Contacts of the strand formed by residues 145 - 151 (chain B) in PDB entry 5DSV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ARG* 6.1 0.2 - - - -
139B SER* 3.9 1.6 + - - +
140B TYR* 3.5 12.5 - - - -
141B SER 2.9 34.9 + - - +
142B VAL 3.6 6.1 + - - -
143B ASN 3.6 1.8 - - - -
144B ASP* 1.3 82.0 - - - +
146B ALA* 1.3 62.6 + - - -
147B GLN* 4.0 3.6 - - - +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 3.1 40.7 + - + +
41B CYS 4.3 3.1 - - - +
42B LYS 4.7 4.5 + - - +
44B GLY* 3.5 42.4 - - - +
139B SER 3.6 5.2 - - - -
140B TYR* 3.5 8.2 - - + -
144B ASP 4.5 1.7 - - - +
145B GLY* 1.3 69.3 - - - -
147B GLN* 1.3 68.7 + - - +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 4.5 4.7 - - - +
45B VAL* 3.5 6.8 - - - +
107B PRO 5.0 0.2 - - - -
108B LEU* 3.4 38.1 - - + +
109B LYS* 3.6 36.3 - - - +
138B GLY* 3.3 4.7 - - - -
139B SER* 2.9 38.0 + - - +
144B ASP* 3.8 35.5 + - - +
145B GLY 4.0 8.3 - - - +
146B ALA* 1.3 82.4 - - - +
148B LEU* 1.3 61.2 + - - +
149B TYR* 4.0 10.2 + - + -
59C GLU* 5.4 3.8 - - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLY 3.7 13.5 - - - +
39B ILE* 3.9 2.7 - - - +
40B ARG* 4.6 7.4 - - + +
45B VAL* 3.9 14.1 - - + -
47B PHE* 3.5 37.9 - - + -
136B MET* 4.2 13.9 - - + -
137B LEU 3.4 7.0 - - - +
147B GLN* 1.3 74.4 - - - +
149B TYR* 1.3 67.6 + - - +
159B GLY* 3.5 4.2 - - - -
160B TYR* 2.9 53.7 + - + +
161B TRP 4.0 2.7 - - - +
162B GLY* 3.7 30.3 - - - -
163B CYS 4.1 2.7 - - - +
59C GLU* 5.5 0.2 - - - +
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Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.7 20.9 - - + -
109B LYS* 3.4 47.4 - - - +
112B ALA* 3.9 17.7 - - + -
113B ASP* 6.6 0.2 - - - -
136B MET* 2.9 8.9 - - - +
137B LEU* 2.8 41.7 + - + +
147B GLN* 4.0 16.8 + - + -
148B LEU* 1.3 78.6 - - - +
150B MET* 1.3 59.7 + - - +
151B ILE* 5.1 3.1 - - + -
157B SER* 3.6 18.2 - - - +
158B TYR 3.1 18.2 - - - -
159B GLY* 3.4 21.8 - - - -
160B TYR* 4.9 0.4 - - - +
59C GLU* 5.0 7.0 + - - -
61C GLY 5.7 1.0 + - - -
62C SER* 5.3 0.9 - - - -
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B SER* 4.4 1.6 - - - -
135B PHE 3.3 11.2 - - - +
136B MET* 4.0 20.6 - - + -
149B TYR* 1.3 75.8 - - - +
151B ILE* 1.3 77.3 + - - +
152B ASP* 4.0 19.1 - - + +
156B VAL 3.3 3.6 - - - +
157B SER* 3.7 0.3 - - - -
158B TYR* 2.8 56.0 + - + -
160B TYR* 3.9 26.9 - - + +
163B CYS* 4.6 6.3 - - - -
165B ILE* 4.1 24.2 - - + -
169B ARG* 5.7 4.5 - - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA* 4.0 34.3 - - + +
115B VAL* 5.2 0.4 - - + -
116B ALA* 4.0 9.6 - - + +
119B VAL* 4.1 16.8 - - + -
134B SER* 3.2 5.2 - - - -
135B PHE* 2.8 75.6 + - + +
137B LEU* 4.4 5.4 - - + -
149B TYR* 5.1 0.2 - - + -
150B MET* 1.3 85.7 - - - +
152B ASP* 1.3 75.2 - - - +
155B GLY* 4.4 6.5 - - - -
156B VAL 3.3 11.7 - - - +
157B SER* 3.9 12.6 - - - +
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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