Contacts of the strand formed by residues 148 - 153 (chain A) in PDB entry 3ECS
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 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 4.6 7.9 - - + -
120A LYS 5.0 0.2 - - - +
122A GLY 4.8 0.7 - - - -
123A ALA 3.2 17.9 - - - +
125A ILE* 4.0 16.6 - - + -
138A LEU* 3.6 44.0 - - + -
141A ALA* 3.6 24.9 - - + -
142A VAL* 3.7 22.2 - - + -
146A LYS* 3.5 19.7 - - + -
147A ARG* 1.3 75.7 - - - +
149A SER* 1.3 64.0 + - - +
150A VAL* 3.9 14.1 - - + -
173A VAL* 3.5 23.9 - - + +
174A PRO* 3.7 20.2 - - - +
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Residues in contact with SER 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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122A GLY 5.5 1.0 + - - -
123A ALA 2.9 7.8 + - - +
124A THR* 3.9 21.9 + - - -
125A ILE* 2.9 25.7 + - - +
148A PHE* 1.3 73.8 - - - +
150A VAL* 1.3 70.7 + - - +
151A TYR* 5.9 2.9 - - - -
174A PRO* 3.6 16.8 - - - +
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Residues in contact with VAL 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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125A ILE* 3.3 13.9 - - + +
127A THR* 4.3 12.6 - - + -
138A LEU* 4.1 15.3 - - + -
148A PHE* 3.9 23.6 - - + -
149A SER* 1.3 83.1 - - - +
151A TYR* 1.3 75.1 + - - +
152A VAL* 4.7 0.4 - - + -
168A LEU* 3.8 23.8 - - + -
173A VAL* 4.1 7.6 - - + -
174A PRO 3.0 11.4 + - - +
175A VAL* 3.1 9.1 - - + -
176A THR* 2.7 32.1 + - - -
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Residues in contact with TYR 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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124A THR* 3.8 27.8 - - + -
125A ILE 2.9 8.1 + - - +
126A LEU* 3.4 20.6 - - + +
127A THR 3.0 25.5 + - - -
149A SER* 5.9 2.7 - - - -
150A VAL* 1.3 78.0 - - - +
152A VAL* 1.3 60.5 + - - +
176A THR* 3.3 36.1 - - + -
178A VAL* 4.0 8.3 - - + -
186A ILE* 3.6 25.1 - - + -
189A LYS* 2.9 45.7 + - + +
190A ALA* 5.3 3.6 - - + -
269C GLU* 3.8 11.9 + - - -
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Residues in contact with VAL 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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126A LEU* 4.9 0.2 - - - -
127A THR* 3.4 24.2 - - + +
129A ALA 3.6 25.1 - - - +
150A VAL* 4.7 2.0 - - + -
151A TYR* 1.3 73.5 - - - +
153A THR* 1.3 78.7 + - - +
161A GLY 3.8 20.2 - - - +
164A MSE 4.3 5.2 - - + -
165A ALA* 4.0 9.6 - - + +
168A LEU* 5.5 0.2 - - + -
175A VAL* 3.8 24.5 - - + -
176A THR 3.0 6.6 + - - +
177A VAL* 3.3 6.5 - - + -
178A VAL* 3.2 23.0 + - - +
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Residues in contact with THR 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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126A LEU* 5.3 1.3 - - + -
127A THR 3.4 2.4 + - - -
128A HIS* 2.7 27.5 + - + +
129A ALA 3.1 12.8 + - - -
152A VAL* 1.3 76.9 - - - +
154A GLU* 1.3 63.8 + - - +
155A SER* 4.2 0.3 - - - -
161A GLY* 3.0 19.4 - - - -
178A VAL* 3.5 13.5 - - + -
180A ASP* 3.5 22.4 - - - +
183A VAL* 3.4 33.2 - - + -
215A MSE 3.5 14.1 - - + -
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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