Contacts of the strand formed by residues 225 - 238 (chain A) in PDB entry 2ARE
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 THR 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLN* 4.0 6.7 - - - +
34A THR* 4.0 4.9 - - - -
36A THR* 3.8 27.6 - - + -
40A GLY 4.1 7.2 - - - +
42A PRO* 3.8 20.9 - - + -
76A SER 4.5 0.3 + - - -
77A LEU* 3.3 25.1 - - - +
78A LYS* 2.9 34.3 + - + +
224A GLN* 1.3 77.2 - - - +
226A HIS* 1.3 60.0 + - - +
227A THR* 3.8 16.8 + - - -
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Residues in contact with HIS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 3.6 0.7 - - - +
32A GLN* 4.0 2.4 + - - -
33A LEU* 3.1 32.7 + - + +
34A THR* 2.9 27.8 + - + +
77A LEU* 3.5 24.0 - - + -
85A ALA 3.6 0.7 - - - -
87A GLY 3.1 42.8 + - - -
88A ILE* 3.9 7.2 - - + -
217A ALA* 3.6 18.2 - - + -
218A ALA 3.3 22.4 - - - -
219A SER* 3.4 8.3 - - - -
224A GLN* 3.2 32.9 + - + -
225A THR* 1.3 70.9 - - - +
227A THR* 1.3 61.0 + - - +
228A LEU 3.8 1.0 + - - -
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.6 22.7 - - + -
31A VAL 3.5 3.4 - - - +
32A GLN* 2.9 36.1 + - - +
75A PHE* 3.0 9.2 - - - +
76A SER* 3.0 46.7 + - - +
77A LEU* 4.8 0.2 - - - +
88A ILE* 5.3 0.2 - - - -
225A THR* 3.8 13.2 + - - -
226A HIS* 1.3 70.4 - - - +
228A LEU* 1.3 62.2 + - - +
229A GLU* 3.6 12.0 + - + +
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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
----------------------------------------------------------
11A PHE* 3.8 22.9 - - + -
30A ALA* 3.5 3.3 - - - +
31A VAL* 2.9 41.4 + - + +
33A LEU* 4.7 11.2 - - + +
50A ILE* 3.8 20.6 - - + -
73A PHE* 4.2 6.7 - - + -
74A SER 3.7 14.6 - - - +
75A PHE* 4.2 6.7 - - + -
88A ILE* 4.7 2.0 - - + -
215A PHE* 3.5 57.2 - - + -
226A HIS 3.8 2.0 + - - -
227A THR* 1.3 70.3 - - - +
229A GLU* 1.3 59.1 + - - +
230A SER 4.0 9.2 - - - +
231A TRP* 4.6 1.3 - - + -
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Residues in contact with GLU 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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9A PRO 3.6 9.5 - - - +
10A THR* 3.8 12.6 - - - +
11A PHE* 3.8 5.3 - - - -
29A ASN 4.5 3.1 - - - +
30A ALA* 4.5 7.4 - - + -
74A SER* 2.9 23.1 + - - +
75A PHE 3.9 4.2 + - - -
76A SER* 2.9 29.2 + - - -
169A SER* 2.8 32.5 + - - -
227A THR* 3.9 16.6 - - + +
228A LEU* 1.3 75.7 - - - +
230A SER* 1.3 64.2 + - - +
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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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8A PHE 3.3 9.6 - - - -
9A PRO* 3.4 18.4 - - - -
11A PHE* 3.8 6.3 - - - -
73A PHE* 3.2 7.3 - - - +
74A SER* 2.8 43.6 + - - +
228A LEU* 3.7 3.4 - - - +
229A GLU* 1.3 80.3 - - - +
231A TRP* 1.3 63.8 + - - +
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Residues in contact with TRP 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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6A PHE* 3.7 38.5 - + - -
7A GLY* 3.7 0.9 - - - -
8A PHE* 2.7 54.9 + + - +
11A PHE* 3.9 18.4 - + + -
18A LEU* 4.4 20.4 - - + -
50A ILE* 4.5 8.5 - - + -
52A PHE* 4.1 5.2 - - + -
71A SER* 3.0 21.9 + - - -
