Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 3DRW
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 VAL 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ALA* 3.8 16.4 - - + +
103A ASN* 3.8 14.6 - - - +
106A ALA* 3.8 20.4 - - + -
113A VAL* 3.7 7.9 - - + +
114A ILE 4.9 0.2 - - - -
115A ALA* 3.7 25.6 - - + +
128A PHE* 3.7 14.8 - - + -
129A LYS 3.3 16.6 + - - +
131A GLY* 1.3 78.9 + - - +
133A LEU* 1.4 70.8 + - - +
146A PRO* 3.8 4.3 - - - +
147A ILE* 3.0 34.3 + - + +
148A GLN* 4.2 2.6 - - - +
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Residues in contact with LEU 133 (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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112A LYS* 3.6 43.3 - - + +
113A VAL 2.8 18.3 + - - +
114A ILE* 4.0 7.0 - - + -
115A ALA 2.9 26.2 + - - +
131A GLY* 3.9 10.8 - - - +
132A VAL* 1.4 84.3 - - - +
134A TYR* 1.3 60.5 + - - +
144A PHE* 4.0 21.3 - - + +
145A LYS* 3.3 22.2 - - - +
146A PRO* 4.0 9.2 - - + -
147A ILE* 4.2 1.5 - - - +
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Residues in contact with TYR 134 (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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114A ILE* 4.3 0.2 - - - -
115A ALA 3.1 19.1 - - - -
116A TYR* 3.4 17.8 - + - -
117A THR* 2.6 44.0 + - + -
120A LEU* 3.8 18.2 - - + -
133A LEU* 1.3 74.2 - - - +
135A PRO* 1.3 93.8 - - + +
136A VAL* 4.0 4.3 - - + +
144A PHE* 3.3 6.0 - - - -
145A LYS* 2.9 28.2 + - - +
147A ILE* 3.6 34.3 - - + -
150A ALA* 3.6 23.8 - - + -
152A ARG* 3.0 29.9 + - - -
204A ILE* 5.7 2.2 - - + -
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Residues in contact with PRO 135 (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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9A TYR* 4.7 0.2 - - + -
114A ILE* 3.9 10.1 - - + -
115A ALA 3.7 11.0 - - - +
116A TYR* 3.9 24.5 - - + -
134A TYR* 1.3 111.5 - - + +
136A VAL* 1.3 58.8 + - - +
142A LEU* 4.0 11.4 - - + -
143A GLN 3.5 6.1 - - - +
144A PHE* 3.9 8.0 - - + -
204A ILE* 3.6 21.3 - - + +
211A ILE* 3.9 29.4 - - + -
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Residues in contact with VAL 136 (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 TYR* 4.0 6.5 - - + +
135A PRO* 1.3 79.6 - - - +
137A VAL* 1.3 62.7 + - - +
138A GLU* 3.8 14.6 - - + -
141A GLU 3.6 0.2 - - - +
142A LEU* 3.6 5.1 - - - +
143A GLN* 2.7 55.8 + - + +
145A LYS* 3.2 39.9 - - + -
150A ALA* 4.2 20.2 - - + +
204A ILE* 4.4 2.7 - - - -
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Residues in contact with VAL 137 (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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136A VAL* 1.3 74.9 - - - +
138A GLU* 1.3 64.0 + - - +
139A ASN 3.9 2.0 + - - +
140A GLY* 3.7 29.4 - - - +
141A GLU 3.5 4.5 - - - +
142A LEU* 5.3 1.3 - - + -
203A ASP* 3.7 12.6 - - + +
204A ILE* 3.7 24.1 - - + +
207A PHE* 3.6 34.3 - - + -
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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