Contacts of the helix formed by residues 99 - 104 (chain D) in PDB entry 1JIQ
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 99 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D MET 3.3 25.6 - - - +
85D PHE 4.4 0.9 - - - +
87D GLY* 4.1 7.4 - - - -
97D ALA* 4.2 10.8 - - + -
98D VAL* 1.3 75.0 - - - +
100D HIS* 1.3 66.0 + - - +
101D VAL* 3.0 17.7 - - + +
102D ALA* 2.9 19.0 + - + +
103D LEU 3.5 2.8 + - - -
111D ILE* 3.8 29.8 - - + -
113D VAL* 3.4 33.2 - - + -
118D VAL* 4.6 6.1 - - + -
269D TRP* 3.1 41.0 + - + -
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Residues in contact with HIS 100 (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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84D MET* 4.2 14.4 - - - -
98D VAL* 3.6 29.7 - - + +
99D LEU* 1.3 76.4 + - - +
101D VAL* 1.3 70.1 + - + +
103D LEU* 3.1 30.0 + - + +
104D ARG* 3.4 30.7 + - - +
269D TRP 4.1 5.2 + - - +
270D VAL* 5.6 2.0 - - + -
271D GLY 5.7 1.2 + - - -
274D TYR* 3.5 57.9 - + + +
277D TRP* 4.3 0.2 - - + -
495D GLU* 3.7 24.7 + - - +
496D HIS* 4.6 6.1 + - - -
510D PHE* 4.1 7.9 - + - -
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D MET* 4.7 5.4 - - + -
85D PHE* 3.9 38.8 - - + -
98D VAL 4.9 2.5 - - - +
99D LEU* 3.0 23.1 - - + -
100D HIS* 1.3 85.3 - - + +
102D ALA* 1.3 62.2 + - - +
104D ARG* 3.5 15.9 + - - +
105D ASN* 3.3 20.8 + - - +
111D ILE* 4.8 6.0 - - + +
301D HIS* 5.2 0.7 + - - -
304D ASP* 3.6 29.7 - - + +
496D HIS* 3.8 18.4 - - + -
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Residues in contact with ALA 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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99D LEU* 2.9 23.3 + - + +
101D VAL* 1.3 78.5 - - - +
103D LEU* 1.3 64.7 + - - +
104D ARG 3.2 0.9 + - - -
105D ASN* 3.2 9.0 + - - -
111D ILE* 3.8 25.4 - - + -
118D VAL* 3.9 24.2 - - + -
119D MET* 3.3 21.0 - - - +
122D VAL* 3.8 3.4 - - + +
269D TRP* 4.4 5.4 - - + -
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Residues in contact with LEU 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 LEU 3.9 2.9 - - - +
100D HIS* 3.1 27.6 + - - +
102D ALA* 1.3 78.9 - - - +
104D ARG* 1.3 56.4 + - - +
105D ASN 4.0 0.3 + - - -
106D ARG* 5.5 0.2 + - - -
122D VAL* 3.8 18.7 - - + +
126D LEU* 4.1 13.0 - - - +
267D TRP* 3.9 24.7 - - + -
269D TRP* 4.0 10.8 - - + -
270D VAL* 3.9 19.7 - - + -
274D TYR 4.0 5.2 - - - +
277D TRP* 3.8 32.0 - - + +
278D SER* 3.9 32.5 - - - +
297D LEU* 4.2 8.0 - - - +
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Residues in contact with ARG 104 (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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100D HIS* 3.4 35.8 + - - -
101D VAL* 3.8 5.4 - - - +
103D LEU* 1.3 79.1 - - - +
105D ASN* 1.3 57.1 + - - +
106D ARG* 2.8 15.7 + - - +
277D TRP* 3.0 36.1 - - - +
297D LEU* 3.5 34.3 - - + +
300D ALA* 3.6 20.6 - - + +
301D HIS* 3.1 22.5 - - - +
304D ASP* 2.8 42.4 + - - +
492D ALA* 3.8 5.3 - - - +
495D GLU* 2.7 30.9 + - - -
496D HIS* 3.8 9.3 + - - -
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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