Contacts of the strand formed by residues 141 - 148 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A THR* 2.6 43.7 + - - +
139A GLU 3.2 3.2 + - - -
140A ASP* 1.3 80.4 - - - +
142A ASN* 1.3 67.6 + - - -
340A PRO* 4.9 1.0 - - - +
378A PRO* 4.6 1.8 - - - -
381A ALA* 3.7 7.9 - - - +
31B ALA 3.3 13.7 - - - -
32B GLY 3.5 9.0 + - - -
33B ASN* 3.6 1.8 - - - -
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 4.1 19.4 - - + +
136A PHE 3.4 5.4 - - - +
137A TYR* 3.3 34.0 - - - +
138A THR 5.1 0.3 - - - +
141A GLY* 1.3 72.8 - - - -
143A TRP* 1.3 60.2 + - - +
144A ASP* 4.1 2.5 - - - +
338A ASN* 3.5 28.1 + - - +
339A MET 4.1 0.2 + - - -
340A PRO* 5.0 0.4 - - - -
371A LEU* 5.8 1.0 - - - +
376A ASN 3.2 25.3 + - - -
377A CYS 3.9 2.4 + - - -
378A PRO* 3.4 24.8 - - - +
31B ALA* 3.0 16.0 + - + +
33B ASN* 3.3 16.3 + - - +
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Residues in contact with TRP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.2 11.0 - - + -
100A PHE* 3.8 32.8 - + - -
135A LYS* 3.5 0.9 - - - -
136A PHE* 2.8 87.8 + + + +
138A THR* 4.5 4.3 - - + -
141A GLY 3.8 0.2 + - - -
142A ASN* 1.3 73.8 - - - +
144A ASP* 1.3 73.7 + - - +
145A LEU* 4.3 17.7 - - + +
220A PHE* 6.1 2.2 - - - -
234A PHE* 3.8 30.0 - + - -
279A PHE* 4.2 11.9 - + - -
338A ASN 3.4 12.3 - - - -
339A MET* 4.2 6.2 - - + +
340A PRO* 3.7 24.2 - - + -
343A ILE* 3.7 28.7 - - + +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL 3.4 2.2 - - - +
135A LYS* 2.8 49.0 + - - +
142A ASN* 5.1 1.3 - - - -
143A TRP* 1.3 80.9 + - - +
145A LEU* 1.3 60.1 + - - +
146A VAL* 3.6 3.3 + - + -
220A PHE* 6.1 0.7 - - - -
333A ALA 3.9 0.3 - - - +
334A PHE* 3.7 12.4 - - + -
335A ASP 2.7 41.9 + - - +
336A PRO* 4.0 16.6 - - - +
338A ASN* 2.9 28.5 + - - +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE 3.8 1.6 - - - +
133A ALA* 3.5 0.3 - - - -
134A VAL* 2.7 39.0 + - + +
136A PHE* 4.0 17.5 - - + -
143A TRP* 3.9 16.0 + - + +
144A ASP* 1.3 71.8 - - - +
146A VAL* 1.3 56.2 + - - +
147A GLY 3.2 5.0 + - - -
216A GLY* 4.2 16.2 - - - -
220A PHE* 4.2 16.2 - - + -
234A PHE* 3.8 28.9 - - + -
236A TYR* 3.8 32.2 + - + +
279A PHE* 3.8 26.0 - - + -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA* 4.0 11.2 - - + -
144A ASP* 3.6 6.7 + - + +
145A LEU* 1.3 71.0 - - - +
147A GLY* 1.3 58.6 + - - +
216A GLY 4.8 1.5 - - - +
334A PHE* 3.6 25.1 - - + -
336A PRO* 3.6 31.1 - - + +
354A ARG* 2.9 38.2 + - - +
358A TYR* 4.0 10.1 - - + -
2000A HEM 3.3 42.5 - - + +
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE 2.7 46.3 + - - -
145A LEU 3.2 4.0 + - - -
146A VAL* 1.3 74.9 - - - +
148A ASN* 1.3 57.3 + - - -
215A TYR 3.1 16.8 - - - -
216A GLY* 4.5 3.1 - - - -
236A TYR* 3.6 3.6 - - - -
2000A HEM 3.3 18.8 - - - +
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Residues in contact with ASN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A HIS* 3.6 14.6 + - - -
116A VAL* 5.7 0.2 - - - +
129A PRO* 4.8 9.4 - - - +
130A ARG 2.9 19.2 - - - +
131A GLY* 3.4 8.1 - - - -
132A PHE* 4.2 5.4 - - - +
147A GLY* 1.3 76.5 - - - +
149A ASN* 1.3 59.0 + - - +
150A THR* 3.0 30.0 + - + +
152A ILE 5.3 0.2 + - - -
153A PHE* 4.0 22.2 - - - -
214A GLY* 3.5 2.6 - - - -
215A TYR* 2.9 29.8 + - - +
217A SER* 4.5 0.4 - - - +
2000A HEM 3.3 34.0 - - + +
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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