Contacts of the strand formed by residues 145 - 151 (chain B) in PDB entry 4DEQ
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 ARG 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ARG 3.5 10.3 - - - +
33B SER 3.6 6.1 - - - -
34B ARG 3.4 23.6 - - - +
35B LEU* 4.6 1.1 - - - -
36B ASN* 3.7 5.9 - - - +
37B TYR* 3.2 30.0 + - - +
40B ASN 3.8 17.1 + - - -
41B GLY* 4.1 3.8 - - - -
68B THR* 3.6 2.3 - - - +
69B GLN* 2.7 72.9 + - + +
70B GLY 2.8 17.4 + - - +
71B ALA* 4.0 6.2 - - - +
72B ILE* 5.1 1.6 - - - +
114B PRO 3.0 26.9 + - - -
115B THR* 4.4 3.0 + - - +
144B MET* 1.3 80.7 - - - +
146B PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 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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8B MET* 3.3 41.5 - - + +
18B ILE* 5.4 1.1 - - + -
33B SER* 3.1 38.7 + - - -
35B LEU* 3.4 15.4 + - - +
53B ILE* 3.9 31.4 - - + -
54B GLN* 4.7 6.1 - - - -
55B VAL* 4.1 16.6 - - + -
66B VAL* 5.6 1.3 - - + -
67B GLY 3.1 15.7 - - - +
68B THR* 4.6 0.2 - - - -
131B VAL* 5.1 2.2 - - + -
133B ILE* 3.9 30.7 - - + -
144B MET* 4.6 7.6 - - + -
145B ARG* 1.3 77.9 - - - +
147B GLU* 1.3 67.7 + - - +
148B VAL* 4.0 21.8 - - + -
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Residues in contact with GLU 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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5B ALA* 3.7 15.7 - - + +
6B LEU 3.4 6.4 + - - -
7B GLY 3.3 12.4 + - - -
8B MET* 3.1 21.7 + - - -
9B GLU* 2.8 41.0 + - - +
10B SER 4.6 0.5 + - - -
35B LEU* 3.8 22.6 - - + +
66B VAL* 3.6 4.9 - - - +
67B GLY 3.0 29.0 + - - +
146B PHE* 1.3 76.5 - - - +
148B VAL* 1.3 72.7 + - - +
149B TYR* 3.7 30.5 - - + +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA* 3.5 2.6 - - - -
6B LEU* 2.9 48.6 + - + +
8B MET* 4.2 5.7 - - + +
13B ILE* 5.6 0.7 - - + -
55B VAL* 4.0 18.8 - - + -
57B LEU* 4.7 3.6 - - + -
63B VAL* 3.3 31.9 - - + -
65B ALA 3.8 5.2 - - - +
66B VAL* 4.5 6.3 - - + -
131B VAL* 4.7 13.7 - - + -
146B PHE* 4.0 22.0 - - + -
147B GLU* 1.3 86.0 + - - +
149B TYR* 1.3 65.8 + - - +
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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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3B MET* 3.8 36.8 - - + -
4B GLU 3.3 1.8 - - - -
5B ALA* 3.9 14.8 - - + -
6B LEU* 4.0 3.1 - - - -
35B LEU* 4.2 5.9 - - - +
63B VAL* 3.6 7.8 - - - +
64B THR* 3.1 24.9 + - - +
65B ALA* 3.0 27.1 + - + +
66B VAL 4.0 1.3 - - - -
67B GLY* 3.5 31.4 - - - -
117B VAL* 4.1 18.5 - - - +
119B VAL* 4.2 16.2 - - + +
147B GLU* 3.7 27.9 - - + +
148B VAL* 1.3 76.4 - - - +
150B GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 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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2B CYS* 3.4 19.4 - - - -
4B GLU* 2.8 40.1 + - - +
6B LEU* 4.0 5.3 - - - +
62B PHE 3.2 12.6 - - - -
63B VAL* 4.3 0.2 - - - -
64B THR* 3.8 2.9 + - - -
149B TYR* 1.3 77.8 - - - +
151B CYS* 1.3 66.0 + - - +
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Residues in contact with CYS 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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1B LYS* 5.5 4.5 - - - +
2B CYS* 2.0 49.4 - - + -
4B GLU* 5.0 8.5 - - + -
6B LEU* 4.0 7.9 - - - +
61B ARG* 3.9 11.1 - - - +
62B PHE* 3.0 33.6 + - - +
150B GLY* 1.3 71.9 - - - +
152B LYS* 1.3 74.9 + - - +
153B ILE 3.7 0.2 + - - -
155B ASP 4.2 10.3 - - - +
156B TYR* 3.7 15.7 - - - -
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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