Contacts of the strand formed by residues 132 - 138 (chain C) in PDB entry 3A4Y
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 LEU 132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.6 31.4 - - + -
19C LEU* 3.9 17.0 - - + +
21C ALA* 4.0 26.9 - - + +
22C GLY* 4.5 0.7 - - - +
24C ARG* 4.8 2.5 - - + +
26C VAL* 3.9 24.0 - - + -
128C ARG* 3.5 8.0 - - - +
129C LEU* 2.6 42.3 + - + +
130C GLY 3.2 0.2 - - - -
131C ALA* 1.3 74.5 - - - +
133C SER* 1.3 72.2 + - - +
134C LEU* 3.4 23.3 - - + -
150C ALA* 4.5 8.1 - - + -
151C GLN 3.8 7.2 - - - +
152C GLY* 4.4 1.8 - - - -
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Residues in contact with SER 133 (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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178B PRO* 3.9 21.7 - - - +
179B LEU* 3.0 33.3 + - - +
126C TRP* 4.0 7.9 - - - -
127C LEU 3.3 6.3 - - - -
128C ARG* 4.1 2.9 - - - +
131C ALA 5.3 0.2 + - - -
132C LEU* 1.3 78.7 + - - +
134C LEU* 1.3 62.5 - - - +
149C VAL 3.9 0.2 - - - +
150C ALA* 3.3 4.0 - - - +
151C GLN* 2.9 44.9 + - - -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.5 13.9 - - + -
26C VAL* 4.1 20.6 - - + -
28C LEU* 4.6 1.1 - - + -
56C LEU* 3.5 33.9 - - + -
121C LEU* 5.2 1.2 - - - +
125C GLU 3.6 0.5 - - - +
126C TRP* 3.3 9.1 - - - -
127C LEU* 2.8 43.0 + - + +
129C LEU* 4.2 14.1 - - + -
132C LEU* 3.4 26.2 - - + -
133C SER* 1.3 84.2 - - - +
135C ALA* 1.3 61.3 + - - +
148C VAL* 4.5 9.2 - - + -
149C VAL 3.3 7.0 - - - +
150C ALA* 4.1 9.6 - - + -
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Residues in contact with ALA 135 (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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126B TRP* 5.4 3.1 - - + +
56C LEU* 5.5 0.6 - - - +
121C LEU* 5.3 3.1 - - - -
124C GLY* 4.8 5.6 - - - -
125C GLU 3.6 15.7 - - - +
126C TRP* 3.6 33.0 - - + +
134C LEU* 1.3 79.8 - - - +
136C PHE* 1.3 69.6 + - - +
148C VAL* 3.8 2.4 - - - +
149C VAL* 3.0 36.8 + - + +
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Residues in contact with PHE 136 (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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124B GLY 4.6 5.0 - - - +
126B TRP* 5.4 2.4 + - - -
56C LEU* 4.1 17.0 - - + -
57C LEU 3.6 24.0 - - - -
58C THR* 4.8 2.2 - - - -
81C TYR 3.9 10.8 - - - -
82C ALA* 3.9 14.6 - - - -
83C THR* 4.1 10.8 - - + -
121C LEU* 3.4 49.7 - - + +
122C GLU 4.6 1.5 + - - +
123C TYR* 3.8 16.9 - - + +
124C GLY* 3.3 22.0 + - - +
125C GLU 4.5 3.4 + - - -
135C ALA* 1.3 78.2 - - - +
137C GLY* 1.3 59.4 + - - +
146C ALA* 3.7 18.6 - - + -
147C PHE* 3.4 11.9 - - - -
148C VAL* 3.8 22.9 - - + -
149C VAL* 5.8 1.1 - - - -
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Residues in contact with GLY 137 (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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124B GLY 4.8 9.4 - - - -
126B TRP* 5.5 1.3 - - - -
123C TYR* 3.7 6.1 - - - -
136C PHE* 1.3 74.1 - - - +
138C GLN* 1.3 62.7 + - - -
146C ALA* 3.1 8.8 - - - +
147C PHE* 2.9 55.4 + - - -
175C SER* 5.6 0.4 - - - -
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Residues in contact with GLN 138 (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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124B GLY 6.2 0.4 - - - -
125B GLU* 6.4 0.9 - - + -
123C TYR* 3.3 41.3 + - + +
137C GLY* 1.3 69.9 - - - -
139C ALA* 1.3 62.0 + - - +
140C GLY* 2.5 30.0 + - - +
142C LEU 5.0 1.2 - - - +
144C GLY 5.7 0.4 - - - +
145C SER* 3.4 8.3 + - - +
147C PHE* 3.2 12.3 - - - -
172C PRO* 3.5 27.1 - - + +
173C ASP 3.5 24.2 - - - +
174C PRO* 3.8 0.5 - - - +
175C SER* 3.0 37.8 + - - +
267C TYR* 5.3 3.0 + - - +
389C TRP* 5.3 0.2 + - - -
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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