Contacts of the strand formed by residues 181 - 187 (chain A) in PDB entry 1U2X
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 ILE 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.3 20.4 - - + +
40A ALA* 4.2 15.3 - - + -
96A LEU* 5.2 1.6 - - - +
102A ASN* 4.2 4.6 + - - +
106A ASP* 4.3 0.4 - - - +
111A TYR* 5.4 0.2 - - - +
145A ARG* 3.7 29.2 - - - +
179A LEU* 3.5 43.2 + - + +
180A LYS* 1.3 80.3 - - - +
182A ASN* 1.3 75.0 + - - +
183A ARG* 3.9 43.5 + - - +
210A VAL 4.2 2.3 - - - +
212A ALA* 3.6 17.7 + - - +
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.5 18.2 + - - +
38A ILE 2.9 6.9 + - - -
39A ASP* 3.3 23.6 - - - +
40A ALA* 2.8 27.5 + - - +
180A LYS* 4.6 7.2 - - - +
181A ILE* 1.3 73.0 - - - +
183A ARG* 1.3 60.7 + - - +
184A ILE* 5.1 4.0 - - + +
209A ILE* 5.2 6.1 - - + -
210A VAL 3.4 7.0 - - - +
211A SER* 3.5 12.2 - - - +
212A ALA* 2.7 41.8 + - - +
1003A SO4 4.7 6.1 + - - -
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Residues in contact with ARG 183 (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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40A ALA* 3.1 5.2 - - + +
42A VAL* 5.6 0.9 - - + -
96A LEU* 4.1 7.7 - - - +
102A ASN* 2.9 39.2 + - - -
105A PHE* 3.1 47.4 - - - +
106A ASP* 2.8 27.9 + - - -
111A TYR* 2.9 28.6 + - + -
181A ILE* 3.9 30.8 + - + +
182A ASN* 1.3 77.7 - - - +
184A ILE* 1.3 63.8 + - - +
185A PHE* 3.9 18.6 - - + -
208A PHE 3.7 1.2 - - - +
209A ILE* 3.4 2.8 - - - +
210A VAL* 2.8 44.8 + - + +
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Residues in contact with ILE 184 (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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39A ASP* 5.4 8.1 - - + +
40A ALA 2.6 14.7 + - - +
41A ILE* 3.3 21.8 - - + +
42A VAL* 2.8 27.5 + - - +
115A ARG* 5.4 7.2 - - - +
182A ASN* 5.1 4.3 - - + +
183A ARG* 1.3 74.8 - - - +
185A PHE* 1.3 65.3 + - - +
186A GLU* 3.8 3.3 + - - +
207A ARG* 3.7 50.0 - - + +
208A PHE 3.7 1.8 - - - -
209A ILE* 3.3 42.2 - - + -
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Residues in contact with PHE 185 (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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42A VAL* 3.4 42.4 - - + -
44A LEU* 3.5 26.0 - - + -
78A PHE* 3.5 35.9 - + - -
82A LEU* 4.7 1.1 - - + -
105A PHE* 4.0 15.0 - + - -
109A PHE* 3.9 22.7 - + - -
183A ARG* 3.9 17.9 - - + -
184A ILE* 1.3 73.6 - - - +
186A GLU* 1.3 62.4 + - - +
187A PHE* 3.8 2.1 + - - -
207A ARG* 3.1 5.9 - - - -
208A PHE* 2.6 56.0 + + + +
210A VAL* 3.8 14.8 - - + -
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Residues in contact with GLU 186 (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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41A ILE* 3.6 34.5 - - + +
42A VAL 2.8 13.8 + - - +
43A LYS* 3.0 41.9 + - + +
44A LEU* 2.9 30.0 + - - +
184A ILE* 3.8 2.8 + - + -
185A PHE* 1.3 71.7 - - - +
187A PHE* 1.3 60.1 + - - +
188A ARG 4.3 0.2 - - - -
206A GLY 3.5 6.5 - - - +
207A ARG* 3.8 26.1 + - - +
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Residues in contact with PHE 187 (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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44A LEU* 4.2 14.1 - - + +
85A THR* 4.0 24.5 - - + -
86A LEU* 3.7 28.3 - - + -
89A GLY* 4.1 15.7 - - - -
90A LYS 4.4 1.1 - - - -
91A PRO 4.4 13.2 - - - -
185A PHE 3.9 6.7 - - - -
186A GLU* 1.3 74.2 - - - +
188A ARG* 1.3 60.4 + - - +
202A ILE* 3.8 18.4 - - + -
204A ASN 3.6 13.7 - - - -
205A SER* 3.0 22.1 - - - -
206A GLY* 2.8 61.0 + - - +
207A ARG 3.3 16.6 - - - -
208A PHE* 3.8 2.7 - - + -
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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