Contacts of the strand formed by residues 127 - 133 (chain B) in PDB entry 4B92
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 ASP 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B THR 3.7 8.2 + - - +
96B MET* 3.5 6.8 - - + -
97B ILE 3.4 9.7 + - - -
126B CYS* 1.3 93.5 - - - +
128B TYR* 1.3 59.1 + - - +
390B ARG* 4.1 2.6 + - - -
391B LYS* 2.7 33.3 + - - +
399B ASP* 4.4 0.7 - - - +
401B ASP* 4.8 1.1 - - - -
441B SER* 4.5 2.0 + - - -
442B ARG* 2.9 45.6 + - - +
460B LYS 3.2 16.6 + - - +
462B CYS* 3.5 20.7 - - - -
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Residues in contact with TYR 128 (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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82B PHE* 4.7 1.6 - + - -
96B MET* 3.8 7.8 - - - +
97B ILE* 3.1 32.3 - - + +
117B ARG* 3.2 16.3 + - - -
120B ALA* 3.7 20.8 - - + +
121B ASP* 2.3 38.9 + - - -
124B VAL* 3.8 32.5 - - + -
126B CYS 4.3 1.6 - - - +
127B ASP* 1.3 75.7 - - - +
129B ALA* 1.3 72.4 + - - +
130B LEU* 4.0 20.0 - - + -
460B LYS 3.2 6.0 + - - -
461B PHE* 3.3 40.4 - + - -
462B CYS* 2.9 27.5 + - - +
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Residues in contact with ALA 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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96B MET* 4.0 6.2 - - + +
97B ILE 3.2 5.1 + - - +
98B ILE* 3.2 23.1 - - + -
99B GLY 2.6 30.2 + - - -
128B TYR* 1.3 79.9 - - - +
130B LEU* 1.3 63.2 + - - +
153B GLY 5.4 0.2 - - - +
461B PHE* 4.1 9.4 - - + -
462B CYS 4.0 4.9 - - - +
464B LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 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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82B PHE* 4.6 3.4 - - + -
98B ILE* 4.0 3.6 - - - -
99B GLY* 3.3 23.3 - - - +
101B VAL* 4.1 9.9 - - + -
113B TYR* 3.8 34.3 - - + +
116B CYS* 3.7 28.5 - - - -
117B ARG* 3.9 22.9 - - + +
128B TYR* 4.0 18.2 - - + -
129B ALA* 1.3 87.5 - - - +
131B HIS* 1.3 69.6 + - - +
132B VAL* 4.1 1.7 + - + -
153B GLY 5.1 1.1 + - - +
154B VAL* 4.1 20.7 - - + +
156B SER* 4.3 3.6 + - - +
461B PHE* 4.1 7.7 - - + -
464B LEU* 5.1 5.2 - - - +
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Residues in contact with HIS 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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65B THR* 2.7 30.4 + - - -
98B ILE* 3.2 27.9 - - + +
99B GLY 2.7 14.9 + - - +
100B HIS* 3.6 34.1 - + + +
101B VAL* 2.9 32.7 + - - +
130B LEU* 1.3 72.9 - - - +
132B VAL* 1.3 60.6 + - - +
156B SER* 2.4 38.2 + - - +
158B GLN* 4.5 10.5 - - + -
189B ARG* 3.5 25.4 + - - -
385B LEU* 4.8 8.5 - - + -
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Residues in contact with VAL 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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101B VAL* 3.8 14.8 - - + -
103B PRO* 4.6 1.1 - - + -
109B LEU* 3.9 40.4 - - + +
113B TYR* 4.3 16.4 - - + -
130B LEU 4.1 1.1 - - - +
131B HIS* 1.3 76.3 - - - +
133B GLY* 1.3 69.3 + - - +
148B LEU* 4.1 12.6 - - + -
154B VAL* 3.9 26.5 - - + -
156B SER 3.4 6.1 + - - -
157B PHE* 3.1 22.7 - - + -
158B GLN* 2.9 19.6 + - - -
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Residues in contact with GLY 133 (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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101B VAL 2.7 21.7 + - - -
102B LEU* 4.4 9.0 - - - -
103B PRO* 3.0 30.2 - - - +
109B LEU* 4.0 2.8 - - - +
132B VAL* 1.3 77.1 - - - +
134B ILE* 1.3 61.7 + - - -
135B THR* 3.5 2.9 + - - -
158B GLN* 3.2 18.8 - - - +
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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