Contacts of the helix formed by residues 229 - 238 (chain A) in PDB entry 1UJP
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 GLY 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.7 28.0 - - - +
62A ILE* 4.1 6.1 - - - -
227A VAL* 4.0 1.0 - - - +
228A VAL* 1.3 75.3 - - - +
230A SER* 1.3 63.6 + - - -
231A ALA 3.2 1.5 - - - +
232A LEU* 3.0 15.1 + - - +
233A VAL* 3.1 13.5 + - - +
1001A CIT 2.9 19.6 + - - -
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Residues in contact with SER 230 (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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61A VAL* 3.6 28.1 - - - +
62A ILE* 3.9 9.1 - - - +
210A GLY* 5.2 3.1 - - - -
229A GLY* 1.3 71.0 - - - -
231A ALA* 1.3 61.7 + - - +
233A VAL* 3.1 12.3 + - - +
234A ARG* 3.1 31.8 + - - +
1001A CIT 2.8 51.1 + - - -
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Residues in contact with ALA 231 (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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210A GLY 5.8 1.0 + - - -
211A VAL 3.5 25.1 + - - +
212A SER* 3.9 9.6 - - - -
228A VAL* 4.0 12.1 - - + -
229A GLY 3.2 1.8 - - - +
230A SER* 1.3 77.2 - - - +
232A LEU* 1.3 57.6 + - - +
234A ARG* 3.4 26.0 + - - +
235A ALA* 3.1 26.0 + - - +
245A LEU* 3.7 16.4 - - + +
1001A CIT 4.5 1.2 + - - -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 4.0 21.5 - - + -
21A TYR 4.0 9.6 - - - +
22A LEU* 4.0 20.4 - - + -
39A VAL* 4.4 5.6 - - + -
228A VAL* 3.4 31.0 - - + +
229A GLY 3.0 9.4 + - - +
231A ALA* 1.3 76.9 - - - +
233A VAL* 1.3 64.2 + - - +
235A ALA* 3.8 2.0 - - - +
236A LEU* 2.9 32.1 + - + +
242A LEU* 4.0 29.4 - - + -
245A LEU* 4.1 15.3 - - + -
246A LEU* 4.2 18.2 - - + -
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Residues in contact with VAL 233 (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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21A TYR 5.9 1.3 - - - +
23A THR* 5.3 3.4 - - - +
26A PHE* 4.0 21.3 - - + -
61A VAL* 3.5 27.1 - - + +
62A ILE* 4.0 18.6 - - + -
64A ARG* 4.8 0.2 - - - +
65A ALA* 3.9 19.7 - - + +
229A GLY 3.1 14.7 + - - +
230A SER 3.1 7.6 + - - +
232A LEU* 1.3 76.1 - - - +
234A ARG* 1.3 58.4 + - - +
236A LEU* 3.3 3.1 + - + +
237A GLU* 2.8 48.6 + - - +
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Residues in contact with ARG 234 (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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61A VAL* 4.5 17.4 - - + +
64A ARG* 4.7 9.4 - - - +
210A GLY 4.9 3.2 + - - -
212A SER* 3.4 26.5 - - - -
230A SER* 3.1 35.6 + - - +
231A ALA* 3.4 27.1 - - - +
232A LEU 3.2 0.2 - - - -
233A VAL* 1.3 77.5 - - - +
235A ALA* 1.3 63.5 + - - +
237A GLU* 3.2 10.0 + - - +
238A GLU* 2.9 42.2 + - - +
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Residues in contact with ALA 235 (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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231A ALA 3.1 17.8 + - - +
232A LEU* 3.8 2.2 - - - +
234A ARG* 1.3 76.1 - - - +
236A LEU* 1.3 58.3 + - - +
238A GLU* 3.4 3.2 + - - -
239A GLY 3.0 7.3 + - - -
240A ARG* 2.9 46.6 + - + +
241A SER 5.0 2.0 - - - +
242A LEU* 3.6 23.6 - - + -
245A LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 236 (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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22A LEU* 4.0 25.8 - - + -
26A PHE* 3.9 35.4 - - + +
27A PRO* 4.4 24.2 - - + +
31A GLY 5.0 2.0 - - - +
35A ALA* 4.1 20.9 - - + -
38A GLU* 6.0 0.9 - - - +
232A LEU* 2.9 22.2 + - + +
233A VAL* 3.6 4.0 - - + +
235A ALA* 1.3 74.5 - - - +
237A GLU* 1.3 65.9 + - - +
239A GLY* 3.0 13.9 + - - +
240A ARG 5.1 1.8 - - - +
242A LEU* 4.2 19.1 - - + -
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Residues in contact with GLU 237 (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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26A PHE* 3.7 20.2 - - + -
27A PRO* 5.9 1.1 - - - -
64A ARG* 2.4 55.5 + - - +
233A VAL* 2.8 28.7 + - - +
234A ARG* 3.5 10.9 - - - +
236A LEU* 1.3 77.0 - - - +
238A GLU* 1.3 65.1 + - + +
239A GLY 3.2 0.7 + - - -
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Residues in contact with GLU 238 (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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234A ARG* 2.9 32.7 + - - +
235A ALA* 5.3 0.3 - - - -
237A GLU* 1.3 78.1 - - + +
239A GLY* 1.3 63.1 + - - +
240A ARG* 2.5 59.7 + - + +
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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