Contacts of the strand formed by residues 144 - 150 (chain D) in PDB entry 5L5E
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 GLY 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D HIS* 3.5 17.8 - - - -
140D ASP 2.9 26.9 + - - -
141D ALA 4.5 1.2 + - - -
142D ASP 3.7 1.2 - - - -
143D ASP* 1.3 77.4 - - - +
145D TYR* 1.3 59.7 + - - -
146D GLN* 3.0 19.6 + - - +
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Residues in contact with TYR 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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33D ALA* 4.9 5.8 - - + +
34D THR 3.5 22.6 - - - +
35D LYS* 3.2 29.6 - - - -
36D GLU* 3.9 6.0 + - - -
37D GLY* 3.7 20.0 - - - -
38D VAL* 3.7 13.5 - - + -
138D GLY 3.5 3.1 - - - -
139D HIS* 3.6 32.3 - + + -
143D ASP 3.7 0.4 + - - +
144D GLY* 1.3 70.1 - - - -
146D GLN* 1.3 59.5 + - - +
158D ARG* 3.5 16.8 + - - -
214D ILE 3.6 20.2 - - - -
215D THR* 3.7 3.7 - - - -
216D LYS* 2.8 35.3 + - + +
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Residues in contact with GLN 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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33D ALA* 4.9 1.6 - - - -
38D VAL* 3.7 8.3 - - - +
101D VAL* 3.9 12.9 - - + +
102D GLU* 4.2 9.9 + - - +
136D ILE 4.6 0.7 - - - -
137D ALA* 3.4 3.3 - - - -
138D GLY 2.9 33.4 + - - +
140D ASP* 3.0 28.6 + - - +
143D ASP* 3.5 25.9 + - - +
144D GLY 3.0 15.3 - - - +
145D TYR* 1.3 80.1 - - - +
147D LEU* 1.3 60.2 + - - +
148D PHE* 3.4 35.8 - - + -
158D ARG* 3.8 19.3 - - - +
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Residues in contact with LEU 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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31D GLY* 3.3 34.3 - - - +
32D ILE* 4.1 2.2 - - - +
33D ALA* 4.2 9.3 - - + +
38D VAL* 4.2 3.8 - - + -
40D LEU* 3.9 27.8 - - + -
135D LEU* 4.4 11.2 - - + -
136D ILE 3.6 4.3 - - - +
137D ALA* 4.0 7.9 - - + -
146D GLN* 1.3 76.2 - - - +
148D PHE* 1.3 68.9 + - - +
158D ARG* 3.4 7.5 - - - +
159D TYR* 2.8 55.8 + - + +
160D ASN 4.2 2.7 - - - +
161D ALA* 4.0 4.9 - - - -
162D LYS* 3.9 16.8 - - + +
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Residues in contact with PHE 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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101D VAL* 3.7 27.6 - - + -
102D GLU* 3.9 23.1 - - + -
105D THR* 3.7 25.4 - - + +
134D LEU 3.8 0.2 - - - +
135D LEU* 3.4 8.5 - - - +
136D ILE* 2.8 38.7 + - + +
146D GLN* 3.4 37.0 - - + -
147D LEU* 1.3 77.9 - - - +
149D HIS* 1.3 60.1 + - - +
150D ALA 4.0 0.4 - - - -
156D PHE* 3.8 32.1 - + - -
157D TYR 3.4 10.8 - - - -
158D ARG* 3.7 26.7 - - + -
159D TYR* 5.1 0.9 - - - -
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Residues in contact with HIS 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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133D ALA* 3.9 14.5 - - + +
134D LEU 3.5 10.5 - - - -
135D LEU* 4.2 8.7 - - + -
148D PHE* 1.3 71.4 - - - +
150D ALA* 1.3 62.2 + - - +
151D GLU* 3.4 39.4 + - + +
155D THR 3.8 0.7 - - - +
156D PHE* 3.3 23.7 - - - -
157D TYR* 2.9 14.0 + - - +
159D TYR* 3.7 28.0 + - + -
162D LYS* 3.7 24.9 + - + -
164D ILE* 3.4 25.6 - - + +
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Residues in contact with ALA 150 (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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80D MET* 5.5 3.5 - - + +
105D THR* 4.4 4.5 - - + -
108D VAL* 5.0 7.9 - - + -
109D CYS* 3.9 20.9 - - - -
132D VAL 4.6 1.0 - - - +
133D ALA* 3.6 4.9 - - - +
134D LEU* 2.8 41.9 + - + +
136D ILE* 4.1 24.0 - - + -
148D PHE 4.0 1.0 - - - -
149D HIS* 1.3 71.2 - - - +
151D GLU* 1.3 62.0 + - - +
155D THR 4.1 4.5 - - - -
156D PHE* 4.3 0.9 - - - -
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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