Contacts of the strand formed by residues 142 - 148 (chain C) in PDB entry 5AJI
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 ALA 142 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TYR* 3.5 28.1 + - + +
136C VAL 3.1 11.2 - - - +
137C ASP* 4.0 16.2 - - + +
140C GLY 4.2 0.4 - - - -
141C VAL* 1.3 75.3 - - - +
143C GLY* 1.3 58.6 + - - +
155C MET* 2.9 9.9 - - - +
157C THR* 3.7 20.6 - - - +
178C PHE* 5.0 2.5 - - + -
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Residues in contact with GLY 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C GLU 3.6 0.7 - - - +
135C TYR* 3.4 18.3 - - - -
136C VAL* 2.9 33.0 + - - +
142C ALA* 1.3 75.0 - - - +
144C THR* 1.3 62.7 + - - -
155C MET* 2.8 14.5 - - - +
156C ARG 3.3 11.2 - - - -
157C THR* 4.0 2.7 - - - -
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLY* 3.3 35.2 - - - +
134C GLU 3.5 7.6 - - - +
135C TYR* 3.8 14.1 - - + +
143C GLY* 1.3 73.7 - - - -
145C VAL* 1.3 65.4 + - - +
146C LEU* 3.4 8.0 + - + +
155C MET* 3.3 1.3 - - - -
156C ARG* 2.9 42.4 + - - +
157C THR 5.4 0.7 - - - -
158C ALA* 5.9 0.5 - - - -
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 3.6 40.2 - - + -
131C ARG 3.9 11.9 - - - +
132C ALA* 3.9 12.3 - - + +
133C GLY* 2.8 26.0 + - - +
134C GLU 3.1 15.7 + - - +
136C VAL* 3.7 22.0 - - + -
138C LEU* 5.6 0.7 - - + -
144C THR* 1.3 72.6 - - - +
146C LEU* 1.3 65.4 + - - +
147C SER 3.8 19.5 - - - +
148C VAL* 4.6 1.8 - - + -
153C THR* 4.2 5.6 - - + -
154C THR 3.8 7.4 - - - +
155C MET* 4.1 4.7 - - + -
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Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLU* 4.9 1.1 - - - +
132C ALA* 3.4 17.8 - - - +
144C THR* 3.7 15.9 - - - +
145C VAL* 1.3 76.9 - - - +
147C SER* 1.3 67.2 + - - +
154C THR* 2.8 31.3 + - + +
155C MET* 4.1 3.6 - - - -
156C ARG* 3.8 34.8 - - + +
162C ILE* 3.9 28.7 - - + -
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ALA* 5.0 3.6 - - - -
145C VAL* 3.8 3.8 - - - +
146C LEU* 1.3 83.7 - - - +
148C VAL* 1.3 64.9 + - - +
149C GLN* 2.9 32.1 + - - -
153C THR* 3.4 8.0 - - - +
154C THR* 3.1 34.4 + - - -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLY* 4.4 2.9 - - - +
124C LEU* 4.3 21.3 - - + -
125C VAL* 4.3 22.0 - - + +
128C ARG* 5.4 9.0 - - - +
130C PHE* 3.6 26.9 - - + +
132C ALA 6.2 0.7 - - - +
145C VAL* 4.6 3.4 - - + -
147C SER* 1.3 76.6 - - - +
149C GLN* 1.3 72.5 + - - +
152C SER 4.0 2.5 - - - -
153C THR* 3.6 20.9 - - + +
167C ASN* 4.1 9.0 - - - +
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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