Contacts of the helix formed by residues 110 - 119 (chain D) in PDB entry 1J0B
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315C PHE* 3.6 19.6 - - - -
109D LYS* 1.3 73.9 - - - +
111D ASN* 1.3 62.2 + - - -
113D LEU* 3.4 4.9 - - - +
114D LEU* 3.4 23.7 + - - +
312D SER* 3.7 18.6 - - - -
315D PHE* 5.4 0.6 - - - +
316D HIS* 3.1 19.4 - - - +
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Residues in contact with ASN 111 (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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50D ILE* 3.7 5.7 - - - +
79D VAL 4.5 1.6 - - - +
80D HIS 2.9 27.3 + - - +
81D SER 2.9 22.9 + - - +
82D ASN* 3.1 27.5 - - - +
85D PHE* 3.7 12.3 - - + +
109D LYS 3.5 0.6 + - - -
110D GLY* 1.3 68.6 - - - -
112D TYR* 1.3 58.8 + - - +
113D LEU 3.1 1.3 - - - -
114D LEU* 3.1 15.3 + - - +
115D ASP* 2.7 35.8 + - - +
312D SER* 2.9 26.3 + - - -
313D GLY 5.3 0.2 - - - +
316D HIS* 3.8 6.5 - - - -
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Residues in contact with TYR 112 (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 VAL* 3.9 23.5 + - + +
80D HIS* 5.0 0.4 - - - +
102D LEU* 3.6 17.7 - - + -
106D GLU* 2.5 48.0 + - + -
107D GLU 3.1 27.4 - - - +
108D LEU* 3.7 23.1 - - + -
109D LYS 3.6 4.6 + - - +
110D GLY 3.4 0.4 - - - -
111D ASN* 1.3 77.2 - - - +
113D LEU* 1.3 66.0 + - - +
115D ASP* 3.2 13.9 + - - +
116D LYS* 3.1 50.7 + - - +
122D THR* 3.3 24.8 - - + +
124D VAL* 3.4 13.8 - - + +
316D HIS* 5.0 0.2 - - - -
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Residues in contact with LEU 113 (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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314C THR 4.1 2.0 - - - +
315C PHE* 3.4 38.6 - - + +
318C GLY* 3.6 22.2 - - - +
319C ASP* 4.4 4.0 - - - +
322C LEU* 4.1 10.8 - - + -
108D LEU* 3.9 15.0 - - - +
109D LYS* 3.6 29.0 + - + +
110D GLY 3.4 12.1 + - - +
112D TYR* 1.3 81.6 - - - +
114D LEU* 1.3 58.6 + - + +
116D LYS* 3.3 1.6 + - - +
117D ILE* 2.9 63.2 + - + +
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Residues in contact with LEU 114 (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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277C ILE* 4.8 9.4 - - + -
311C ILE* 6.0 0.2 - - + -
314C THR* 3.8 28.7 - - + +
315C PHE* 3.7 20.6 - - + -
50D ILE* 3.7 17.7 - - + -
85D PHE* 3.4 23.1 - - + -
110D GLY 3.4 10.7 + - - +
111D ASN* 3.1 30.5 + - - +
113D LEU* 1.3 76.4 - - + +
115D ASP* 1.3 70.7 + - - +
117D ILE* 3.5 5.7 + - - +
118D MET* 3.1 26.4 + - + +
312D SER* 3.2 16.2 - - - +
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Residues in contact with ASP 115 (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 VAL 4.8 0.2 - - - +
85D PHE* 3.1 27.2 - - - -
100D LEU* 3.3 30.6 - - - +
102D LEU* 4.0 10.4 - - - +
111D ASN* 2.7 18.5 + - - +
112D TYR* 3.3 15.8 - - - +
114D LEU* 1.3 74.1 - - - +
116D LYS* 1.3 57.6 + - + +
118D MET* 2.5 31.9 + - - +
119D GLY 2.9 7.1 + - - -
120D ILE* 3.4 23.5 + - + +
122D THR* 4.1 9.2 + - - +
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Residues in contact with LYS 116 (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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268C ARG* 2.7 31.4 + - - -
322C LEU* 3.3 22.8 - - + +
108D LEU* 4.1 15.7 - - + -
112D TYR* 3.1 54.4 + - - +
113D LEU 3.6 4.3 - - - +
115D ASP* 1.3 78.6 - - - +
117D ILE* 1.3 51.4 + - - +
119D GLY* 2.8 7.4 + - - +
120D ILE 4.3 9.3 + - - +
122D THR* 3.1 40.3 + - - +
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Residues in contact with ILE 117 (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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264C ALA 5.7 0.4 - - - +
267C ILE* 4.3 24.2 - - + -
268C ARG* 2.7 33.5 + - - +
314C THR* 3.3 36.1 - - + +
318C GLY* 3.7 11.2 - - - +
321C LEU* 4.2 15.3 - - + -
322C LEU* 3.3 17.3 - - + -
325C LEU* 4.2 9.2 - - + +
113D LEU* 2.9 49.6 + - + +
114D LEU* 3.7 6.7 - - - +
115D ASP 2.9 2.0 + - - -
116D LYS* 1.3 70.6 - - - +
118D MET* 1.3 55.6 + - + +
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Residues in contact with MET 118 (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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267C ILE* 3.6 42.4 - - + +
268C ARG* 3.2 22.8 + - - +
271C GLY* 3.8 20.4 - - - -
272C THR* 3.1 27.5 - - + +
277C ILE* 3.9 30.7 - - + -
314C THR* 5.0 3.1 - - + -
85D PHE* 4.3 6.5 - - + -
89D LEU* 3.9 17.9 - - + -
92D LYS* 4.1 2.4 - - - -
114D LEU* 3.1 13.2 + - + +
115D ASP 2.5 13.8 + - - +
117D ILE* 1.3 75.7 - - + +
119D GLY* 1.3 59.8 + - - -
120D ILE* 3.4 8.9 + - + -
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Residues in contact with GLY 119 (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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268C ARG* 3.3 16.8 - - - +
92D LYS* 3.5 14.5 + - - -
115D ASP 2.9 0.2 + - - -
116D LYS* 2.8 17.7 + - - -
117D ILE 3.2 0.2 - - - -
118D MET* 1.3 79.7 - - - +
120D ILE* 1.3 64.4 + - - +
121D GLU* 3.6 2.1 + - - +
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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