Contacts of the strand formed by residues 133 - 141 (chain D) in PDB entry 5FLZ
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 PHE 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D GLU* 3.2 16.6 - - + -
6D ILE* 3.5 42.8 - - + -
65D ARG* 4.4 0.2 - - - -
127D ILE* 5.2 13.0 - - + -
130D THR* 3.6 26.3 - - + +
132D ASN* 1.4 81.9 + - - +
134D GLU* 1.4 64.6 + - - +
135D GLY* 2.9 35.9 - - - -
136D PHE* 3.7 30.3 - + - -
162D TYR* 6.3 0.9 - + + -
165D LYS* 3.7 42.3 + - + +
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Residues in contact with GLU 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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2D GLY 5.2 0.7 - - - +
3D GLY* 3.4 25.8 - - - +
4D GLU 2.7 17.3 + - - +
5D ILE* 4.4 12.6 - - + -
132D ASN* 3.5 4.6 + - - +
133D PHE* 1.4 73.9 - - - +
135D GLY* 1.4 56.8 - - - +
165D LYS* 4.0 4.1 - - - +
166D ILE* 3.5 46.6 + - + +
242D ILE* 5.6 2.2 - - + -
252D MET* 5.9 4.7 - - + +
253D SER* 3.0 41.7 + - - -
256D TYR* 5.4 1.0 - - - +
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Residues in contact with GLY 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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4D GLU 3.2 1.8 + - - -
5D ILE* 3.2 18.3 - - - +
133D PHE* 2.9 34.9 - - - -
134D GLU* 1.4 82.9 - - - +
136D PHE* 1.3 59.7 + - - -
165D LYS* 4.3 0.9 - - - -
166D ILE* 3.2 18.6 - - - -
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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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5D ILE* 4.3 0.4 - - - -
6D ILE* 3.4 12.3 - - + +
8D LEU* 3.8 26.9 - - + -
123D ILE* 4.9 5.8 - - + -
127D ILE* 4.4 22.2 - - + -
133D PHE* 3.7 29.6 - + - -
135D GLY* 1.3 75.8 - - - -
137D GLN* 1.4 66.4 + - - +
138D LEU* 6.2 0.7 - - + -
155D LEU* 6.1 2.5 - - + -
158D LEU* 3.7 38.1 - - + -
162D TYR* 4.6 15.3 - + + -
165D LYS* 4.8 8.3 - - + -
166D ILE* 3.0 20.1 + - - +
167D LEU* 4.1 21.5 - - + -
168D THR* 3.0 27.7 + - - +
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Residues in contact with GLN 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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5D ILE* 3.6 35.7 - - + +
6D ILE 2.9 8.9 + - - +
7D THR* 3.2 12.3 - - + +
8D LEU* 2.8 32.6 + - - +
53D PHE* 3.6 19.4 - - - -
136D PHE* 1.4 77.5 - - - +
138D LEU* 1.3 51.2 + - - +
139D LEU* 3.7 8.9 - - + +
168D THR* 3.3 9.4 - - - -
170D TYR* 3.4 38.2 - - + -
235D ILE* 4.4 16.4 - - - +
239D THR* 4.1 9.2 - - - +
252D MET* 6.1 1.0 - - - +
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Residues in contact with LEU 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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8D LEU* 3.4 38.1 - - + +
10D ALA* 3.8 19.7 - - + -
136D PHE* 6.2 0.7 - - + -
137D GLN* 1.3 70.3 - - - +
139D LEU* 1.3 67.9 + - - +
140D HIS* 4.1 14.6 - - + +
151D GLY* 3.9 30.5 - - - +
154D LEU* 5.6 2.0 - - + -
155D LEU* 4.1 23.3 - - + -
168D THR 3.0 9.5 + - - +
169D THR* 3.1 22.7 + - - +
170D TYR* 2.8 32.7 + - - +
194D LEU* 5.4 0.9 - - + -
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Residues in contact with LEU 139 (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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7D THR* 4.0 21.8 - - + -
8D LEU 2.8 19.2 + - - +
9D GLN* 4.0 15.5 - - + +
10D ALA 3.2 21.8 + - - +
14D GLY* 4.0 19.7 - - - +
17D VAL* 5.1 6.7 - - + -
18D GLY 6.0 0.2 - - - +
21D LEU* 5.1 5.6 - - + -
137D GLN* 3.7 20.0 - - + +
138D LEU* 1.3 73.6 - - - +
140D HIS* 1.4 65.7 - - - +
170D TYR* 3.6 22.9 - - + +
235D ILE* 3.6 35.4 - - + -
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Residues in contact with HIS 140 (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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10D ALA* 3.9 22.2 - - + +
13D CYS* 5.4 3.8 - - - -
14D GLY* 4.9 4.0 - - - +
138D LEU* 4.1 15.4 - - + +
139D LEU* 1.4 74.7 - - - +
141D SER* 1.3 59.8 + - - +
142D VAL* 4.1 9.6 - - + -
147D GLY 2.9 26.4 + - - +
148D SER* 5.1 6.1 - - - -
151D GLY* 4.8 3.8 - - - -
152D SER* 5.4 0.2 - - - -
169D THR* 3.2 23.0 + - - -
170D TYR 3.2 11.4 + - - +
171D SER* 3.0 26.5 + - - -
172D VAL* 3.1 25.7 + - - +
190D ALA* 6.1 0.7 - - + -
194D LEU* 3.8 30.7 - - + +
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Residues in contact with SER 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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10D ALA 5.0 0.6 + - - -
11D GLY* 6.1 0.4 - - - -
13D CYS* 4.3 24.7 - - - +
140D HIS* 1.3 72.5 + - - +
142D VAL* 1.3 74.7 + - - +
143D ALA 5.6 0.2 - - - -
144D GLY* 4.4 5.3 + - - -
147D GLY* 3.0 34.2 - - - +
148D SER 3.3 0.3 + - - -
172D VAL* 3.8 23.8 + - - +
206D ASN* 5.4 1.6 + - - -
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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