Contacts of the strand formed by residues 210 - 219 (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 TRP 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLN* 3.7 28.9 - - - -
55A GLN* 3.6 37.9 - - + +
56A VAL 3.4 7.6 - - - -
57A HIS* 3.5 57.3 + + + -
95A PRO* 3.4 17.9 - - + +
208A PRO* 3.4 10.6 - - - +
209A GLU* 1.3 86.0 - - + +
211A VAL* 1.3 66.6 + - - +
14B ASP* 2.7 48.9 + - - -
15B GLN* 4.9 2.5 - - - -
16B LYS* 3.4 40.6 - - + +
17B ASN* 3.9 4.0 - - - -
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Residues in contact with VAL 211 (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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55A GLN* 3.4 6.4 - - - -
56A VAL* 2.8 51.9 + - + +
58A LEU* 4.1 17.9 - - + -
92A ILE* 3.5 25.1 - - + -
93A ALA 3.2 15.5 - - - +
95A PRO* 4.0 5.4 - - - -
207A LEU* 4.0 18.8 - - + -
208A PRO* 3.6 22.2 - - + +
210A TRP* 1.3 81.2 - - - +
212A ARG* 1.3 65.9 + - - +
213A VAL* 4.7 1.8 - - + -
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Residues in contact with ARG 212 (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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19A ILE* 3.8 23.9 - - - +
51A LEU* 4.3 22.4 - - + +
52A PHE 3.6 16.2 + - - +
53A SER* 2.9 30.3 + - - -
54A ALA 4.5 2.0 - - - +
55A GLN* 4.1 25.2 - - + +
56A VAL* 5.0 0.9 - - - +
91A PHE 4.1 0.2 - - - +
92A ILE* 3.5 3.3 - - - +
93A ALA 2.8 32.3 + - - +
94A PRO 4.7 1.6 - - - +
95A PRO* 2.9 47.3 + - + +
96A ASP* 5.0 0.8 - - - +
211A VAL* 1.3 79.4 - - - +
213A VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 213 (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* 4.2 12.6 - - + -
51A LEU* 3.4 6.1 - - - -
52A PHE* 3.0 30.3 + - + +
56A VAL* 4.3 18.6 - - + +
90A PHE* 4.2 8.5 - - + -
91A PHE 3.4 6.1 - - - +
92A ILE* 4.1 25.8 - - + -
211A VAL* 4.7 2.5 - - + -
212A ARG* 1.3 80.1 - - - +
214A GLY* 1.3 59.2 + - - +
231A TRP* 3.7 21.0 - - + -
233A PHE* 4.1 26.5 - - + -
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Residues in contact with GLY 214 (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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50A ILE 3.1 13.9 - - - -
51A LEU* 4.1 4.3 - - - +
90A PHE* 3.3 13.0 - - - -
91A PHE* 2.9 34.0 + - - -
213A VAL* 1.3 77.7 - - - +
215A PHE* 1.3 65.4 + - - -
231A TRP* 4.1 12.6 - - - -
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Residues in contact with PHE 215 (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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33A LEU* 4.1 18.1 - - + +
49A ARG* 3.1 7.6 - - - +
50A ILE* 3.0 41.7 + - + +
73A PHE* 3.6 55.9 - + + -
88A ILE* 4.5 9.4 - - + -
89A ALA 3.1 17.3 - - - +
90A PHE* 3.8 18.4 - + + -
91A PHE* 3.5 4.4 - - - -
214A GLY* 1.3 77.4 - - - -
216A SER* 1.3 60.1 + - - +
228A LEU* 3.5 29.4 - - + -
231A TRP* 3.4 36.1 - + - -
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Residues in contact with SER 216 (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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33A LEU* 4.4 2.5 - - - -
48A GLY 3.5 6.3 - - - -
49A ARG* 3.1 29.3 - - - +
87A GLY 4.2 0.2 - - - +
88A ILE* 3.3 2.1 - - - +
89A ALA* 2.8 33.6 + - - +
91A PHE* 3.9 9.2 - - - -
108A LEU* 2.6 27.0 + - - +
109A GLY* 3.7 4.0 - - - -
110A LEU* 4.0 14.6 - - - -
215A PHE* 1.3 75.8 - - - +
217A ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 217 (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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33A LEU* 3.8 17.3 - - + -
34A THR* 3.8 3.4 - - + +
47A VAL* 3.5 3.5 - - - +
48A GLY 3.0 30.8 + - - +
87A GLY 3.4 15.3 - - - +
88A ILE* 4.1 2.0 - - - -
108A LEU* 4.2 4.9 - - - -
216A SER* 1.3 77.4 + - - +
218A ALA* 1.3 65.1 + - - +
226A HIS* 3.6 31.0 - - + +
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Residues in contact with ALA 218 (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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34A THR* 3.7 4.7 - - - +
46A THR 3.2 12.6 - - - +
47A VAL* 3.9 15.9 - - + -
86A ASP* 2.8 32.6 + - - +
87A GLY 3.5 3.9 + - - -
105A GLY 3.7 24.2 - - - +
108A LEU* 4.0 15.8 + - - +
217A ALA* 1.3 79.7 - - - +
219A SER* 1.3 56.3 + - - +
226A HIS* 3.3 6.8 + - - -
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Residues in contact with SER 219 (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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34A THR* 4.3 1.7 - - - +
43A VAL 4.0 1.5 + - - -
45A SER* 3.2 4.7 + - - -
46A THR* 2.9 46.5 + - - +
47A VAL* 5.5 0.3 - - - +
85A ALA 2.7 18.0 + - - -
86A ASP* 3.7 4.3 - - - -
105A GLY* 4.3 5.0 + - - -
218A ALA* 1.3 70.8 - - - +
220A GLY* 1.3 59.9 + - - +
222A GLN 3.5 13.2 - - - -
223A TYR* 3.6 13.3 - - - +
224A GLN 3.5 8.7 + - - -
226A HIS* 3.4 13.9 + - - -
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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