Contacts of the strand formed by residues 140 - 150 (chain A) in PDB entry 1K4C
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 MET 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A THR* 4.7 0.7 - - - -
138A ASN* 3.0 25.8 + - + +
139A SER* 1.3 92.9 - - - +
141A VAL* 1.3 62.1 + - - +
187A THR* 3.4 29.4 - - + +
188A VAL* 3.3 28.3 - - - +
189A PRO* 3.5 24.7 - - + -
190A SER* 3.7 4.7 - - - +
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Residues in contact with VAL 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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131A PRO* 4.1 15.0 - - + -
137A THR* 5.1 9.9 - - - -
140A MET* 1.3 75.8 - - - +
142A THR* 1.3 65.3 + - - +
143A LEU* 4.1 22.0 + - + +
186A VAL 3.8 0.5 - - - +
187A THR* 3.3 4.2 - - - -
188A VAL* 2.9 53.3 + - + +
189A PRO 4.1 0.2 - - - +
190A SER* 3.8 20.2 - - - -
193A TRP* 4.3 23.8 - - + -
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Residues in contact with THR 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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131A PRO* 3.8 6.9 - - - +
140A MET 5.7 0.2 - - - -
141A VAL* 1.3 77.6 - - - +
143A LEU* 1.3 72.9 + - - +
185A SER* 3.6 23.8 - - - +
186A VAL 3.4 6.3 - - - +
187A THR* 3.1 18.5 + - - +
114B THR* 4.8 10.6 - - - +
116B SER* 3.7 23.9 + - - +
118B PHE* 3.4 18.8 - - + -
135B PHE* 4.1 13.9 - - + -
137B ASN* 4.2 7.0 + - - +
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Residues in contact with LEU 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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129A LEU 3.5 9.9 - - - +
131A PRO* 3.4 32.5 - - + -
141A VAL* 4.1 8.1 - - + +
142A THR* 1.3 83.5 - - - +
144A GLY* 1.3 60.0 + - - +
185A SER* 3.6 4.0 - - - -
186A VAL* 2.8 41.1 + - + +
188A VAL* 4.9 6.1 - - + -
193A TRP* 3.5 56.5 - - + +
198A VAL* 4.2 16.8 - - + -
215A ILE* 4.1 14.6 - - + -
118B PHE* 4.3 4.7 - - - -
135B PHE* 4.1 0.9 - - - -
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Residues in contact with GLY 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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129A LEU* 2.9 39.5 + - - +
143A LEU* 1.3 79.1 - - - +
145A CYS* 1.3 59.8 + - - -
159A TRP* 3.6 12.3 - - - -
184A SER 3.1 14.6 - - - -
215A ILE* 3.4 13.2 - - - +
135B PHE* 4.4 1.6 - - - -
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Residues in contact with CYS 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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126A VAL* 4.3 4.7 - - + -
127A TYR 3.2 12.6 - - - +
129A LEU* 3.5 6.6 - - - +
144A GLY* 1.3 74.8 - - - +
146A LEU* 1.3 59.8 + - - +
147A VAL* 3.9 12.8 + - - +
157A VAL* 4.1 8.3 - - - -
159A TRP* 3.9 9.4 - - + -
183A SER* 3.2 4.9 - - - -
184A SER* 3.1 42.0 + - - -
200A CYS* 3.2 44.0 - - + -
202A VAL* 4.6 0.7 - - - -
215A ILE* 4.7 2.5 - - + -
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Residues in contact with LEU 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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125A SER 3.2 4.9 - - - +
126A VAL* 3.3 2.8 - - - -
127A TYR* 2.7 51.9 + - + +
129A LEU* 3.9 13.4 - - + +
145A CYS* 1.3 72.9 - - - +
147A VAL* 1.3 64.2 + - - +
148A LYS* 4.0 18.4 - - + -
181A THR* 3.9 20.2 - - + -
182A LEU 3.9 4.0 - - - +
183A SER* 3.2 21.8 - - - +
124B GLN* 4.2 7.6 - - - +
131B SER* 3.6 33.7 - - - +
133B VAL* 4.3 13.7 - - + -
178B THR* 5.0 6.5 - - + +
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Residues in contact with VAL 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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124A PRO* 3.4 28.5 - - + -
125A SER 3.5 3.4 - - - +
126A VAL* 4.5 3.6 - - + -
145A CYS* 4.3 12.8 - - - +
146A LEU* 1.3 77.2 - - - +
148A LYS* 1.3 58.4 + - - +
150A TYR* 3.7 15.7 - - + -
155A VAL* 4.6 4.3 - - + -
157A VAL* 4.5 2.7 - - + -
181A THR* 3.2 3.2 - - - -
182A LEU* 2.7 54.3 + - + +
202A VAL* 3.8 38.8 - - + -
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Residues in contact with LYS 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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124A PRO* 3.7 1.2 - - - +
125A SER* 3.0 32.6 + - - -
127A TYR* 4.2 17.7 - - + -
146A LEU* 4.1 12.6 - - + -
147A VAL* 1.3 72.7 - - - +
149A GLY* 1.3 63.7 - - - +
150A TYR* 3.4 2.7 - - - -
176A GLN* 5.9 1.0 + - - -
180A TYR 3.6 1.6 - - - -
181A THR* 2.9 45.6 + - + +
124B GLN* 3.6 27.6 - - - +
131B SER* 4.1 11.4 + - - +
180B THR* 4.9 13.7 + - - +
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Residues in contact with GLY 149 (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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122A THR* 3.1 26.5 - - - +
123A PRO 3.4 4.8 - - - +
148A LYS* 1.3 79.5 - - - +
150A TYR* 1.3 60.0 + - - +
179A LEU* 3.7 28.0 - - - +
180A TYR 2.9 9.1 + - - -
181A THR* 3.6 2.2 + - - -
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Residues in contact with TYR 150 (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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122A THR 3.1 11.4 - - - +
124A PRO* 3.3 24.5 - - + -
147A VAL* 3.7 37.2 - - + -
149A GLY* 1.3 78.8 - - - +
151A PHE* 1.3 66.4 + - - +
152A PRO 3.8 15.3 - - - -
153A GLU* 2.7 30.2 + - - -
155A VAL* 3.6 27.5 - - + +
173A ALA* 3.2 18.4 - - - +
179A LEU* 3.7 1.2 - - - -
180A TYR* 2.8 55.8 + + + -
182A LEU* 3.3 14.5 - - + +
204A HIS* 4.0 2.0 - - - +
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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