Contacts of the strand formed by residues 141 - 148 (chain C) in PDB entry 1DGH
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 GLY 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C THR* 2.6 39.8 + - - +
139C GLU 3.2 6.3 + - - -
140C ASP* 1.3 80.4 - - - +
142C ASN* 1.3 67.4 + - - -
143C TRP* 4.8 0.2 - - - -
340C PRO* 4.9 1.0 - - - +
378C PRO* 4.6 0.9 - - - -
381C ALA* 3.6 9.3 - - - +
31D ALA 3.3 13.9 - - - -
32D GLY 3.3 10.8 + - - -
33D ASN* 3.6 1.1 + - - -
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Residues in contact with ASN 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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135C LYS* 4.2 11.1 - - + +
136C PHE 3.4 4.3 - - - +
137C TYR* 3.4 37.4 - - - -
138C THR 5.0 0.3 - - - +
141C GLY* 1.3 72.4 - - - -
143C TRP* 1.3 59.1 + - - +
144C ASP* 4.1 10.1 - - - +
338C ASN* 3.5 20.9 + - - +
340C PRO* 4.5 0.3 - - - +
371C LEU* 5.8 0.4 - - - +
376C ASN 3.3 24.5 + - - -
377C CYS 3.8 3.0 + - - -
378C PRO* 3.5 25.7 - - - +
31D ALA* 3.0 20.5 + - + +
33D ASN* 3.2 17.2 + - - +
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Residues in contact with TRP 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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99C VAL* 4.1 16.6 - - + -
100C PHE* 3.7 33.0 - + - -
136C PHE* 2.7 90.7 + + + +
138C THR* 4.3 4.0 - - + -
141C GLY 3.7 0.2 + - - -
142C ASN* 1.3 73.4 - - - +
144C ASP* 1.3 73.8 + - - +
145C LEU* 4.4 16.6 - - + +
220C PHE* 6.3 1.2 - - - -
234C PHE* 3.8 31.8 - + - -
279C PHE* 4.3 8.7 - + - -
338C ASN 3.3 13.5 - - - -
339C MET* 4.3 6.2 - - + +
340C PRO* 3.7 25.1 - - + -
343C ILE* 3.7 20.5 - - + +
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Residues in contact with ASP 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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134C VAL 3.4 2.9 - - - +
135C LYS* 2.8 49.5 + - - +
142C ASN* 4.7 1.2 - - - +
143C TRP* 1.3 81.9 + - - +
145C LEU* 1.3 59.7 + - - +
146C VAL* 3.6 3.3 + - + -
333C ALA 3.8 0.3 - - - +
334C PHE* 3.8 11.7 - - + -
335C ASP 2.8 41.8 + - - +
336C PRO* 3.9 16.3 - - - +
338C ASN* 3.0 26.7 + - - +
339C MET* 5.7 0.2 - - - +
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Residues in contact with LEU 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 PHE 3.9 1.4 - - - +
133C ALA* 3.6 0.2 - - - -
134C VAL* 2.8 37.1 + - + +
136C PHE* 3.9 17.7 - - + -
143C TRP* 3.9 14.7 + - + +
144C ASP* 1.3 71.2 - - - +
146C VAL* 1.3 59.7 + - - +
147C GLY 3.3 4.9 + - - -
216C GLY* 4.0 16.4 - - - -
220C PHE* 4.4 13.0 - - + -
234C PHE* 3.7 32.5 - - + -
236C TYR* 3.6 34.0 + - + +
279C PHE* 3.8 25.8 - - + -
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Residues in contact with VAL 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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133C ALA* 4.1 10.3 - - + +
144C ASP* 3.6 7.3 + - + +
145C LEU* 1.3 73.6 - - - +
147C GLY* 1.3 58.1 + - - +
216C GLY 4.7 1.8 - - - +
220C PHE* 6.2 0.4 - - - -
334C PHE* 3.5 26.5 - - + +
336C PRO* 3.7 29.7 - - + +
354C ARG* 3.0 37.2 + - - +
358C TYR* 4.1 7.2 - - + -
2002C HEM 3.2 46.3 - - + +
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Residues in contact with GLY 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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132C PHE* 2.7 45.5 + - - -
145C LEU 3.3 3.4 + - - -
146C VAL* 1.3 76.7 - - - +
148C ASN* 1.3 56.6 + - - -
215C TYR 3.0 19.7 - - - -
216C GLY* 4.5 2.0 - - - -
236C TYR* 3.7 4.2 + - - -
2002C HEM 3.3 17.2 - - - +
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Residues in contact with ASN 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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75C HIS* 3.5 24.6 - - - -
116C VAL* 5.7 0.2 - - - +
129C PRO* 4.9 8.6 - - - +
130C ARG 3.1 16.3 - - - +
131C GLY* 3.5 3.1 - - - -
132C PHE* 4.5 4.5 - - - -
147C GLY* 1.3 73.1 - - - +
149C ASN* 1.3 59.6 + - - +
150C THR* 3.0 28.0 + - + +
152C ILE 5.1 0.6 + - - -
153C PHE* 3.8 25.5 - - - -
214C GLY* 3.6 1.6 - - - -
215C TYR 2.9 29.5 + - - +
217C SER* 4.4 0.7 - - - +
2002C HEM 3.2 35.1 - - + +
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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