9 - - + -
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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