72A GLN 3.3 10.1 - - - -
73A PHE* 4.1 2.2 - - + -
90A PHE* 4.2 8.3 - + - -
213A VAL* 3.7 34.3 - - + -
214A GLY* 4.1 5.6 - - - -
215A PHE* 3.4 33.6 - + + -
228A LEU* 4.6 0.9 - - + -
230A SER* 1.3 78.4 - - - +
232A SER* 1.3 77.3 + - - +
233A PHE* 4.1 4.3 - - + +
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Residues in contact with SER 232 (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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6A PHE* 3.5 10.1 - - - -
7A GLY* 4.3 6.5 - - - -
8A PHE 5.1 0.2 - - - -
70A GLN* 4.6 3.7 + - - -
71A SER* 3.3 3.6 - - - -
72A GLN* 2.8 58.3 + - - +
231A TRP* 1.3 79.9 - - - +
233A PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 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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4A LEU* 4.6 4.5 - - + -
5A SER* 3.2 3.6 - - - -
6A PHE* 2.9 71.4 + + + +
56A VAL* 3.9 20.2 - - + -
69A PHE* 4.0 38.1 - + + -
70A GLN 3.4 13.9 - - - -
71A SER* 3.9 13.9 - - - -
90A PHE* 4.4 7.4 - + - -
92A ILE* 6.0 0.2 - - + -
213A VAL* 4.1 30.5 - - + -
231A TRP* 4.1 3.6 - - - +
232A SER* 1.3 76.0 - - - +
234A THR* 1.3 63.7 + - - +
235A SER* 3.7 25.4 - - - -
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU 3.3 6.2 + - - -
5A SER* 2.8 22.7 + - - -
68A ASN 4.6 0.2 - - - -
69A PHE* 3.1 5.8 - - - +
70A GLN* 2.9 59.6 + - + +
233A PHE* 1.3 78.7 - - - +
235A SER* 1.3 65.5 + - - +
236A THR* 4.5 5.5 + - - -
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP 4.5 1.5 + - - -
3A SER* 3.2 5.1 - - - -
4A LEU* 2.9 43.3 + - - +
5A SER* 5.3 0.2 + - - -
56A VAL* 3.4 23.8 - - - +
57A HIS 5.0 2.4 + - - -
67A ALA* 4.5 8.7 - - - -
68A ASN 3.3 6.3 - - - -
69A PHE* 3.8 12.1 - - - -
233A PHE* 3.7 16.4 - - - -
234A THR* 1.3 76.9 + - - +
236A THR* 1.3 64.8 + - - +
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Residues in contact with THR 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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2A ASP* 3.6 5.2 - - + +
3A SER* 4.2 15.2 - - - +
67A ALA* 4.0 3.8 - - - +
68A ASN* 2.9 32.6 + - - +
234A THR* 4.5 6.6 + - - -
235A SER* 1.3 80.7 + - - +
237A LEU* 1.3 74.8 + - - +
238A LEU* 3.4 18.4 + - + +
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Residues in contact with LEU 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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2A ASP* 3.0 29.8 + - + +
57A HIS* 3.6 50.5 - - + +
58A LEU 3.8 5.2 - - - +
59A TRP* 3.9 12.3 - - - -
60A GLU* 4.1 6.5 - - + -
65A ARG* 3.9 47.0 + - + +
66A VAL* 3.7 9.2 - - - +
67A ALA* 3.5 22.2 - - - +
236A THR* 1.3 76.5 - - - +
238A LEU* 1.3 68.0 + - - +
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Residues in contact with LEU 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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65A ARG* 3.4 8.0 - - - +
66A VAL 3.1 35.3 + - - +
68A ASN* 3.8 27.1 - - + +
178A PRO* 4.6 10.7 - - + +
236A THR* 3.8 21.8 - - + +
237A LEU* 1.3 84.6 - - - +
239A TYR* 1.3 67.3 + - - +
240A THR* 3.7 7.5 + - - +
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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