Contacts of the strand formed by residues 137 - 142 (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 GLY 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLN 3.3 13.7 + - - -
24A GLY* 3.2 3.5 - - - -
25A MSE 2.8 25.0 + - - -
136A VAL* 1.3 80.1 - - - +
138A ASP* 1.3 66.1 + - - -
139A TYR* 3.4 5.0 - - - -
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Residues in contact with ASP 138 (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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25A MSE 3.3 26.5 - - - +
67A ASP* 3.4 21.3 - - - +
68A SER 5.0 0.3 + - - -
136A VAL 5.0 0.3 - - - +
137A GLY* 1.3 74.1 - - - -
139A TYR* 1.3 67.9 + - - +
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Residues in contact with TYR 139 (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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24A GLY* 4.3 2.0 - - - -
25A MSE 2.8 11.3 + - - +
26A VAL* 4.1 14.1 - - + -
27A THR* 2.9 26.6 + - - -
65A LEU* 3.8 22.2 - - + -
66A THR 3.4 10.3 - - - +
67A ASP* 3.8 14.9 + - + +
116A LEU* 3.5 33.4 - - + -
134A PRO 4.1 3.3 + - - -
135A LEU* 3.5 27.2 - - + +
136A VAL 3.0 39.8 + - - -
137A GLY 3.4 18.8 - - - -
138A ASP* 1.3 79.2 - - - +
140A THR* 1.3 64.1 + - - +
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Residues in contact with THR 140 (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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27A THR* 3.4 8.2 - - - +
29A TYR* 3.7 25.8 - - + -
64A LEU 3.4 1.9 - - - +
65A LEU* 3.4 5.6 - - - +
66A THR* 2.9 41.7 + - - +
67A ASP* 5.0 1.3 - - - +
139A TYR* 1.3 76.7 + - - +
141A LEU* 1.3 62.3 + - - +
142A TYR* 3.6 38.8 + - + +
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Residues in contact with LEU 141 (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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26A VAL* 4.0 17.9 - - + +
27A THR 2.8 10.9 + - - +
28A ILE* 3.5 19.4 - - + +
29A TYR* 2.8 31.0 + - - +
48A LEU* 5.0 6.3 - - + -
54A LEU* 4.9 4.3 - - + -
58A LEU* 3.8 27.6 - - + -
60A TRP* 4.3 11.4 - - + -
63A ALA* 4.1 2.0 - - + -
64A LEU 3.3 28.7 - - - +
65A LEU* 3.8 14.6 - - + +
120A LEU* 3.9 17.7 - - + -
140A THR* 1.3 73.6 - - - +
142A TYR* 1.3 59.5 + - - +
143A THR* 4.2 7.0 - - + -
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Residues in contact with TYR 142 (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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29A TYR* 3.9 28.9 - + + -
33A GLU* 3.7 32.8 - - + -
62A GLY 4.2 0.8 - - - +
63A ALA* 3.4 3.3 - - - +
64A LEU* 2.8 54.8 + - + +
66A THR* 4.1 15.3 - - + -
113A THR* 4.1 17.4 - - + +
140A THR* 3.6 23.6 + - + +
141A LEU* 1.3 74.4 - - - +
143A THR* 1.3 62.0 + - - +
249A LEU* 3.8 28.9 - - + -
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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