Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 3P42
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A PRO* 3.5 9.7 - - - +
148A VAL* 1.3 95.3 + - + +
150A ILE* 1.3 68.4 + - - +
161A GLN* 3.3 37.2 + - + +
162A LEU 3.1 20.9 - - - +
163A PRO* 4.3 3.6 - - + -
164A TRP* 3.7 3.8 - - - +
214A PRO* 3.9 0.9 - - - +
215A GLY* 2.9 28.1 + - - -
248A GLU* 5.6 0.2 + - - -
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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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149A THR* 1.3 81.1 - - - +
151A THR* 1.3 64.7 + - - +
161A GLN* 3.4 5.2 - - - +
162A LEU* 2.9 51.4 + - + +
163A PRO 5.0 0.4 - - - +
164A TRP* 3.8 18.4 - - + -
173A TYR* 3.8 34.8 - - + -
212A PRO* 4.5 3.8 - - + +
213A PRO 3.7 22.7 - - - +
215A GLY* 3.9 2.5 - - - +
216A SER* 3.5 17.3 - - - +
218A LEU* 3.7 32.8 - - + -
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Residues in contact with THR 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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150A ILE* 1.3 79.0 + - - +
152A LEU* 1.3 58.0 + - - +
153A LEU* 3.5 27.2 - - + +
160A GLY* 3.6 12.6 - - - +
161A GLN* 4.3 14.7 + - + +
215A GLY 5.5 0.9 + - - -
216A SER 3.0 12.0 + - - -
217A GLN* 3.2 9.1 - - - -
218A LEU* 2.7 33.4 + - - +
245A ARG* 4.2 11.2 - - - +
247A PRO* 3.8 20.2 - - + +
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Residues in contact with LEU 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 4.2 0.6 - - - -
151A THR* 1.3 74.3 - - - +
153A LEU* 1.3 64.4 + - - +
156A VAL* 3.7 24.5 - - + -
158A GLY 4.3 4.5 - - - +
159A ALA* 3.5 5.6 - - - +
160A GLY* 2.9 37.6 + - - +
162A LEU* 3.9 17.4 - - + +
173A TYR* 6.4 0.2 - - + -
174A LEU* 4.0 19.3 - - + -
177A HIS* 3.5 49.4 - - + +
188A VAL* 6.0 0.9 - - + -
218A LEU* 3.5 31.4 - - + +
220A LEU* 5.4 4.3 - - + -
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Residues in contact with LEU 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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106A GLN* 3.4 18.8 - - + +
107A LEU* 3.9 28.5 - - + -
151A THR* 3.5 35.7 - - + +
152A LEU* 1.3 76.0 - - - +
154A GLY* 1.3 60.9 + - - +
156A VAL* 4.0 6.9 - - - +
159A ALA* 4.5 0.7 - - - -
217A GLN* 3.8 24.7 - - + +
218A LEU 2.8 12.6 + - - +
219A TRP* 3.4 9.8 - - + -
220A LEU* 2.9 25.8 + - - +
242A LEU* 4.0 15.7 - - + -
245A ARG* 3.7 15.5 - - - +
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Residues in contact with GLY 154 (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 VAL* 3.6 11.9 - - - +
106A GLN* 2.8 34.6 + - - +
153A LEU* 1.3 75.9 - - - +
155A ALA* 1.3 58.1 - - - -
156A VAL* 2.8 13.8 + - - +
180A LEU* 4.4 1.4 - - - +
219A TRP* 3.4 19.6 - - - -
220A LEU 3.3 8.5 - - - -
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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