Contacts of the strand formed by residues 206 - 212 (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 GLY 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PRO* 4.9 8.5 - - - -
186A GLU* 3.5 6.1 - - - +
187A PHE* 2.8 42.1 + - - +
205A SER* 1.3 79.8 - - - +
207A ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 207 (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* 5.0 6.3 - - - +
91A PRO* 3.4 15.1 - - + +
92A ALA 3.3 23.4 + - - +
115A ARG* 5.1 9.3 - - - +
184A ILE* 3.7 36.4 - - + +
185A PHE 3.1 9.9 - - - +
186A GLU* 3.8 22.4 + - - +
187A PHE* 3.3 6.7 - - - -
206A GLY* 1.3 75.8 + - - +
208A PHE* 1.3 57.7 + - - +
209A ILE* 4.0 23.4 - - + +
451A VAL* 5.8 4.0 - - - +
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Residues in contact with PHE 208 (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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72A ILE* 4.5 2.0 - - + -
78A PHE* 3.8 31.9 - + - -
81A ARG* 3.7 30.7 - - + -
82A LEU* 3.5 32.5 - - + -
85A THR* 3.7 28.9 - - + -
92A ALA* 3.4 11.0 - - + -
94A VAL* 3.4 35.7 - - + -
185A PHE* 2.6 49.5 + + + +
187A PHE* 3.8 2.6 - - + -
207A ARG* 1.3 73.4 - - - +
209A ILE* 1.3 57.6 + - - +
210A VAL* 3.9 13.7 - - + -
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Residues in contact with ILE 209 (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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92A ALA 2.8 16.7 + - - +
93A ALA* 3.2 12.3 - - + -
94A VAL* 2.8 30.0 + - - +
182A ASN* 5.2 4.0 - - + -
183A ARG 3.4 5.2 - - - +
184A ILE* 3.3 34.1 - - + -
207A ARG* 4.0 26.9 - - + +
208A PHE* 1.3 78.4 - - - +
210A VAL* 1.3 67.8 + - - +
211A SER* 3.9 17.4 + - - +
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Residues in contact with VAL 210 (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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72A ILE* 3.8 15.5 - - + -
78A PHE* 4.1 8.1 - - + -
94A VAL 3.2 11.9 - - - +
96A LEU* 3.8 27.5 - - + +
105A PHE* 4.2 10.5 - - + -
181A ILE 4.2 2.1 - - - +
182A ASN* 3.4 3.6 - - - -
183A ARG* 2.8 43.9 + - + +
185A PHE* 3.8 25.8 - - + -
208A PHE* 3.9 20.0 - - + -
209A ILE* 1.3 76.8 - - - +
211A SER* 1.3 59.9 + - - +
212A ALA 3.9 0.2 + - - -
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Residues in contact with SER 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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93A ALA* 5.4 4.3 - - - +
94A VAL 3.2 11.8 + - - -
95A PRO* 3.4 7.2 - - - +
96A LEU* 2.7 32.5 + - - -
182A ASN* 3.5 13.2 + - - +
209A ILE* 3.9 13.4 - - - +
210A VAL* 1.3 73.2 - - - +
212A ALA* 1.3 62.6 + - - +
213A ARG* 3.3 7.9 + - - -
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Residues in contact with ALA 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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96A LEU* 4.2 6.0 - - - +
180A LYS* 3.5 33.9 - - + -
181A ILE 3.6 19.1 + - - +
182A ASN* 2.7 21.0 + - - +
211A SER* 1.3 69.9 - - - +
213A ARG* 1.3 64.3 + - - +
214A PHE* 3.9 20.6 - - + -
217A ILE* 3.8 10.8 - - + +
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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