Contacts of the strand formed by residues 143 - 153 (chain C) in PDB entry 3OF6
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 LYS 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C GLU* 3.3 29.3 + - - +
138C ILE* 4.0 5.6 - - - +
141C THR* 2.9 20.1 - - - +
142C GLN* 1.3 82.0 - - - +
144C ALA* 1.3 60.8 + - - +
198C ARG* 3.3 46.1 - - + +
199C VAL* 3.5 18.4 + - - +
200C SER* 5.1 5.3 - - - +
201C ALA 4.3 1.3 - - - +
67F ASP* 5.8 3.8 - - - -
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Residues in contact with ALA 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 PRO* 3.5 26.7 - - + -
137C GLU* 4.2 0.2 - - - -
138C ILE* 4.7 5.4 - - + -
143C LYS* 1.3 72.7 - - - +
145C THR* 1.3 61.9 + - - +
146C LEU* 4.3 0.6 - - - +
197C LEU 3.2 3.8 - - - +
198C ARG* 3.3 1.6 - - - -
199C VAL* 2.9 42.5 + - + +
200C SER 4.8 1.6 - - - +
201C ALA* 4.5 3.5 - - - +
204C TRP* 3.7 28.3 - - + -
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Residues in contact with THR 145 (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 GLU 4.3 0.9 - - - -
133C PRO* 3.5 21.1 - - - +
137C GLU* 2.6 33.2 + - - +
144C ALA* 1.3 71.8 - - - +
146C LEU* 1.3 67.6 + - - +
147C VAL* 4.1 4.0 + - - +
196C ARG* 3.8 24.9 - - + -
197C LEU 3.3 7.9 - - - +
198C ARG* 3.0 24.9 + - + +
32F LEU* 3.6 28.8 - - + +
34F LEU* 4.7 2.8 - - + +
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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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130C VAL* 4.4 12.6 - - + -
131C PHE 3.6 8.3 - - - +
132C GLU* 5.6 0.2 - - - -
133C PRO* 3.9 22.2 - - + -
144C ALA 4.3 4.9 - - - +
145C THR* 1.3 78.7 - - - +
147C VAL* 1.3 61.6 + - - +
162C TRP* 3.7 25.3 - - + -
195C SER 3.5 1.2 - - - +
196C ARG* 3.4 7.6 - - - -
197C LEU* 3.1 38.5 + - + +
199C VAL* 4.6 11.2 - - + -
204C TRP* 3.9 20.4 - - + -
211C PHE* 3.6 39.0 - - + -
242C ALA* 5.3 1.3 - - + -
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Residues in contact with VAL 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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129C ALA 3.6 1.6 - - - +
130C VAL* 3.4 3.7 - - - -
131C PHE* 2.9 47.5 + - + -
145C THR* 4.1 4.0 + - + +
146C LEU* 1.3 77.6 - - - +
148C CYS* 1.3 63.1 + - - +
149C LEU* 3.8 16.8 - - + -
162C TRP* 4.5 2.0 - - - -
195C SER 3.4 4.5 - - - +
196C ARG* 4.2 6.1 - - + -
30F VAL* 4.4 11.2 - - + -
32F LEU* 4.1 28.0 - - + -
73F LEU* 3.5 37.9 - - + -
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Residues in contact with CYS 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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128C VAL* 3.5 20.9 - - - -
129C ALA 3.4 5.4 - - - -
130C VAL* 4.4 0.7 - - + -
147C VAL* 1.3 73.7 - - - +
149C LEU* 1.3 69.2 + - - +
160C LEU* 4.2 11.3 - - + +
162C TRP* 3.6 13.8 - - + -
193C LEU 4.4 0.2 - - - -
194C SER* 3.1 8.7 - - - -
195C SER* 3.1 28.0 + - - +
213C CYS* 2.0 53.4 - - + -
215C VAL* 4.8 2.0 - - - -
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Residues in contact with LEU 149 (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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127C GLU 2.8 22.6 - - - +
128C VAL* 3.1 13.1 - - - -
129C ALA* 3.0 16.1 + - + +
131C PHE* 3.5 31.4 - - + -
147C VAL* 3.8 14.8 - - + -
148C CYS* 1.3 87.2 - - - +
150C ALA* 1.3 55.8 + - - +
151C THR* 4.0 6.5 - - + -
193C LEU 3.4 0.7 - - - -
194C SER* 3.5 13.7 - - - -
28F VAL* 5.4 1.8 - - + -
30F VAL* 4.8 2.5 - - + -
60F TYR* 3.4 39.3 - - + +
73F LEU* 3.9 1.6 - - + -
75F HIS* 3.9 24.9 - - + -
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Residues in contact with ALA 150 (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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126C PRO* 4.1 20.6 - - + -
127C GLU 3.6 4.7 - - - -
128C VAL* 4.3 10.5 - - + -
148C CYS* 4.3 0.4 - - - -
149C LEU* 1.3 72.8 - - - +
151C THR* 1.3 62.1 + - - +
153C PHE* 3.0 17.2 - - + -
158C VAL* 5.9 0.4 - - + -
160C LEU* 5.6 2.7 - - + +
193C LEU* 2.8 47.2 + - + +
215C VAL* 4.4 14.4 - - + -
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Residues in contact with THR 151 (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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126C PRO* 3.7 0.9 - - - +
127C GLU* 3.0 42.7 + - - +
149C LEU* 4.7 6.7 - - + -
150C ALA* 1.3 81.3 - - - +
152C GLY* 1.3 68.0 + - - +
153C PHE* 3.4 3.1 + - - -
182C GLU* 3.4 10.3 - - - +
191C TYR 3.6 5.2 - - - -
192C CYS* 4.2 8.1 - - + -
60F TYR* 3.8 21.8 - - - +
75F HIS* 4.8 11.4 - - + +
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Residues in contact with GLY 152 (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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124C PHE* 3.3 14.6 - - - +
125C PRO 3.0 15.1 - - - +
151C THR* 1.3 71.8 - - - +
153C PHE* 1.3 58.0 + - - +
182C GLU* 2.8 21.8 + - - -
190C ARG* 3.6 34.2 + - - -
191C TYR 3.1 2.8 + - - -
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Residues in contact with PHE 153 (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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124C PHE 3.1 11.2 - - - +
126C PRO* 3.6 24.9 - - + -
150C ALA* 3.0 35.7 - - + -
151C THR 4.0 0.9 - - - -
152C GLY* 1.3 79.5 - - - +
154C TYR* 1.3 61.1 + - - +
155C PRO 3.4 11.2 - - - -
156C ASP* 3.7 13.0 - - - -
158C VAL* 3.5 35.9 - - + -
179C PRO* 3.5 18.8 - - + -
190C ARG* 4.5 0.2 - - - -
191C TYR* 2.9 69.0 + - + +
192C CYS* 3.5 5.4 - - - -
193C LEU* 3.9 4.3 - - + -
217C PHE* 4.4 1.6 - - + -
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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