Contacts of the strand formed by residues 136 - 143 (chain C) in PDB entry 5KC6
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 TRP 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C MET* 3.3 6.4 - - - -
133C LEU* 2.7 44.2 + - + +
134C ASN* 3.3 18.1 + - + -
135C GLY* 1.3 81.2 - - - +
137C PRO* 1.3 74.6 - - + +
138C VAL* 3.6 0.6 + - + -
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Residues in contact with PRO 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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130C SER* 4.5 7.6 - - - +
131C LEU 3.7 2.0 - - - +
132C MET* 3.5 28.4 - - + -
135C GLY 4.3 2.9 - - - +
136C TRP* 1.3 94.9 - - + +
138C VAL* 1.3 61.7 + - - +
139C ILE 5.2 0.2 - - - +
140C SER* 5.2 3.1 - - - +
172C GLU* 4.2 9.2 - - - +
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Residues in contact with VAL 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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67A ILE* 4.0 19.1 - - - +
90A LEU* 3.6 19.9 - - + +
131C LEU* 2.8 23.9 + - + +
132C MET 4.5 1.1 - - - -
133C LEU* 3.7 32.8 - - + +
136C TRP* 4.1 0.9 - - + +
137C PRO* 1.3 78.5 - - - +
139C ILE* 1.3 73.1 + - + +
157C VAL* 4.1 5.4 - - + -
159C ILE* 3.6 36.8 - - + -
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Residues in contact with ILE 139 (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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67A ILE* 4.2 7.2 - - + -
182A TYR* 5.7 1.8 - - - +
184A THR* 3.7 22.2 - - + -
116C PHE* 3.9 17.5 - - + -
130C SER* 3.2 6.2 - - - -
131C LEU* 2.9 44.3 + - + +
137C PRO 5.2 0.4 - - - -
138C VAL* 1.3 90.4 + - + +
140C SER* 1.3 65.5 + - - +
155C ASN* 3.9 10.3 - - + +
156C GLY* 3.7 29.2 - - - +
157C VAL* 3.5 31.0 - - + -
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Residues in contact with SER 140 (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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119A VAL* 5.1 2.4 - - - +
182A TYR* 3.7 40.8 + - - +
116C PHE* 4.9 0.7 - - - -
128C GLN* 3.6 18.5 + - - -
129C VAL 3.2 7.4 - - - -
130C SER* 2.5 24.0 + - - -
137C PRO* 5.2 3.5 - - - +
139C ILE* 1.3 74.9 + - - +
141C ALA* 1.3 59.9 + - - +
142C PHE* 4.4 5.6 - - - -
155C ASN* 3.1 21.8 + - - -
172C GLU* 4.7 0.2 + - - -
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Residues in contact with ALA 141 (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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116C PHE* 4.1 10.1 - - + -
128C GLN* 3.4 5.9 - - - +
129C VAL 2.8 29.5 + - - +
140C SER* 1.3 74.7 - - - +
142C PHE* 1.3 69.6 + - - +
153C ALA* 3.4 10.9 - - + +
154C SER 3.4 43.7 - - - +
155C ASN* 4.2 0.2 - - + -
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Residues in contact with PHE 142 (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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119A VAL* 4.4 8.1 - - + -
149A THR* 3.9 14.4 - - - +
150A ARG* 3.9 42.4 - - + +
151A GLU* 5.9 0.5 - - - -
182A TYR* 3.6 50.0 - + + -
127C ILE 3.7 8.1 - - - +
128C GLN* 3.3 45.1 - - + -
140C SER* 4.4 0.9 - - - -
141C ALA* 1.3 84.3 - - - +
143C ALA* 1.3 64.7 + - - +
152C ALA 3.8 4.9 - - - +
153C ALA* 3.3 14.3 - - - -
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Residues in contact with ALA 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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149A THR* 3.7 5.1 + - - -
150A ARG 5.2 0.2 - - - -
120C LYS* 4.1 14.2 - - + +
126C THR* 3.6 3.8 - - - -
127C ILE* 3.3 48.9 + - + +
142C PHE* 1.3 79.7 - - - +
144C GLY* 1.3 64.6 + - - +
151C GLU* 4.2 14.4 - - + +
152C ALA 4.3 1.6 - - - -
153C ALA 4.0 15.9 - - - +
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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