Contacts of the strand formed by residues 226 - 230 (chain A) in PDB entry 1EUQ
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 HIS 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 5.7 0.2 - - - +
14A ILE* 4.8 0.7 - - + -
15A ILE* 3.8 37.5 - - + +
18A ASP* 3.5 30.8 - - + +
19A LEU* 6.2 1.2 - - - +
24A HIS* 3.9 8.7 - + - +
27A VAL* 4.6 9.2 - - + +
28A HIS 3.9 1.6 + - - -
29A THR* 4.4 13.4 - - + -
30A ARG* 4.5 0.7 + - - -
50A ASN* 4.2 3.8 - - - +
224A ILE* 3.5 7.1 - - - +
225A THR* 1.3 115.6 + - - +
227A SER* 1.3 65.7 + - - +
228A LEU* 3.0 28.4 + - + +
254A ARG* 3.4 6.5 - - + -
256A TYR* 3.2 25.4 - + + -
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Residues in contact with SER 227 (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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30A ARG* 3.1 22.8 + - - +
215A HIS* 3.3 3.5 + - - -
219A ASP* 2.7 28.7 + - - -
224A ILE* 3.7 5.2 - - - +
225A THR 4.3 0.2 - - - -
226A HIS* 1.3 69.9 - - - +
228A LEU* 1.3 58.8 + - - +
240A TYR* 3.8 12.3 - - - -
253A PRO* 4.8 0.4 - - - +
254A ARG 3.2 6.6 + - - -
255A GLN* 3.2 31.2 + - - +
256A TYR 3.1 24.1 + - - -
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Residues in contact with LEU 228 (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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11A ILE* 3.7 33.9 - - + -
29A THR* 4.8 5.2 - - + -
30A ARG* 2.7 23.2 + - - +
49A LEU* 3.8 22.4 - - + -
50A ASN* 3.2 32.4 + - - +
53A ILE* 3.9 7.9 - - + -
226A HIS* 3.0 29.4 + - + +
227A SER* 1.3 76.0 - - - +
229A CYS* 1.3 62.9 + - - +
256A TYR* 3.3 17.9 - - + +
258A PHE* 4.1 10.6 - - + -
998A QSI 3.9 9.7 + - - +
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Residues in contact with CYS 229 (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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30A ARG* 3.0 18.2 - - - -
227A SER 4.0 0.4 + - - -
228A LEU* 1.3 73.0 - - - +
230A THR* 1.3 57.5 + - - +
233A PHE* 4.0 13.5 - - + -
255A GLN* 3.8 14.6 - - - +
256A TYR 3.1 8.5 + - - -
257A GLU* 2.8 8.9 - - + -
258A PHE* 2.6 43.1 + - - -
998A QSI 2.3 57.2 - - - +
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Residues in contact with THR 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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229A CYS* 1.3 76.7 - - - +
231A LEU* 1.3 66.4 + - - +
232A GLU* 2.9 29.3 + - - -
233A PHE* 3.2 24.3 + - - -
257A GLU* 3.6 6.4 - - - +
258A PHE* 3.0 27.6 - - + +
260A ARG* 3.5 33.2 + - + -
998A QSI 4.3 23.4 - - + -
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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