Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 2D7I
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 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASN* 1.3 76.6 - - - +
148A SER* 1.3 62.3 + - - +
149A ILE* 3.7 11.7 + - + -
176A LEU 2.8 22.3 + - - +
177A VAL* 3.8 3.8 - - - +
178A ALA* 2.9 24.4 + - - +
179A GLU 3.6 2.9 + - - +
230A GLY* 4.4 0.4 - - - -
232A VAL* 2.7 31.0 + - - +
234A THR* 2.9 24.6 + - - +
247A LEU* 3.9 32.1 - - + -
251A LEU* 4.1 4.5 - - + -
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Residues in contact with SER 148 (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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147A THR* 1.3 74.3 + - - +
149A ILE* 1.3 58.2 + - - +
150A ILE* 3.1 13.6 - - - +
178A ALA* 4.5 0.5 - - - +
179A GLU* 2.7 35.2 + - - +
228A ALA* 3.5 24.0 - - - -
229A THR 3.2 1.0 + - - -
230A GLY* 2.8 23.5 + - - -
232A VAL 2.9 8.5 + - - -
233A ILE* 3.6 2.2 - - - -
234A THR 3.0 21.0 + - - -
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Residues in contact with ILE 149 (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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147A THR* 4.3 13.2 - - + +
148A SER* 1.3 73.0 - - - +
150A ILE* 1.3 59.6 + - - +
151A ILE* 3.9 17.8 + - + -
168A VAL* 3.4 31.4 - - + -
177A VAL* 4.2 21.1 - - + -
179A GLU 2.9 14.1 + - - +
180A ILE* 3.5 7.0 - - + +
181A VAL 2.8 28.4 + - - +
234A THR* 3.4 21.1 - - + +
236A LEU* 4.1 23.6 - - + -
246A TRP* 4.2 17.9 - - + -
247A LEU* 4.9 0.7 - - + -
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Residues in contact with ILE 150 (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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148A SER* 3.1 33.2 - - - +
149A ILE* 1.3 74.6 - - - +
151A ILE* 1.3 65.2 + - - +
152A PRO* 3.5 9.3 - - + +
181A VAL* 3.5 13.5 - - + -
183A VAL* 4.0 20.0 - - + -
221A ARG* 4.4 5.2 - - - +
224A GLY* 3.8 32.8 - - - +
225A ALA 4.3 0.9 - - - +
228A ALA* 4.3 3.1 - - + -
233A ILE* 4.1 12.6 - - + -
234A THR 2.9 10.3 + - - +
235A PHE* 3.6 29.0 - - + -
236A LEU 3.2 22.9 + - - -
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Residues in contact with ILE 151 (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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149A ILE* 4.1 18.2 - - + +
150A ILE* 1.3 79.3 - - - +
152A PRO* 1.3 61.3 - - - +
153A PHE* 3.9 2.8 - - + -
161A LEU* 4.7 9.2 - - + -
164A THR* 4.0 21.1 - - + -
165A VAL* 4.6 6.5 - - + -
168A VAL* 4.8 4.7 - - + -
180A ILE* 4.2 7.6 - - + -
181A VAL 2.8 9.1 + - - -
182A LEU* 3.3 27.0 - - + -
183A VAL 2.8 22.8 + - - -
236A LEU* 3.6 23.6 - - + +
237A ASP 4.0 1.1 - - - +
238A SER* 3.6 36.6 - - - -
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Residues in contact with PRO 152 (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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150A ILE* 3.5 14.1 - - + +
151A ILE* 1.3 83.2 - - - +
153A PHE* 1.3 64.4 + - - +
183A VAL* 3.3 11.0 - - + +
217A LEU 4.8 1.3 - - - +
220A THR* 3.7 22.2 - - + -
221A ARG* 3.7 35.0 - - + +
236A LEU 3.5 13.2 - - - +
237A ASP* 5.0 0.4 - - - +
238A SER* 3.7 4.0 - - - -
705A UDP 2.7 46.0 + - - +
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Residues in contact with PHE 153 (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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151A ILE 3.9 9.4 - - - -
152A PRO* 1.3 78.3 - - - +
154A HIS* 1.3 60.6 + - - +
156A GLU* 4.1 11.2 - - + -
161A LEU* 4.5 13.7 - - + -
182A LEU* 3.8 20.6 - - + -
183A VAL 2.8 12.7 + - - -
184A ASP* 3.5 34.3 - - + -
185A ASP* 2.7 32.7 + - - +
187A SER* 3.6 13.5 - - - -
192A LEU* 3.5 29.2 - - + -
196A LEU* 3.8 23.6 - - + -
208A ILE* 5.0 2.2 - - + -
210A ARG* 4.7 2.2 - - - -
238A SER* 3.7 20.6 - - - +
705A UDP 3.3 11.3 + - - -
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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