Contacts of the helix formed by residues 98 - 103 (chain D) in PDB entry 1JLH
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 98 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D MET 3.3 25.4 - - - +
84D PHE 4.3 1.8 - - - +
86D GLY* 4.0 9.2 - - - -
96D ALA* 4.3 7.0 - - + -
97D VAL* 1.3 76.3 - - - +
99D HIS* 1.3 63.0 + - - +
100D VAL* 3.0 18.2 - - + +
101D ALA* 3.2 13.8 + - + +
102D LEU 3.7 1.4 + - - -
110D ILE* 3.7 29.8 - - + -
112D VAL* 3.3 34.1 - - + -
117D VAL* 4.5 4.7 - - + -
268D TRP* 3.0 50.1 + - + +
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Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D MET* 4.2 12.4 - - + +
97D VAL* 3.8 26.6 + - + +
98D LEU* 1.3 76.3 - - - +
100D VAL* 1.3 69.6 + - + +
102D LEU* 3.2 29.4 + - + +
103D ARG* 3.4 25.0 + - - +
268D TRP 4.2 4.6 + - - +
269D VAL* 5.4 1.8 - - + -
270D GLY 5.5 1.6 - - - -
273D TYR* 3.5 64.4 - + + +
494D GLU* 3.7 22.6 + - + -
495D HIS* 4.7 6.3 - + - -
498D PHE* 6.3 0.9 - - + -
509D PHE* 3.9 7.9 - + - -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D MET* 4.6 10.3 - - + -
84D PHE* 4.0 35.7 - - + -
98D LEU* 4.1 22.7 - - + -
99D HIS* 1.3 81.5 - - - +
101D ALA* 1.3 67.7 + - - +
103D ARG* 3.3 18.2 + - - +
104D ASN* 3.1 20.5 + - - +
110D ILE* 4.9 5.8 - - + -
300D HIS* 5.1 0.3 + - - -
303D ASP* 3.8 28.9 - - + +
495D HIS* 3.8 16.8 - - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.2 26.6 + - + +
100D VAL* 1.3 82.7 - - - +
102D LEU* 1.3 63.0 + - - +
104D ASN* 3.1 9.5 + - - -
110D ILE* 3.7 27.1 - - + -
117D VAL* 4.1 23.6 - - + -
118D MET* 3.3 21.0 - - - +
121D VAL* 3.9 3.6 - - - +
268D TRP* 4.3 1.6 - - + -
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU 3.9 6.5 - - - +
99D HIS* 3.2 27.1 - - - +
100D VAL 3.2 0.2 - - - -
101D ALA* 1.3 78.9 - - - +
103D ARG* 1.3 57.4 + - - +
104D ASN 3.9 0.2 + - - -
105D ARG* 5.4 0.3 + - - -
118D MET* 5.5 0.2 - - - +
121D VAL* 3.8 20.9 - - + +
125D LEU* 4.2 5.7 - - - +
266D TRP* 3.9 19.3 - - + -
268D TRP* 4.0 4.3 - - + -
269D VAL* 3.8 30.7 - - + -
273D TYR 4.0 8.3 - - - +
276D TRP* 3.9 18.2 - - + +
277D SER* 3.6 40.2 - - - +
296D LEU* 4.0 13.5 - - - +
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 3.4 32.0 + - - -
100D VAL* 3.6 7.4 - - - +
101D ALA 3.2 0.2 - - - -
102D LEU* 1.3 78.1 - - - +
104D ASN* 1.3 53.2 + - - +
105D ARG* 2.7 24.1 + - - +
276D TRP* 3.0 35.0 - - + +
296D LEU* 3.4 35.7 - - + +
299D ALA* 3.5 21.4 - - + +
300D HIS* 3.2 17.8 - - - +
303D ASP* 2.8 42.5 + - - +
491D ALA* 3.9 5.2 - - - +
494D GLU* 2.8 29.9 + - - -
495D HIS* 3.9 11.9 + - - -
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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