Contacts of the helix formed by residues 95 - 104 (chain D) in PDB entry 4J1R
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 ASN 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D VAL* 4.3 15.4 - - - +
89D GLN* 3.4 28.3 + - + +
94D LYS* 1.3 72.6 - - - +
96D ARG* 1.3 64.1 + - - +
97D GLU* 3.0 17.8 + - - +
98D LEU* 2.7 36.0 + - + +
99D GLN* 3.1 28.1 + - - +
128D LEU* 3.6 28.8 - - + +
130D LEU* 5.2 0.3 - - - +
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Residues in contact with ARG 96 (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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94D LYS 3.7 5.0 + - - +
95D ASN* 1.3 72.1 + - - +
97D GLU* 1.3 64.3 + - - +
99D GLN* 3.3 7.5 + - - +
100D ILE* 3.0 33.3 + - + +
180D ARG* 4.0 7.5 - - - +
204D ALA 4.2 19.2 + - - +
205D LYS* 3.5 32.7 - - + +
501D PO4 2.4 42.4 + - - -
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Residues in contact with GLU 97 (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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85D LYS* 3.1 37.1 + - - +
87D VAL* 5.0 3.8 - - - +
95D ASN* 3.0 13.0 + - - +
96D ARG* 1.3 78.7 - - - +
98D LEU* 1.3 57.0 + - - +
100D ILE* 3.3 5.9 + - - +
101D MET* 2.8 41.8 + - + +
130D LEU* 3.6 25.9 - - + +
132D LEU* 5.1 6.4 - - - +
200D ASP* 4.9 1.4 - - - -
201D PHE* 3.5 45.9 + - + +
202D GLY* 3.6 7.5 - - - +
204D ALA 5.9 0.2 - - - -
502D I5R 5.7 0.2 - - - -
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Residues in contact with LEU 98 (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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95D ASN* 2.7 26.2 + - + +
97D GLU* 1.3 74.8 - - - +
99D GLN* 1.3 73.2 + - - +
100D ILE 3.3 0.5 + - - -
101D MET* 3.5 2.1 + - - -
102D ARG* 3.0 39.8 + - + +
112D LEU* 4.0 10.8 - - + -
115D PHE* 3.8 50.9 - - + -
117D TYR* 4.0 14.6 - - - +
128D LEU* 4.0 16.8 - - + -
130D LEU* 3.9 17.2 - - + +
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Residues in contact with GLN 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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94D LYS* 4.1 28.8 - - + +
95D ASN 3.1 23.4 + - - +
96D ARG* 3.3 8.0 + - - +
98D LEU* 1.3 92.3 - - - +
100D ILE* 1.3 62.2 + - + +
102D ARG* 3.9 12.5 + - - +
103D LYS* 3.6 25.5 + - - +
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Residues in contact with ILE 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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96D ARG* 3.0 22.3 + - + +
97D GLU* 3.8 5.6 - - - +
99D GLN* 1.3 78.3 - - + +
101D MET* 1.3 65.7 + - + +
102D ARG 3.1 1.6 - - - -
103D LYS* 3.1 21.1 + - + +
104D LEU* 3.3 28.7 + - + +
177D ILE* 3.5 35.7 - - + -
201D PHE* 4.6 9.4 - - + -
204D ALA* 3.8 37.2 - - + +
205D LYS* 3.9 10.1 - - - +
206D GLN* 4.4 6.7 - - + +
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Residues in contact with MET 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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45D GLY 4.7 0.3 - - - +
46D GLN* 4.1 3.3 - - - +
97D GLU* 2.8 40.2 + - + +
98D LEU* 3.5 3.3 + - - +
100D ILE* 1.3 75.1 - - - +
102D ARG* 1.3 59.8 + - - +
103D LYS 3.4 0.2 - - - -
104D LEU* 3.7 24.7 - - + +
109D ILE* 5.3 1.6 - - + -
110D VAL* 3.4 28.9 - - + +
112D LEU* 3.6 42.3 + - + +
130D LEU* 5.0 4.3 - - + -
132D LEU* 3.7 28.3 - - + -
201D PHE* 3.7 34.8 - - + -
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Residues in contact with ARG 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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43D THR* 4.1 4.2 - - - +
44D PRO 4.0 14.3 + - - -
45D GLY 3.7 21.3 + - - +
46D GLN* 3.4 18.3 + - - +
47D GLY 4.6 5.5 + - - -
49D ASP* 3.6 40.2 + - - +
98D LEU* 3.0 33.8 - - + +
99D GLN* 4.2 12.1 + - - +
100D ILE 3.1 1.4 - - - -
101D MET* 1.3 76.7 - - - +
103D LYS* 1.3 64.0 + - - +
112D LEU* 4.4 3.6 - - + -
115D PHE* 3.8 27.1 - - + -
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Residues in contact with LYS 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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46D GLN* 4.1 6.9 + - - -
99D GLN* 3.6 21.3 - - - +
100D ILE* 3.1 8.5 + - - +
102D ARG* 1.3 80.0 - - - +
104D LEU* 1.3 68.5 - - + +
105D ASP* 3.6 3.1 + - - +
171D TYR* 3.9 5.9 + - - -
175D PHE* 4.6 24.1 + - + +
177D ILE* 4.5 15.4 - - + +
206D GLN* 2.7 33.3 + - - +
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Residues in contact with LEU 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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46D GLN* 3.1 17.0 - - - +
100D ILE* 3.3 28.4 + - + +
101D MET* 3.7 17.7 + - + +
102D ARG 3.5 0.6 - - - -
103D LYS* 1.3 76.2 - - + +
105D ASP* 1.3 58.7 + - - +
106D HIS 4.0 0.7 - - - -
109D ILE* 4.4 13.5 - - + -
111D ARG* 6.2 0.2 - - - -
112D LEU 6.0 0.2 + - - -
171D TYR* 3.5 25.6 - - + -
172D ILE* 3.9 16.4 - - + -
175D PHE* 4.1 15.5 - - + -
177D ILE* 4.4 11.2 - - + -
201D PHE* 3.6 37.7 - - + -
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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