Contacts of the strand formed by residues 151 - 155 (chain B) in PDB entry 4EUT
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 SER 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 2.7 28.7 + - - -
114B ILE* 3.4 24.0 - - - +
117B ARG* 4.0 6.9 + - - -
143B ARG* 2.7 38.2 + - - +
144B VAL 3.3 7.0 - - - -
145B ILE* 4.5 2.0 - - - +
149B GLY 4.1 1.2 + - - -
150B GLN* 1.3 77.3 + - - +
152B VAL* 1.3 61.5 + - - +
153B TYR* 3.7 15.9 - - - -
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 3.7 29.8 - - + +
66B ASN* 3.8 10.3 - - - +
117B ARG* 5.4 4.3 - - - +
118B ASP* 3.5 6.5 - - - +
142B MET 3.6 1.4 - - - +
143B ARG* 3.6 1.2 - - - -
144B VAL* 2.6 50.5 + - + +
146B GLY* 4.1 18.4 - - - -
148B ASP* 5.9 1.1 - - - +
150B GLN 4.2 1.1 - - - +
151B SER* 1.3 78.8 - - - +
153B TYR* 1.3 65.4 + - - +
154B LYS* 4.1 9.4 - - - +
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Residues in contact with TYR 153 (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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66B ASN* 2.8 32.8 + - - +
94B LEU* 4.2 25.8 - - + +
97B VAL* 4.1 9.2 - - - +
111B GLU* 2.6 34.1 + - - +
114B ILE* 3.7 21.8 - - + -
115B VAL* 3.9 27.1 - - + -
118B ASP* 2.8 27.1 + - + +
119B VAL* 5.2 2.2 - - + +
141B ILE* 3.9 24.7 - - + -
142B MET 3.3 14.6 - - - +
143B ARG* 3.6 30.0 + - + -
151B SER* 3.7 10.1 - - - -
152B VAL* 1.3 73.2 - - - +
154B LYS* 1.3 61.9 + - - +
155B LEU* 6.3 0.2 - - - -
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Residues in contact with LYS 154 (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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64B HIS 4.9 1.2 + - - -
65B LYS* 2.8 42.0 + - - +
66B ASN 3.1 7.2 - - - -
67B ILE 4.2 1.7 + - - +
68B VAL* 3.6 24.2 - - + +
87B GLU* 3.4 35.1 + - - +
89B CYS* 4.6 0.2 - - - -
141B ILE* 3.4 1.3 - - - +
142B MET* 2.6 40.4 + - - +
144B VAL* 3.6 35.9 - - + -
152B VAL* 4.1 10.4 - - + +
153B TYR* 1.3 76.7 - - - +
155B LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 155 (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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66B ASN 2.7 16.6 + - - +
67B ILE* 3.8 14.8 - - + -
68B VAL* 3.0 21.8 + - - +
118B ASP 5.6 0.2 - - - +
119B VAL* 4.7 17.7 - - + +
122B GLY* 4.1 29.4 - - - -
123B MET* 4.2 3.8 - - + +
126B LEU* 4.2 15.9 - - + -
133B HIS* 5.1 4.3 - - + -
136B ILE* 4.7 21.5 - - + -
140B ASN* 3.7 2.9 - - - +
141B ILE* 3.8 31.0 - - + -
154B LYS* 1.3 72.1 - - - +
156B THR* 1.3 62.9 + - - +
158B PHE* 3.8 13.3 - - + -
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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