Contacts of the helix formed by residues 95 - 108 (chain D) in PDB entry 5DQZ
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 ARG 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C ALA* 4.6 0.4 - - - -
93D GLY* 3.5 1.0 - - - -
94D ALA* 1.3 84.8 - - + +
96D SER* 1.3 66.1 + - - +
97D ASP* 2.7 35.5 + - - +
98D LYS* 3.4 39.0 - - + +
99D LEU* 3.4 26.7 + - - +
198D ALA 5.9 0.2 - - - -
199D GLY* 4.7 8.0 + - - +
280D PRO* 4.4 3.6 - - - +
281D ALA* 3.8 27.9 - - - +
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Residues in contact with SER 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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203C ALA* 3.1 30.1 + - - +
204C ILE* 4.9 4.9 - - - -
210C GLY* 3.7 28.0 + - - -
211C LYS 3.9 7.4 + - - -
94D ALA 4.0 2.2 + - - -
95D ARG* 1.3 71.2 - - - +
97D ASP* 1.3 58.0 + - - +
98D LYS 3.3 0.3 + - - -
99D LEU* 3.3 6.1 + - - +
100D LEU* 2.9 46.2 + - - +
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Residues in contact with ASP 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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95D ARG* 2.7 49.2 + - - +
96D SER* 1.3 75.7 + - - +
98D LYS* 1.3 60.6 + - - -
100D LEU* 3.8 8.3 - - - +
101D TYR* 2.9 29.6 + - - +
280D PRO* 3.2 25.0 - - + +
281D ALA* 4.8 1.4 + - - +
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Residues in contact with LYS 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 ARG* 3.4 47.1 - - + +
96D SER 3.3 0.6 - - - -
97D ASP* 1.3 82.0 + - - +
99D LEU* 1.3 65.3 + - - +
101D TYR* 3.1 7.0 + - - +
102D GLN 3.0 19.8 + - - -
198D ALA* 2.7 27.9 + - - +
199D GLY* 3.4 18.6 - - - +
200D TYR* 3.4 27.6 - - + +
269D GLU* 3.2 21.2 + - - -
280D PRO* 4.0 21.3 - - + -
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Residues in contact with LEU 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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201C ALA* 4.3 12.8 - - + -
203C ALA* 4.3 19.3 - - + -
204C ILE* 4.1 15.9 - - + +
92D GLY 3.3 26.9 - - - +
93D GLY* 4.3 8.1 - - - -
95D ARG 3.4 15.5 + - - +
96D SER 3.3 5.5 + - - +
98D LYS* 1.3 78.5 - - - +
100D LEU* 1.3 59.5 + - - +
102D GLN* 3.5 8.3 + - - +
103D ALA* 2.9 30.2 + - - +
199D GLY 3.7 17.3 - - - +
200D TYR 4.0 1.8 - - - -
201D ALA* 3.8 31.4 - - + +
204D ILE* 5.3 3.0 - - + +
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Residues in contact with LEU 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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103C ALA* 4.4 9.4 - - + +
106C ALA* 4.8 4.3 - - + -
107C LEU* 3.9 39.4 - - + +
204C ILE* 4.0 34.8 - - + -
96D SER* 2.9 33.6 + - - +
97D ASP* 4.0 6.5 - - - +
99D LEU* 1.3 73.3 - - - +
101D TYR* 1.3 60.7 + - - +
103D ALA* 4.0 2.6 - - - +
104D LYS* 2.9 32.1 + - - +
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Residues in contact with TYR 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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97D ASP 2.9 18.4 + - - +
98D LYS* 3.1 5.6 + - - +
100D LEU* 1.3 76.5 - - - +
102D GLN* 1.3 64.2 + - - +
104D LYS* 3.8 4.4 - - - +
105D LEU* 3.0 40.3 + - + +
200D TYR* 3.6 24.7 - + - -
269D GLU* 4.8 5.0 + - - -
272D LEU* 3.2 43.5 + - + -
273D ALA* 3.4 9.9 + - - -
277D ILE* 3.6 40.0 + - + -
278D GLN 3.9 15.9 - - - -
279D PRO* 4.0 12.2 - - + +
280D PRO* 4.2 16.4 - - + -
