Contacts of the strand formed by residues 156 - 164 (chain D) in PDB entry 4FQX
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 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ASP 4.0 8.0 + - - -
39C GLU* 4.9 3.1 + - - +
40C ASP* 2.6 31.0 + - - -
121D GLY 3.1 22.0 + - - -
122D PHE* 2.6 47.7 + - + +
123D TYR* 3.7 26.0 - + - -
125D ALA* 3.5 37.0 - - + +
148D ALA* 3.9 9.9 - - + -
149D GLN 3.3 9.0 - - - +
150D PRO* 3.4 41.4 - - + +
151D ASN* 3.5 4.0 - - - +
155D THR* 1.3 78.6 - - - +
157D GLN* 1.3 60.6 + - - +
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Residues in contact with GLN 157 (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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106C PHE* 3.5 17.1 - - - +
107C THR 2.8 28.0 + - - +
108C LEU 3.6 9.1 + - - +
119D VAL 3.2 10.3 - - - +
120D TRP* 3.9 13.5 - - + -
122D PHE* 3.7 2.7 - - - -
148D ALA* 3.5 0.7 - - - -
149D GLN* 2.8 48.1 + - + +
151D ASN* 2.9 27.8 + - - +
156D TYR* 1.3 76.1 - - - +
158D THR* 1.3 65.9 + - - +
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Residues in contact with THR 158 (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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118D TYR* 3.9 2.3 - - - +
119D VAL* 2.7 39.8 + - + +
122D PHE* 4.1 2.9 - - + -
127D VAL* 4.0 21.8 - - + -
129D ILE* 3.8 23.2 - - + +
146D LYS* 4.9 10.2 - - - +
147D THR 4.8 4.3 + - - -
148D ALA* 4.2 15.5 + - - -
157D GLN* 1.3 79.1 - - - +
159D LEU* 1.3 77.3 + - - +
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Residues in contact with LEU 159 (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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116D ALA* 5.1 0.9 - - + -
117D CYS 3.2 18.8 - - - +
118D TYR* 4.4 22.9 - - + -
129D ILE* 4.2 5.6 - - - +
142D SER* 4.7 2.1 + - - -
146D LYS* 5.0 12.9 - - + +
158D THR* 1.3 89.0 + - - +
160D SER* 1.3 64.7 + - - +
161D HIS* 3.5 35.9 - - + +
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ALA* 3.4 3.1 - - - +
117D CYS* 2.8 30.5 + - - -
129D ILE* 3.6 32.7 + - - +
131D TRP* 2.9 26.2 + - - -
140D PRO* 4.4 2.6 - - - +
142D SER* 3.9 16.3 + - - -
146D LYS* 5.9 2.8 + - - -
159D LEU* 1.3 77.0 - - - +
161D HIS* 1.3 68.9 + - - +
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Residues in contact with HIS 161 (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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104D THR* 3.9 15.5 - - + +
107D PHE* 4.0 29.3 - + - -
114D MET* 3.6 16.5 - - + +
115D LEU 3.2 13.8 + - - +
116D ALA* 3.9 15.1 - - + +
131D TRP* 3.6 10.6 + - - -
140D PRO* 3.6 4.7 - - - +
141D HIS* 3.2 28.4 + - + +
142D SER* 3.5 11.5 + - - -
159D LEU* 3.5 38.7 - - + +
160D SER* 1.3 82.3 + - - +
162D LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D VAL 4.1 0.2 - - - +
114D MET* 3.5 4.2 - - - -
115D LEU* 3.1 30.2 + - + +
131D TRP* 3.5 48.7 - - + -
132D ARG 5.4 0.4 - - - +
138D VAL* 4.3 16.6 - - + -
139D MET 3.6 23.8 - - - +
140D PRO* 4.2 6.7 - - + -
141D HIS 4.3 2.5 - - - +
161D HIS* 1.3 77.1 - - - +
163D ALA* 1.3 75.1 + - - +
164D LEU* 4.0 9.3 + - + +
172D TYR* 3.9 28.9 - - + -
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Residues in contact with ALA 163 (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 THR* 3.7 27.4 - - + +
111D GLU* 3.8 12.5 - - + +
113D VAL 3.5 7.6 - - - +
114D MET* 3.2 20.0 - - + +
141D HIS* 4.2 8.6 - - + +
162D LEU* 1.3 83.8 - - - +
164D LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 164 (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 GLU* 3.2 12.6 - - - +
112D PRO* 3.4 17.2 - - - +
113D VAL* 3.2 34.2 + - + +
115D LEU* 3.7 37.7 - - + -
162D LEU* 4.1 11.2 - - + +
163D ALA* 1.3 75.8 - - - +
165D THR* 1.3 58.0 + - - +
166D PRO* 3.5 26.9 - - + -
172D TYR* 3.9 40.4 - - + +
189D TRP* 4.5 3.8 - - + -
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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