Contacts of the strand formed by residues 130 - 135 (chain B) in PDB entry 1JHH
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 LEU 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU* 4.0 23.8 - - + -
98B TYR* 4.0 30.7 - - + +
112B LEU* 4.4 18.6 - - + -
113B LEU 3.5 1.6 - - - +
114B ARG* 3.4 39.5 - - - +
128B GLY 4.7 1.8 - - - +
129B ASP* 1.3 73.0 - - - +
131B LEU* 1.3 60.4 + - - +
132B ALA 3.7 0.7 + - - -
195B VAL* 3.3 6.9 - - - +
196B ILE* 2.8 58.0 + - + +
198B ASN* 4.2 18.2 - - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 4.5 4.3 - - + -
112B LEU* 3.3 4.4 - - - -
113B LEU* 2.7 39.3 + - + +
115B VAL* 3.8 11.0 - - + -
125B ILE* 4.0 28.7 - - + -
129B ASP 3.8 0.8 + - - -
130B LEU* 1.3 71.9 - - - +
132B ALA* 1.3 66.1 + - - +
133B VAL* 3.6 7.8 + - + +
146B VAL* 3.8 18.6 - - + -
155B VAL* 3.4 35.9 - - + -
192B ALA* 3.9 19.7 - - + -
194B GLY 3.7 13.9 - - - +
195B VAL* 4.1 7.2 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 4.2 15.3 - - + -
109B ALA* 4.0 17.5 - - + -
111B PHE 3.7 0.4 - - - -
112B LEU* 3.7 20.6 - - + +
130B LEU 3.7 2.6 + - - -
131B LEU* 1.3 71.9 - - - +
133B VAL* 1.3 59.9 + - - +
192B ALA* 3.6 4.9 - - - -
193B VAL* 3.0 29.3 + - + -
194B GLY* 2.8 28.7 + - - +
195B VAL* 5.2 0.4 - - - -
196B ILE* 5.7 0.4 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA* 4.2 3.7 - - - +
110B ASP* 2.7 32.6 + - - +
111B PHE* 2.8 52.9 + - + +
113B LEU* 4.4 5.2 - - + -
131B LEU* 3.6 19.5 - - + +
132B ALA* 1.3 80.5 - - - +
134B HIS* 1.3 59.3 + - - +
146B VAL* 3.9 24.0 - - + -
190B GLY* 3.8 23.8 - - - +
191B LEU 3.4 11.2 - - - +
192B ALA* 5.0 0.4 - - - -
193B VAL* 4.4 0.7 - - - -
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Residues in contact with HIS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 3.5 30.9 - - + +
108B ASN* 2.6 31.2 + - + +
110B ASP* 3.3 15.8 + - - -
133B VAL* 1.3 73.9 - - - +
135B LYS* 1.3 73.7 + - - +
136B THR* 3.3 19.1 + - + +
190B GLY* 3.2 1.0 - - - -
191B LEU* 2.8 37.5 + - + +
193B VAL* 3.9 21.0 - - + +
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Residues in contact with LYS 135 (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 ASP* 2.7 28.3 + - + +
111B PHE* 4.4 14.8 - - + -
133B VAL* 4.0 1.8 + - - +
134B HIS* 1.3 81.4 + - - +
136B THR* 1.3 64.2 + - - +
189B GLU 3.9 15.7 - - - +
190B GLY* 4.4 0.2 - - - -
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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