Contacts of the strand formed by residues 133 - 137 (chain R) in PDB entry 3J0S
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 HIS 133 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E ASP* 4.9 16.0 + - - -
98R ASP* 4.1 35.0 + - + +
99R LEU 3.9 2.1 + - - +
100R VAL* 3.5 32.7 - - + -
101R PHE 3.5 3.3 + - - -
131R ILE* 4.1 8.9 - - - +
132R LYS* 1.3 102.8 + - + +
134R GLU* 1.3 63.1 + - - +
152R LYS* 4.1 28.1 + - + +
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Residues in contact with GLU 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G THR* 3.9 12.1 + - - -
166G TYR* 5.2 2.6 - - - -
167G GLU* 3.7 15.6 - - - +
100R VAL* 4.8 1.6 - - - -
101R PHE 3.6 12.8 - - - +
103R PHE* 3.2 16.7 - - + -
121R LYS* 3.0 39.2 + - - -
125R LYS* 5.6 2.0 - - - +
131R ILE* 5.0 10.5 - - + +
133R HIS* 1.3 79.6 - - - +
135R LEU* 1.3 71.2 + - - +
136R GLN* 4.4 3.7 + - + -
152R LYS* 6.2 0.2 - - - +
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Residues in contact with LEU 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R TYR* 4.9 6.1 - - + +
100R VAL* 4.9 3.1 - - + +
101R PHE 3.3 4.7 + - - +
102R ILE* 3.5 32.7 - - + +
103R PHE* 3.0 24.9 + - - +
134R GLU* 1.3 82.3 - - - +
136R GLN* 1.3 61.9 + - - +
148R THR* 3.3 37.9 - - + +
149R LEU* 3.9 25.1 - - + +
151R GLU* 5.6 3.1 - - - +
152R LYS* 3.2 36.8 - - + +
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Residues in contact with GLN 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G GLY 2.9 23.0 + - - -
147G ARG* 3.0 46.9 + - - +
148G THR 4.0 1.2 + - - -
149G THR 5.2 0.2 + - - -
296G ASN* 5.9 0.7 + - - -
103R PHE* 3.3 42.6 - - + +
105R ALA* 4.6 4.2 - - + +
121R LYS* 3.9 20.7 + - - +
134R GLU* 4.2 3.8 - - + +
135R LEU* 1.3 77.5 - - - +
137R ALA* 1.3 69.7 + - - +
142R GLU* 4.1 5.4 - - - +
148R THR* 5.6 6.2 - - - +
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Residues in contact with ALA 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ARG* 4.7 2.0 - - - +
102R ILE* 6.1 0.2 - - - +
103R PHE 3.4 4.5 + - - +
104R TRP* 3.1 20.5 - - - -
105R ALA 3.6 11.8 + - - -
136R GLN* 1.3 80.5 - - - +
138R ASN* 1.3 59.5 + - - +
139R CYS 3.4 3.4 - - - +
142R GLU* 3.4 36.8 - - + +
143R VAL* 3.5 25.5 - - + +
148R THR* 6.0 2.5 - - + -
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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