Contacts of the strand formed by residues 135 - 143 (chain A) in PDB entry 1DCT
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 TYR 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.0 16.8 - - + -
102A LYS* 3.0 15.6 - - + +
103A PRO* 2.6 46.3 + - - +
104A ILE 3.6 8.7 - - - -
105A PHE* 4.6 0.9 - - - -
106A PHE* 3.8 28.9 - + + -
130A PHE 3.4 17.0 + - - +
131A ASP* 3.3 23.2 + - - +
133A ALA* 3.7 26.9 - - + -
134A GLY* 1.3 80.0 - - - +
136A ASP* 1.3 63.8 + - - +
137A VAL* 3.3 5.6 + - + +
160A GLY 3.8 4.0 - - - -
161A PHE* 2.9 30.7 - - - +
162A ARG* 3.4 11.0 - - + +
163A LYS* 3.6 10.6 + - - +
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Residues in contact with ASP 136 (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 TYR* 1.3 70.0 - - - +
137A VAL* 1.3 62.4 + - - +
138A HIS* 3.7 16.9 - - + +
160A GLY* 3.2 3.1 - - - -
161A PHE* 2.8 33.4 + - + +
162A ARG 4.6 1.0 - - - +
163A LYS* 3.5 46.0 + - - +
166A ASN* 4.0 13.6 - - - +
167A ILE 4.8 7.5 + - - +
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Residues in contact with VAL 137 (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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106A PHE* 4.7 4.3 - - + -
127A ILE* 4.4 13.5 - - + +
130A PHE* 3.3 45.3 - - + -
131A ASP* 4.3 4.7 - - + +
135A TYR 3.3 10.4 + - - +
136A ASP* 1.3 77.1 - - - +
138A HIS* 1.3 81.2 + - - +
139A ILE* 3.7 27.4 - - + -
158A TYR* 4.6 8.5 - - + -
159A ILE 3.3 7.4 - - - +
160A GLY* 4.2 0.9 - - - -
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Residues in contact with HIS 138 (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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136A ASP* 3.7 22.2 + - + +
137A VAL* 1.3 82.5 + - - +
139A ILE* 1.3 62.6 + - - +
140A ILE* 4.1 4.5 - - + -
157A PHE 3.1 1.4 - - - +
158A TYR* 3.3 3.5 - - - -
159A ILE* 2.5 49.9 + - + +
161A PHE* 3.8 22.8 - + - -
167A ILE 4.5 7.0 + - - -
168A ASN* 5.6 1.6 - - - -
169A TYR* 3.6 48.5 + + + +
171A PRO* 6.3 0.2 - - + -
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Residues in contact with ILE 139 (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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115A MET* 5.0 7.9 - - + -
123A VAL* 5.8 0.4 - - + -
127A ILE* 3.4 37.7 - - + -
137A VAL* 3.7 16.8 - - + -
138A HIS* 1.3 78.7 - - - +
140A ILE* 1.3 64.7 + - - +
141A LEU 4.2 0.7 + - - +
156A VAL* 4.8 16.6 - - + -
157A PHE 3.4 4.0 - - - +
158A TYR* 4.1 20.6 - - + -
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Residues in contact with ILE 140 (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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138A HIS* 5.0 4.0 - - + -
139A ILE* 1.3 81.8 - - - +
141A LEU* 1.3 62.2 + - - +
142A LEU* 3.6 30.5 - - + -
155A ARG 3.6 0.7 - - - +
156A VAL* 3.1 6.7 - - - +
157A PHE* 2.9 42.9 + - + -
159A ILE* 3.7 29.2 - - + -
169A TYR* 4.3 9.9 - - + +
171A PRO* 4.1 23.6 - - + -
172A PRO* 4.6 7.0 - - + -
316A ILE* 4.6 3.6 - - + -
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Residues in contact with LEU 141 (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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112A LYS* 3.8 36.6 - - + +
115A MET* 5.5 6.1 - - + -
139A ILE* 4.2 1.4 + - - +
140A ILE* 1.3 76.6 - - - +
142A LEU* 1.3 82.6 + - - +
154A LYS* 3.7 28.7 - - + -
155A ARG 3.3 15.3 - - - +
156A VAL* 4.1 12.3 - - + -
15M C 4.9 3.6 - - - +
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Residues in contact with LEU 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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140A ILE* 3.6 33.0 - - + -
141A LEU* 1.3 85.9 - - - +
143A ASN* 1.3 58.6 + - - +
147A TYR* 3.6 33.0 - - + +
153A ARG 3.5 1.0 - - - +
154A LYS* 3.0 4.3 - - - -
155A ARG* 2.7 40.0 + - - +
157A PHE* 3.7 23.1 - - + -
171A PRO* 6.3 1.1 - - + -
172A PRO* 4.4 8.7 - - + +
312A LEU* 4.1 11.7 - - + +
316A ILE* 4.1 13.9 - - + -
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Residues in contact with ASN 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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142A LEU* 1.3 77.0 - - - +
144A ALA* 1.3 75.4 + - - +
145A ASN* 3.2 16.2 + - - +
146A ASP* 3.3 28.7 + - - +
147A TYR* 3.5 14.0 - - - -
151A GLN 3.4 1.9 - - - +
152A ASP* 3.5 25.8 + - - +
153A ARG 2.9 25.8 + - - +
154A LYS* 4.0 21.0 - - + +
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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