Contacts of the strand formed by residues 129 - 134 (chain C) in PDB entry 3C5C
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C PHE* 3.3 9.2 - - + +
96C VAL* 4.9 2.0 - - + -
113C LEU* 4.4 10.1 - - + -
116C LEU* 3.9 28.5 - - + -
128C PRO* 1.3 74.3 - - - +
130C LEU* 1.3 67.8 + - - +
158C CYS* 3.1 32.9 - - + +
159C LEU* 3.1 11.1 + - - +
182C GLU* 4.8 3.1 + - - +
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Residues in contact with LEU 130 (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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93C ALA* 5.2 2.0 - - + -
94C PHE 2.9 11.8 + - - +
95C LEU* 3.3 20.6 - - + +
96C VAL* 2.7 32.6 + - - -
113C LEU* 6.0 0.2 - - - -
128C PRO 5.1 1.1 - - - -
129C ALA* 1.3 83.3 - - - +
131C LEU* 1.3 56.1 + - - +
132C LEU* 3.8 7.4 + - + +
158C CYS* 4.9 0.4 - - - -
159C LEU* 3.6 19.5 - - + +
161C PHE* 3.9 22.4 - - + -
175C VAL* 3.4 27.4 - - + +
178C GLU* 4.2 4.5 - - + -
179C ALA* 3.8 26.0 - - + +
182C GLU* 4.0 18.4 - - + -
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Residues in contact with LEU 131 (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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96C VAL* 3.4 17.9 - - + +
98C TYR* 3.8 28.5 - - + -
109C SER* 3.9 17.0 - - - +
113C LEU* 3.9 16.2 - - + -
129C ALA 4.3 0.4 - - - -
130C LEU* 1.3 71.2 - - - +
132C LEU* 1.3 61.8 + - - +
149C GLY* 3.5 25.4 - - - +
152C LEU* 3.7 24.9 - - + -
153C ALA* 3.8 9.0 - - + +
158C CYS* 4.0 11.7 - - - -
159C LEU 2.8 16.3 + - - +
160C PHE* 3.4 11.1 - - + -
161C PHE* 3.0 25.6 + - - -
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Residues in contact with LEU 132 (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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36C LEU* 4.3 13.5 - - + -
95C LEU* 3.9 30.1 - - + -
96C VAL 2.7 14.2 + - - +
97C VAL* 3.5 20.1 - - + +
98C TYR* 2.9 34.7 + - - +
130C LEU* 4.3 12.3 - - + +
131C LEU* 1.3 82.5 - - - +
133C GLY* 1.3 59.4 + - - +
134C ASN 3.5 0.4 + - - -
161C PHE* 3.4 33.2 - - + +
163C VAL* 4.2 12.6 - - + -
175C VAL* 4.1 24.2 - - + -
176C PHE* 5.7 0.7 - - + -
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Residues in contact with GLY 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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98C TYR* 3.5 33.3 - - - -
100C VAL* 3.7 9.5 - - - +
132C LEU* 1.3 68.6 - - - +
134C ASN* 1.3 63.2 + - - +
136C LEU 4.7 0.5 + - - -
160C PHE* 4.0 2.6 - - - -
161C PHE 2.9 13.4 + - - -
162C GLU* 3.2 10.0 - - - +
163C VAL* 2.9 25.2 + - - +
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Residues in contact with ASN 134 (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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31C ALA 3.1 23.5 + - - +
32C GLY* 3.6 10.1 + - - -
36C LEU* 3.6 11.8 - - + +
97C VAL* 3.8 11.0 - - + -
98C TYR 2.7 19.0 + - - +
99C SER* 3.4 0.2 - - - -
100C VAL* 2.9 26.5 + - - +
132C LEU 3.5 0.2 + - - -
133C GLY* 1.3 71.7 - - - +
135C LYS* 1.3 76.7 + - - +
136C LEU 3.3 2.2 - - - -
163C VAL* 3.2 22.9 - - + +
164C SER* 3.3 14.0 - - - -
165C ALA 3.5 4.9 + - - -
201C GDP 3.3 27.0 + - - -
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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