Contacts of the strand formed by residues 132 - 136 (chain C) in PDB entry 5J13
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 SER 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B SO4 3.2 31.4 + - - -
129C LYS* 4.2 11.3 + - - -
130C GLY 4.0 0.4 + - - -
131C PRO* 1.3 72.0 - - - +
133C VAL* 1.3 60.4 + - - +
134C PHE* 3.8 21.2 + - - -
153C LEU 3.2 2.4 - - - +
155C LYS* 2.8 44.8 + - - +
156C ASP* 5.4 2.0 + - - +
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Residues in contact with VAL 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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131C PRO* 4.0 3.3 + - + +
132C SER* 1.3 76.7 - - - +
134C PHE* 1.3 70.3 + - - +
152C CYS* 3.7 26.7 - - + -
153C LEU 3.3 5.6 - - - +
154C VAL* 4.7 7.2 - - + -
208C CYS* 4.2 8.3 - - - -
210C VAL* 3.8 25.1 - - + -
219C VAL* 3.7 35.8 - - + +
221C LYS* 3.5 37.5 + - + +
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Residues in contact with PHE 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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126B SER* 3.7 8.1 - - - +
128B GLU* 4.1 14.8 - - + -
129B GLU* 3.6 45.1 - - + +
132B ALA* 4.9 4.9 - - + -
134B LYS* 5.9 1.1 - - + -
302B SO4 3.6 24.9 - - - -
132C SER* 3.8 26.2 - - - -
133C VAL* 1.3 82.3 - - - +
135C PRO* 1.3 69.5 - - + +
152C CYS* 3.1 6.1 - - - -
153C LEU* 2.6 51.8 + - + +
155C LYS* 3.8 29.6 - - + -
221C LYS* 5.8 0.9 - - - -
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Residues in contact with PRO 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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124B PRO 5.4 0.3 - - - +
126B SER* 3.4 33.1 + - - +
128B GLU* 3.2 34.1 - - + +
133C VAL 4.7 0.2 - - - +
134C PHE* 1.3 89.9 - - + +
136C LEU* 1.3 65.1 + - - +
137C ALA* 4.0 3.2 + - + -
151C GLY 3.7 5.4 - - - +
152C CYS* 4.3 1.1 - - + -
221C LYS* 5.4 6.2 - - + -
222C THR 5.3 2.2 - - - +
223C VAL* 3.9 28.5 - - + -
224C GLU 5.3 1.6 - - - +
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Residues in contact with LEU 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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123B PHE* 3.8 44.6 - - + -
124B PRO 4.9 6.5 - - - +
136B THR 5.9 0.2 - - - +
138B VAL* 4.0 18.4 - - + -
134C PHE* 6.2 0.2 - - + -
135C PRO* 1.3 77.0 - - - +
137C ALA* 1.3 60.3 + - - +
150C LEU* 3.2 10.7 - - - +
151C GLY* 2.6 44.6 + - - +
152C CYS 3.6 25.4 - - - +
153C LEU* 3.7 20.2 - - + +
191C SER* 4.0 23.1 - - - +
192C SER 4.8 2.0 - - - +
193C VAL* 4.8 1.6 - - + -
223C VAL* 4.1 1.2 - - - +
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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