Contacts of the strand formed by residues 128 - 132 (chain B) in PDB entry 5N4D
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B TRP* 3.8 12.1 - - - -
110B TYR* 3.7 10.1 - - - -
111B ARG 3.2 11.4 - - - -
113B LYS* 3.7 3.6 - - - +
124B ASP 2.9 12.6 + - - +
125B ASP* 3.3 18.9 - - - +
126B ASN 3.6 0.4 - - - -
127B VAL* 1.3 78.7 - - - +
129B ASP* 1.3 70.1 + - - +
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Residues in contact with ASP 129 (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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110B TYR* 3.3 8.6 - - - -
111B ARG* 2.9 44.3 + - + +
113B LYS* 2.6 47.3 + - - +
128B GLY* 1.3 73.2 - - - +
130B VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 130 (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 VAL* 3.8 20.2 - - + -
109B LEU 4.0 3.6 - - - -
110B TYR* 3.7 31.3 - - + +
111B ARG* 5.5 0.4 - - - +
125B ASP* 5.5 0.4 - - - +
129B ASP* 1.3 77.8 - - - +
131B PHE* 1.3 61.9 + - - +
132B PHE 4.0 7.6 - - - +
133B ASP* 4.2 6.1 - - + +
179B PRO* 3.8 13.5 - - - +
180B LEU 4.1 4.3 - - - +
181B SER* 4.0 27.4 - - - -
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Residues in contact with PHE 131 (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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96B TYR* 4.2 7.4 - + + -
109B LEU* 2.8 29.2 + - + +
110B TYR 4.5 0.9 - - - -
111B ARG* 4.1 22.4 - - + +
129B ASP 3.3 1.8 + - - -
130B VAL* 1.3 76.4 - - - +
132B PHE* 1.3 65.5 + - + +
150B PHE* 3.6 27.4 - + - -
157B PHE* 3.7 35.7 - + + -
174B ARG* 4.2 5.6 - - + -
175B SER 3.7 9.0 - - - -
176B THR* 3.4 38.1 - - - -
178B SER 3.9 10.1 - - - -
179B PRO* 3.1 16.1 - - + +
180B LEU 2.8 24.9 + - - -
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Residues in contact with PHE 132 (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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98B PHE* 5.8 0.2 - + - -
108B VAL* 4.1 2.2 - - - -
109B LEU* 2.8 41.3 + - + -
130B VAL 3.9 0.2 - - - -
131B PHE* 1.3 95.9 - - + +
133B ASP* 1.4 56.3 + - - +
134B PRO* 3.3 28.5 - - + +
137B LEU* 4.1 7.6 - - + -
145B MET* 3.4 29.2 - - + -
157B PHE* 3.5 19.3 - + + -
159B TYR* 3.5 45.1 - + - -
174B ARG* 3.8 11.0 - - - -
180B LEU* 3.5 36.1 - - + -
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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