Contacts of the helix formed by residues 293 - 301 (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 LEU 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B VAL* 6.5 0.4 - - + -
34B ILE* 4.2 33.7 - - + -
37B ALA* 6.0 1.1 - - + -
38B LEU* 6.3 0.7 - - + -
174B LEU* 4.6 13.7 - - + -
176B ASN* 4.7 7.9 - - + +
291B TYR* 3.2 9.3 + - + +
292B ASN* 1.3 70.7 - - - +
294B THR* 1.3 60.8 + - - +
296B VAL* 3.8 12.1 - - + -
297B LEU* 2.9 50.4 + - + +
326B ALA* 2.8 25.4 + - + +
327B VAL 4.2 7.2 - - - +
328B HIS* 3.6 40.2 - - + +
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASN* 3.0 13.7 + - - -
293B LEU* 1.3 78.1 - - - +
295B SER* 1.3 62.8 + - - +
298B MET* 3.0 38.4 + - - +
306B PHE* 3.6 45.4 - - + -
324B SER 4.9 2.7 + - - +
325B GLN* 4.2 6.1 + - - -
326B ALA* 3.7 17.5 + - - +
1F NAG 3.9 25.4 - - - -
2F NAG 5.3 2.5 - - - +
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Residues in contact with SER 295 (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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17B GLU* 5.2 0.2 - - - +
292B ASN* 2.9 27.9 + - - +
294B THR* 1.3 79.7 - - - +
296B VAL* 1.3 61.6 + - - +
298B MET* 4.1 6.2 - - - +
299B ALA* 3.2 23.0 + - - +
68D SEP 3.6 35.3 + - - -
1F NAG 4.0 24.2 - - - -
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Residues in contact with VAL 296 (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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14B VAL* 4.5 13.0 - - + -
17B GLU* 3.7 20.0 - - + +
18B LEU* 3.6 29.4 - - + -
22B HIS* 6.2 0.2 - - - +
291B TYR* 4.7 7.4 - - + -
292B ASN 3.4 17.6 + - - +
293B LEU* 4.0 12.8 - - + +
294B THR 3.3 0.4 - - - -
295B SER* 1.3 80.2 + - - +
297B LEU* 1.3 66.2 + - + +
299B ALA* 3.3 5.9 + - - +
300B MET* 3.2 39.4 + - - +
68D SEP 5.2 5.4 - - - +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 4.4 11.4 - - + -
14B VAL* 5.6 0.9 - - + -
34B ILE* 5.0 4.0 - - + -
38B LEU* 3.9 37.9 - - + -
174B LEU* 6.1 0.7 - - + -
293B LEU* 2.9 42.7 + - + +
296B VAL* 1.3 75.9 - - + +
298B MET* 1.3 64.8 + - - +
300B MET* 3.1 23.5 + - + +
301B GLY 3.1 6.4 + - - -
302B ILE* 2.9 45.3 + - + +
306B PHE* 4.0 22.9 - - + -
326B ALA* 5.8 0.7 - - + -
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Residues in contact with MET 298 (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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294B THR* 3.0 35.1 + - - +
295B SER* 4.1 4.5 - - - +
297B LEU* 1.3 75.8 - - - +
299B ALA* 1.3 63.4 + - - +
301B GLY* 3.0 11.8 + - - -
302B ILE 3.0 19.3 - - - +
303B THR* 3.7 27.3 - - + +
306B PHE* 3.4 20.2 - - + -
1F NAG 3.6 31.0 - - - +
2F NAG 3.9 20.9 - - + +
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Residues in contact with ALA 299 (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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17B GLU* 3.2 39.7 - - - +
295B SER 3.2 16.0 + - - +
296B VAL 3.6 1.8 - - - +
297B LEU 3.2 0.4 - - - -
298B MET* 1.3 79.2 - - - +
300B MET* 1.3 59.9 + - - +
301B GLY 3.6 0.2 + - - -
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Residues in contact with MET 300 (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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10B PHE* 3.6 29.2 - - + -
13B ASP* 3.8 31.6 - - + +
14B VAL* 3.8 19.1 - - + -
17B GLU* 4.3 13.2 - - + +
56B VAL* 3.4 30.5 - - + +
296B VAL* 3.2 30.6 + - - +
297B LEU* 3.1 17.9 + - - +
298B MET 3.1 1.0 - - - -
299B ALA* 1.3 77.2 - - - +
301B GLY* 1.3 56.7 + - - +
302B ILE 3.8 0.2 - - - -
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Residues in contact with GLY 301 (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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52B GLN* 3.6 21.3 + - - +
56B VAL* 3.9 6.8 - - - +
298B MET 3.0 10.7 + - - -
299B ALA 3.3 1.0 + - - -
300B MET* 1.3 80.5 - - - +
302B ILE* 1.3 64.9 + - - +
303B THR* 3.5 7.6 + - - -
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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