Contacts of the strand formed by residues 213 - 219 (chain A) in PDB entry 4U7D
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 PHE 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.7 31.2 - + + -
135A LEU* 3.7 14.8 - - + -
204A LEU* 3.6 26.9 - - + -
207A ALA 3.5 1.2 + - - -
208A TYR* 3.8 48.9 - + + +
211A ARG* 3.3 1.9 - - - -
212A ARG* 1.3 79.3 - - - +
214A THR* 1.3 63.4 + - - +
215A ARG 3.2 26.0 - - - -
216A ILE* 3.4 30.5 - - + -
241A LEU* 5.5 0.2 - - + -
245A PHE* 3.8 29.4 - + + -
247A ASN 5.7 0.2 - - - -
248A ALA* 4.1 4.7 - - + +
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Residues in contact with THR 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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130A SER* 2.8 26.6 + - - +
131A ASP* 3.6 13.5 + - + +
133A PHE 3.8 6.7 + - - -
134A THR* 5.2 0.3 + - - -
211A ARG* 3.9 22.2 - - + +
213A PHE* 1.3 76.8 - - - +
215A ARG* 1.3 75.5 + - - +
247A ASN 4.3 4.4 - - - +
248A ALA* 3.5 10.3 - - - +
249A SER* 3.0 20.1 + - - -
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Residues in contact with ARG 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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103A THR* 2.5 49.7 + - + -
104A MET* 3.5 30.5 + - - +
106A GLY* 4.6 1.8 - - - +
123A TYR* 5.0 2.5 - - - +
126A PRO* 3.5 23.6 + - - +
129A CYS 4.9 0.2 + - - -
130A SER* 3.4 28.6 + - - -
133A PHE 4.3 0.8 + - - -
134A THR* 3.1 29.1 + - + +
135A LEU 2.8 30.0 + - - -
213A PHE* 3.2 10.1 - - - -
214A THR* 1.3 84.2 + - - +
216A ILE* 1.3 60.9 + - - +
249A SER* 3.1 30.8 + - - +
251A ILE* 6.0 1.3 - - + -
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Residues in contact with ILE 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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134A THR* 4.8 1.3 - - - -
135A LEU* 3.4 5.4 - - + +
137A ILE* 4.0 23.8 - - + -
213A PHE* 3.4 27.8 - - + -
215A ARG* 1.3 73.3 - - - +
217A ALA* 1.3 57.3 + - - +
218A VAL* 4.2 5.6 - - + -
241A LEU* 4.3 33.7 - - + +
242A LYS* 5.0 2.0 - - + -
245A PHE* 4.7 2.0 - - + +
248A ALA* 3.9 26.7 - - + +
249A SER 2.6 12.0 + - - +
250A LEU* 3.3 28.3 - - + +
251A ILE* 2.7 35.5 + - - +
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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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123A TYR* 3.7 41.5 - - + -
134A THR* 4.4 2.2 - - + +
135A LEU 2.4 22.2 + - - +
136A VAL* 3.1 11.6 - - + +
137A ILE* 2.6 36.0 + - - +
215A ARG 4.3 0.4 - - - -
216A ILE* 1.3 69.8 - - - +
218A VAL* 1.3 56.4 + - - +
219A ASP 3.9 0.4 - - - -
251A ILE* 3.4 12.1 - - + +
253A LEU* 4.5 1.3 - - + -
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Residues in contact with VAL 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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137A ILE* 3.7 15.9 - - + -
216A ILE* 4.2 16.6 - - + -
217A ALA* 1.3 75.1 - - - +
219A ASP* 1.3 60.7 + - - +
221A VAL* 3.9 20.4 + - + -
235A TYR* 3.8 29.8 - - + +
238A LEU* 4.5 13.7 - - + -
241A LEU* 5.0 2.2 - - + -
250A LEU* 4.2 16.2 - - + -
251A ILE 2.9 12.7 + - - +
252A GLY* 3.7 2.0 - - - -
253A LEU* 3.2 23.3 + - - +
269A LEU* 4.8 9.4 - - + -
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Residues in contact with ASP 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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119A LYS* 5.3 4.9 - - - +
120A SER* 5.2 2.1 + - - -
123A TYR* 4.0 19.2 + - + -
136A VAL* 5.1 6.3 - - + +
137A ILE 2.8 17.6 + - - +
138A CYS* 4.5 20.0 - - + -
139A PRO* 4.2 0.5 - - - +
143A LEU* 5.6 2.3 - - - +
147A GLN* 4.6 5.9 - - - +
188A TYR* 5.9 0.9 - - - -
217A ALA* 3.9 2.0 - - - +
218A VAL* 1.3 72.6 - - - +
220A GLU* 1.3 86.0 + - + +
235A TYR* 2.4 31.0 + - - -
253A LEU* 3.8 24.2 - - + +
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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