Contacts of the strand formed by residues 131 - 138 (chain D) in PDB entry 1DGB
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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D HIS* 3.6 9.4 - - - -
112D ARG 4.0 3.1 - - - -
113D PHE* 3.1 28.1 - - - +
114D SER* 2.7 24.4 + - - -
130D ARG* 1.3 73.1 - - - +
132D PHE* 1.3 59.1 + - - +
133D ALA 3.9 2.0 - - - -
147D GLY 3.6 1.8 - - - -
148D ASN* 3.6 1.1 - - - -
212D MET* 4.3 1.6 - - - +
1203D HEM 3.5 22.0 - - - -
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 3.4 21.5 - - + -
112D ARG 3.8 2.0 - - - -
113D PHE* 3.4 33.0 - + + -
130D ARG 4.5 0.9 - - - +
131D GLY* 1.3 74.3 - - - +
133D ALA* 1.3 58.2 + - - +
134D VAL* 4.0 9.4 - - + -
147D GLY 2.7 26.0 + - - +
148D ASN 4.4 8.5 - - - +
212D MET* 4.4 9.0 - - + -
213D ASN 4.0 6.3 - - - -
214D GLY* 3.6 17.0 - - - -
236D TYR* 3.0 47.9 + + + +
277D TRP* 3.5 43.7 - + - -
316D LEU* 5.2 3.4 - - + -
318D LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA 3.6 0.7 - - - +
111D VAL* 3.1 9.2 - - - +
112D ARG 3.1 33.9 + - - +
131D GLY 3.9 0.2 - - - -
132D PHE* 1.3 74.8 - - - +
134D VAL* 1.3 60.8 + - - +
145D LEU 3.6 4.0 - - - -
146D VAL* 4.1 19.7 - - + -
147D GLY 4.0 1.3 - - - +
334D PHE* 3.7 38.1 - - + -
1203D HEM 4.2 8.7 - - + -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ILE* 4.1 22.4 - - + -
110D ALA 3.4 2.5 - - - -
111D VAL* 4.0 9.4 - - + -
132D PHE* 4.0 25.4 - - + -
133D ALA* 1.3 78.9 - - - +
135D LYS* 1.3 62.6 + - - +
136D PHE* 3.3 33.9 - - + -
143D TRP 3.5 1.7 - - - +
144D ASP* 3.5 2.8 - - - -
145D LEU* 2.8 42.8 + - + +
236D TYR* 4.1 19.1 - - + +
316D LEU* 4.5 10.1 - - + -
334D PHE* 4.0 2.9 - - - -
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ILE* 2.9 9.8 - - - -
110D ALA* 2.6 43.2 + - + +
134D VAL* 1.3 74.0 - - - +
136D PHE* 1.3 64.6 + - - +
137D TYR* 3.7 36.9 + - + +
142D ASN* 4.2 16.5 - - - +
144D ASP* 2.6 39.1 + - - +
332D ILE* 4.0 19.3 - - - -
333D ALA 2.9 28.3 + - - -
334D PHE* 3.6 9.2 - - + -
338D ASN* 4.7 1.6 + - - -
375D VAL 3.9 7.2 - - - +
376D ASN* 4.3 6.4 + - - +
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 3.9 33.0 - + + -
99D VAL* 4.2 11.9 - - + -
107D THR* 4.4 3.4 - - + -
108D PRO 3.6 3.8 - - - -
109D ILE* 3.8 12.6 - - + -
134D VAL* 3.3 30.1 - - + -
135D LYS* 1.3 74.9 - - - +
137D TYR* 1.3 62.4 + - - +
138D THR* 3.2 17.8 + - + +
142D ASN* 3.2 7.4 - - - -
143D TRP* 2.8 85.5 + + + +
145D LEU* 3.9 17.7 - - + -
279D PHE* 4.8 6.5 - + - -
316D LEU* 4.3 7.4 - - + -
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PHE* 4.6 4.4 - + - -
107D THR* 3.2 13.9 - - - +
108D PRO* 3.1 30.1 + - + +
109D ILE 4.0 8.5 - - - -
110D ALA* 3.6 29.2 - - + +
135D LYS* 3.7 17.6 - - + +
136D PHE* 1.3 69.9 - - - +
138D THR* 1.3 59.8 + - - +
142D ASN* 3.2 25.1 - - - +
374D PRO 5.1 0.7 - - - -
375D VAL* 2.9 35.8 + - - +
377D CYS 3.9 10.5 - - - -
379D TYR* 3.4 44.4 - + + -
380D ARG* 3.3 25.5 + - + +
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LYS* 5.5 1.1 - - - -
99D VAL* 4.0 34.3 - - + +
107D THR* 4.1 4.9 - - + -
136D PHE* 3.2 25.8 + - + +
137D TYR* 1.3 76.2 - - - +
139D GLU* 1.3 70.7 + - - +
140D ASP* 2.9 18.6 + - - +
141D GLY* 2.5 36.8 + - - +
142D ASN* 5.0 0.7 - - - +
143D TRP* 4.5 5.6 - - + -
340D PRO* 4.5 3.3 - - + +
378D PRO* 5.6 0.2 - - - +
380D ARG* 3.4 17.6 + - - +
381D ALA* 3.9 0.9 + - - +
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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