Contacts of the strand formed by residues 140 - 149 (chain D) in PDB entry 1KTD
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 ASN 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D PRO* 5.1 7.3 - - - +
131D THR 3.9 2.8 + - - +
132D LYS* 2.9 36.5 + - + +
139D HIS* 1.3 75.4 - - - +
141D LEU* 1.3 95.4 + - - +
142D LEU* 5.5 0.2 - - - +
188D LEU 3.8 1.4 - - - +
189D GLU* 3.9 3.5 - - - -
190D THR* 3.3 35.6 + - - +
191D VAL* 5.4 1.5 - - + +
192D PRO* 4.3 21.2 - - + +
215D TRP* 5.9 0.5 - - - -
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Residues in contact with LEU 141 (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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130D PRO* 3.6 3.5 - - - +
131D THR* 3.1 45.7 + - - +
132D LYS* 3.9 15.0 - - - +
139D HIS* 5.9 0.7 - - + +
140D ASN* 1.3 86.8 + - - +
142D LEU* 1.3 59.5 + - - +
143D VAL* 4.8 3.1 - - + -
170D VAL* 5.0 6.7 - - + -
187D MET* 4.0 35.0 - - + -
188D LEU 3.5 12.3 - - - +
189D GLU* 3.5 36.8 - - + +
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Residues in contact with LEU 142 (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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128D VAL* 3.7 18.4 - - + -
129D TYR 4.0 4.9 - - - +
130D PRO* 4.8 1.6 - - + -
140D ASN 4.1 0.4 + - - +
141D LEU* 1.3 73.5 - - - +
143D VAL* 1.3 61.9 + - - +
158D TRP* 3.5 31.3 - - + -
187D MET* 3.4 2.7 - - - -
188D LEU* 2.9 46.8 + - + +
190D THR* 4.2 7.2 - - - +
192D PRO* 4.9 5.4 - - + -
198D TYR* 3.4 50.5 - - + -
215D TRP* 3.8 31.6 - - + -
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Residues in contact with VAL 143 (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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127D THR 3.7 0.5 - - - +
128D VAL* 3.2 7.8 - - - +
129D TYR* 2.9 69.7 + - + +
131D THR* 3.5 37.5 - - + +
141D LEU* 4.7 0.4 - - + -
142D LEU* 1.3 75.4 - - - +
144D CYS* 1.3 69.4 + - - +
158D TRP* 3.9 2.7 - - - -
185D LEU* 4.2 13.5 - - + -
187D MET* 4.0 30.5 - - + -
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Residues in contact with CYS 144 (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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126D VAL* 3.9 18.4 - - - -
127D THR 3.7 2.0 - - - -
128D VAL* 4.1 2.2 - - - -
143D VAL* 1.3 76.0 - - - +
145D SER* 1.3 60.5 + - - +
146D VAL* 3.8 7.1 + - - +
156D VAL* 4.1 7.6 - - + -
158D TRP* 3.4 17.7 - - + +
185D LEU* 3.7 2.4 - - - -
186D VAL* 3.1 38.8 + - - +
200D CYS* 2.0 50.0 - - - -
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Residues in contact with SER 145 (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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96C PRO* 3.3 26.6 - - - +
125D THR 3.2 1.9 + - - +
126D VAL* 3.2 9.4 - - - +
127D THR* 2.7 42.8 + - - -
129D TYR* 4.1 16.8 - - - -
143D VAL 3.8 0.8 - - - -
144D CYS* 1.3 73.1 - - - +
146D VAL* 1.3 60.6 + - - +
147D SER* 3.8 8.5 + - - -
184D THR 3.8 4.8 + - - -
185D LEU* 3.9 19.4 - - - +
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Residues in contact with VAL 146 (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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124D PRO* 3.5 22.9 - - + -
125D THR 3.7 3.4 - - - -
126D VAL* 4.5 3.4 - - + -
144D CYS* 4.3 8.3 - - - +
145D SER* 1.3 76.2 + - - +
147D SER* 1.3 57.8 + - - +
149D PHE* 3.4 9.1 - - + -
154D ILE* 3.4 30.1 - - + -
156D VAL* 3.7 30.7 - - + -
184D THR* 3.1 40.2 + - + -
202D VAL* 3.9 18.2 - - + -
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Residues in contact with SER 147 (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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94C ARG 4.3 12.8 - - - -
95C SER* 4.2 6.4 + - - -
96C PRO* 3.8 28.0 - - - +
124D PRO* 3.5 1.9 - - - +
125D THR* 3.0 47.5 + - - +
145D SER* 4.3 4.9 - - - -
146D VAL* 1.3 75.3 - - - +
148D ASP* 1.3 69.9 + - - +
149D PHE* 3.5 3.3 + - - -
182D PHE 4.2 1.8 - - - -
183D GLN* 4.3 9.4 - - - +
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Residues in contact with ASP 148 (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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94C ARG* 2.6 41.2 + - - +
95C SER* 3.3 18.1 + - - -
122D VAL* 3.3 23.7 - - + +
123D GLU 3.6 5.9 - - - +
125D THR* 5.3 5.1 + - - +
147D SER* 1.3 77.4 + - - +
149D PHE* 1.3 57.8 - - - +
177D ASN* 4.3 1.4 + - - -
181D THR* 3.0 28.7 + - + -
182D PHE 3.1 11.6 + - - -
183D GLN* 4.5 1.6 - - - +
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Residues in contact with PHE 149 (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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122D VAL* 3.0 13.5 - - - +
124D PRO* 3.6 17.3 - - + -
146D VAL* 3.4 37.2 - - + -
148D ASP* 1.3 76.2 - - - +
150D TYR* 1.3 63.1 + - - +
151D PRO 2.9 27.6 - - - -
152D GLY 3.6 15.5 - - - -
154D ILE* 3.6 23.8 - - + -
174D LEU* 3.5 21.5 - - + -
181D THR* 3.6 2.0 - - - -
182D PHE* 2.9 51.6 + - + -
183D GLN* 4.1 0.4 - - - -
184D THR* 4.0 9.0 - - + -
204D HIS* 3.3 15.0 - + - +
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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