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Residues in contact with GLN 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 LYS 3.0 11.9 + - - +
99D LEU* 3.6 10.7 - - - +
101D TYR* 1.3 78.3 - - - +
103D ALA* 1.3 58.6 + - - +
105D LEU* 3.2 13.7 + - - +
106D ALA* 2.9 26.2 + - - +
200D TYR* 3.5 18.6 - - + +
201D ALA* 2.9 51.5 + - - +
204D ILE* 3.0 33.5 + - + +
206D PHE* 3.9 10.9 - - + -
215D PHE* 3.4 17.2 - - - -
272D LEU* 4.8 6.1 - - + -
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Residues in contact with ALA 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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100C LEU* 4.3 15.9 - - + -
103C ALA* 3.5 31.6 - - + -
107C LEU* 5.0 1.1 - - + -
204C ILE* 6.0 0.2 - - + -
99D LEU 2.9 18.6 + - - +
100D LEU* 4.0 5.2 - - - +
101D TYR 3.3 0.2 - - - -
102D GLN* 1.3 74.0 - - - +
104D LYS* 1.3 60.4 + - - +
106D ALA* 3.1 2.4 + - - +
107D LEU* 2.9 37.0 + - + +
204D ILE* 4.7 8.1 - - + -
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Residues in contact with LYS 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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107C LEU* 4.1 22.8 - - + +
100D LEU 2.9 20.5 + - - +
101D TYR* 3.8 5.4 - - + +
103D ALA* 1.3 75.3 - - - +
105D LEU* 1.3 64.1 + - + +
107D LEU* 4.0 4.3 - - - +
108D ASP* 3.3 26.0 + - + +
111D LEU* 4.0 17.3 - - + +
277D ILE* 4.9 22.4 - - + +
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Residues in contact with LEU 105 (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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101D TYR* 3.0 36.7 + - + +
102D GLN* 3.3 7.9 - - - +
104D LYS* 1.3 80.2 - - + +
106D ALA* 1.3 58.5 + - - +
108D ASP 3.5 2.4 - - - +
111D LEU* 3.8 19.9 - - + +
112D ARG* 3.2 28.2 + - - -
115D VAL* 4.3 4.7 - - + -
206D PHE* 3.7 13.0 - - + -
272D LEU* 3.5 45.1 - - + +
275D GLY* 3.9 27.1 - - - -
277D ILE* 4.6 13.9 - - + -
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Residues in contact with ALA 106 (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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100C LEU* 4.0 12.0 - - + +
283C PRO* 5.7 1.6 - - - +
102D GLN 2.9 15.9 + - - +
103D ALA 3.1 5.1 + - - +
105D LEU* 1.3 76.9 - - - +
107D LEU* 1.3 62.3 + - - +
112D ARG* 4.0 19.1 - - - -
204D ILE* 3.7 26.0 - - + -
205D GLY 4.7 5.6 - - - +
206D PHE* 3.6 18.4 - - + -
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Residues in contact with LEU 107 (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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100C LEU* 4.1 33.9 - - + +
103C ALA* 4.4 5.2 - - + -
104C LYS* 3.7 48.5 - - + +
107C LEU* 4.5 9.6 - - + -
280C PRO* 4.4 13.9 - - + -
103D ALA 2.9 22.2 + - - +
104D LYS* 4.1 4.3 - - - +
105D LEU 3.4 0.4 - - - -
106D ALA* 1.3 77.1 - - - +
108D ASP* 1.3 62.4 + - + +
109D GLU* 3.6 10.6 + - - +
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Residues in contact with ASP 108 (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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104D LYS* 3.3 8.3 + - + +
105D LEU 3.5 0.3 - - - +
106D ALA 3.5 0.2 - - - -
107D LEU* 1.3 78.3 - - - +
109D GLU* 1.3 77.2 + - - +
110D ASP* 3.5 15.3 + - - +
111D LEU* 3.3 37.6 + - + +
112D ARG* 2.8 35.8 + - - +
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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