Contacts of the strand formed by residues 145 - 151 (chain D) in PDB entry 3SDI
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 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D HIS* 3.3 19.6 - - - -
142D ASP* 2.9 28.7 + - - -
143D ALA 4.5 1.6 + - - -
144D ASP* 1.3 79.1 - - - +
146D TYR* 1.3 58.2 + - - -
147D GLN* 2.9 18.7 - - - +
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Residues in contact with TYR 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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41D ALA* 4.8 5.8 - - + +
42D THR 3.5 23.0 - - - +
43D LYS* 3.7 17.9 - - - -
44D GLU* 4.0 5.9 + - - -
45D GLY* 3.4 38.4 - - - -
46D VAL* 3.6 13.9 - - + -
140D GLY 3.4 4.3 - - - -
141D HIS* 3.9 26.2 - + + -
144D ASP 3.7 0.6 + - - +
145D GLY* 1.3 70.6 - - - -
147D GLN* 1.3 64.4 + - - +
159D ARG* 3.4 14.6 + - - -
215D ILE* 3.5 15.0 - - + -
216D THR* 3.7 4.0 - - - -
217D LYS* 2.9 35.5 + - + +
218D GLN 4.9 0.2 + - - -
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Residues in contact with GLN 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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41D ALA* 4.7 2.0 - - - -
46D VAL* 4.0 6.0 - - - +
109D VAL* 3.7 11.3 - - + +
110D GLU* 4.4 9.9 - - - +
138D ILE 3.8 1.2 - - - +
139D ALA* 3.2 8.3 - - - +
140D GLY 2.9 32.0 + - - +
142D ASP* 3.3 21.9 + - - +
144D ASP* 3.4 30.5 - - - +
145D GLY 2.9 18.3 - - - +
146D TYR* 1.3 79.7 - - - +
148D LEU* 1.3 60.5 + - - +
149D PHE* 3.8 31.8 - - + -
159D ARG* 3.6 27.3 - - - +
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Residues in contact with LEU 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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39D GLY* 3.2 33.9 - - - +
40D ILE* 4.1 1.8 - - - +
41D ALA* 4.2 9.7 - - + +
46D VAL* 4.2 2.9 - - + -
48D LEU* 3.8 29.4 - - + -
137D LEU* 4.4 14.4 - - + -
138D ILE 3.6 2.7 - - - +
139D ALA* 4.0 11.2 - - + -
147D GLN* 1.3 75.9 - - - +
149D PHE* 1.3 67.6 + - - +
159D ARG* 3.2 12.8 - - - +
160D TYR* 3.0 49.5 + - + +
161D ASN 4.3 2.5 - - - +
162D ALA* 3.9 11.9 - - - +
163D LYS* 4.0 8.5 - - + +
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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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109D VAL* 4.1 12.1 - - + -
110D GLU* 3.7 32.8 - - + -
113D THR* 3.7 30.5 - - + +
136D LEU 3.5 0.9 - - - +
137D LEU* 3.3 10.5 - - - +
138D ILE* 2.8 36.4 + - + +
147D GLN* 3.8 33.4 - - + -
148D LEU* 1.3 76.9 - - - +
150D HIS* 1.3 59.4 + - - +
151D ALA 3.9 0.4 - - - -
157D PHE* 3.5 34.3 - + - -
158D TYR 3.2 12.6 - - - -
159D ARG* 3.7 27.4 - - + -
160D TYR* 5.2 1.1 - - - -
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Residues in contact with HIS 150 (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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31D ILE* 5.9 0.4 - - - +
135D ALA* 3.7 12.7 - - + +
136D LEU 3.4 9.4 - - - -
137D LEU* 4.4 8.3 - - + -
149D PHE* 1.3 72.9 - - - +
151D ALA* 1.3 67.1 + - - +
152D GLU* 3.2 41.2 + - + +
156D THR 3.7 0.9 - - - +
157D PHE* 3.0 27.1 - - - -
158D TYR* 2.8 15.1 + - + +
160D TYR* 3.6 26.2 + - + -
163D LYS* 3.7 27.1 + - + -
165D ILE* 3.4 26.1 - - + +
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Residues in contact with ALA 151 (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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88D MET* 5.7 4.4 - - + +
113D THR* 4.4 5.2 - - + -
116D VAL* 4.8 5.8 - - + -
117D CYS* 4.2 16.6 - - - -
134D VAL 4.6 0.5 - - - +
135D ALA* 3.4 7.1 - - - +
136D LEU* 2.8 57.5 + - + +
138D ILE* 4.3 17.3 - - + -
149D PHE 3.9 0.6 - - - -
150D HIS* 1.3 73.7 - - - +
152D GLU* 1.3 60.8 + - - +
156D THR 4.0 3.8 - - - -
157D PHE* 4.3 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