Contacts of the helix formed by residues 75 - 85 (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 GLY 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ALA 3.2 0.2 + - - -
72D LYS* 2.9 16.2 + - - -
73D SER 3.2 2.0 + - - -
74D ARG* 1.3 80.4 - - - +
76D VAL* 1.3 66.2 + - - +
77D GLU 3.3 2.5 - - - -
78D ALA* 3.5 10.4 + - - +
79D ALA* 3.1 25.3 + - - +
82D ARG* 4.6 2.4 + - - -
502D ILE* 4.1 0.4 - - - +
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA* 3.0 39.0 + - + +
72D LYS* 5.0 0.2 - - - +
74D ARG* 4.8 1.1 - - + -
75D GLY* 1.3 76.8 - - - +
77D GLU* 1.3 59.8 + - + +
79D ALA* 3.3 2.8 + - - +
80D ARG* 2.9 28.3 + - + +
306D PHE* 5.1 6.3 - - + -
311D LEU* 4.5 15.7 - - + -
317D VAL* 4.6 3.8 - - + -
498D PHE* 4.9 2.4 - - + -
499D VAL* 4.1 33.4 - - + +
502D ILE* 4.1 16.2 - - + -
503D ILE* 4.0 21.5 - - + -
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Residues in contact with GLU 77 (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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71D ALA 4.9 0.2 + - - -
72D LYS* 5.4 5.2 - - - +
75D GLY* 3.3 0.6 - - - -
76D VAL* 1.3 74.3 - - - +
78D ALA* 1.3 65.5 + - - +
80D ARG* 3.1 33.2 + - - +
81D GLU* 3.0 29.6 + - + +
309D THR 5.2 2.1 - - - +
310D PRO* 5.2 2.1 - - - +
311D LEU* 3.4 48.9 + - + +
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Residues in contact with ALA 78 (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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75D GLY* 3.5 13.2 + - - +
77D GLU* 1.3 77.3 - - - +
79D ALA* 1.3 57.8 + - - +
81D GLU* 3.2 10.1 + - - +
82D ARG* 3.0 39.7 + - - +
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Residues in contact with ALA 79 (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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75D GLY 3.1 16.1 + - - +
76D VAL 3.5 4.7 - - - +
78D ALA* 1.3 75.1 - - - +
80D ARG* 1.3 65.3 + - - +
82D ARG* 3.2 32.7 + - - +
83D MET* 3.0 18.5 + - - +
89D ILE* 4.7 2.5 - - + +
498D PHE* 3.7 8.5 - - + -
502D ILE* 3.7 34.8 - - + -
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Residues in contact with ARG 80 (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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76D VAL* 2.9 16.4 + - + +
77D GLU* 3.1 40.9 + - - +
79D ALA* 1.3 75.6 - - - +
81D GLU* 1.3 86.4 + - - +
83D MET* 3.1 3.3 + - - +
84D PHE* 3.0 38.9 + - + -
306D PHE* 2.9 61.4 + - + -
307D ARG* 3.3 30.3 + - - +
309D THR 4.6 4.9 + - - -
311D LEU* 5.0 4.2 - - - +
314D ASN* 4.2 7.1 - - - +
498D PHE* 3.7 15.7 - - + -
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Residues in contact with GLU 81 (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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77D GLU* 3.0 17.5 + - + +
78D ALA* 3.5 9.6 - - - +
80D ARG* 1.3 118.2 + - - +
82D ARG* 1.3 51.1 + - + +
84D PHE* 3.3 1.1 + - - +
85D ASN* 2.7 52.2 + - - +
307D ARG* 2.9 42.6 + - - +
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Residues in contact with ARG 82 (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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75D GLY 4.6 2.2 + - - -
78D ALA* 3.0 19.6 + - + +
79D ALA* 3.2 43.1 + - - +
81D GLU* 1.3 74.9 - - - +
83D MET* 1.3 64.1 + - - +
85D ASN 3.2 4.5 + - - -
87D GLU* 3.0 62.6 + - - +
89D ILE* 3.6 31.4 - - + +
365D LYS* 4.5 22.3 - - - +
502D ILE* 5.3 3.4 - - - +
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Residues in contact with MET 83 (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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79D ALA 3.0 11.8 + - - +
80D ARG 3.1 8.9 + - - +
82D ARG* 1.3 75.2 - - - +
84D PHE* 1.3 80.1 + - + +
86D GLY* 3.0 13.5 + - - -
87D GLU 5.1 1.6 - - - +
89D ILE* 3.8 17.0 - - + +
97D VAL* 3.4 30.6 - - + +
98D LEU* 3.3 15.1 - - - +
99D HIS* 4.2 11.2 - - + +
100D VAL* 4.6 15.5 - - + -
495D HIS* 4.7 5.4 - - - -
498D PHE* 3.4 46.4 - - + -
509D PHE* 3.5 19.3 - - + -
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Residues in contact with PHE 84 (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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80D ARG* 3.0 46.1 + - + +
81D GLU 3.9 0.4 - - - +
83D MET* 1.3 94.4 - - + +
85D ASN* 1.3 61.9 + - - +
86D GLY 3.2 1.3 + - - -
98D LEU* 4.3 4.2 - - - +
100D VAL* 4.0 28.7 - - + -
110D ILE* 3.7 26.4 - - + +
303D ASP* 3.9 35.7 - - + -
304D GLN* 5.1 5.2 - - - -
306D PHE* 4.0 16.2 - + - -
307D ARG* 3.3 50.8 + - + +
495D HIS* 4.3 1.1 - - - -
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Residues in contact with ASN 85 (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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81D GLU* 2.7 44.6 + - - +
82D ARG 3.9 3.1 - - - +
83D MET 3.1 0.4 - - - -
84D PHE* 1.3 73.6 - - - +
86D GLY* 1.3 61.2 + - - +
87D GLU* 3.3 20.5 + - + +
110D ILE* 4.8 2.7 - - - -
111D LEU* 3.3 14.8 + - - +
307D ARG* 3.6 16.2 + - - +
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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