Contacts of the helix formed by residues 84 - 100 (chain D) in PDB entry 4Q96
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 VAL 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL* 3.4 31.9 - - + +
42D SER* 6.1 1.3 - - - -
44D TRP* 4.3 18.4 - - + -
45D HIS* 3.6 28.3 - - + +
81D PHE* 2.8 16.7 + - + +
83D SER* 1.3 86.6 - - - +
85D LEU* 1.3 59.5 + - - +
86D VAL 3.4 2.5 - - - -
87D ASP* 3.4 11.3 + - - +
88D ALA* 2.9 25.3 + - - +
207D UNX 3.6 20.2 - - - +
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Residues in contact with LEU 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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44D TRP* 4.3 24.5 - - + -
60D LEU* 4.6 2.7 - - + -
63D ALA* 4.8 2.9 - - + -
67D ILE* 4.0 1.6 - - + -
81D PHE* 3.1 33.0 + - + +
82D GLU* 4.1 2.9 + - - +
83D SER 3.9 0.8 - - - -
84D VAL* 1.3 74.9 - - + +
86D VAL* 1.3 62.1 + - - +
88D ALA* 3.9 3.1 - - + -
89D PHE* 2.9 54.3 + - + +
111E TRP* 4.0 16.6 - - + -
117E TYR* 3.4 38.4 - - + +
121E PHE* 4.3 7.2 - - + -
125E LEU* 3.7 14.6 - - + -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU 5.1 0.9 + - - +
83D SER 5.6 0.2 - - - -
84D VAL 3.4 0.4 - - - -
85D LEU* 1.3 78.8 - - - +
87D ASP* 1.3 61.9 + - - +
90D SER* 3.0 29.9 + - - -
121E PHE* 3.8 27.3 - - + -
124E GLN* 4.0 25.4 - - + +
125E LEU* 3.8 14.1 - - + -
128E SER* 3.7 20.3 + - - -
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Residues in contact with ASP 87 (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 HIS* 3.9 20.5 + - + +
49D ARG* 5.0 3.9 + - - +
84D VAL* 3.4 12.7 + - - +
85D LEU 3.3 0.2 - - - -
86D VAL* 1.3 83.5 - - - +
88D ALA* 1.3 62.1 + - - +
90D SER* 3.5 6.1 + - - -
91D HIS* 3.1 25.5 + - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D TRP* 4.0 19.3 - - + -
45D HIS* 4.1 8.0 + - - +
48D LEU* 3.9 21.3 - - + +
60D LEU* 4.5 3.6 - - + -
84D VAL 2.9 17.2 + - - +
85D LEU* 3.2 13.0 + - + +
87D ASP* 1.3 78.3 - - - +
89D PHE* 1.3 57.7 + - - +
91D HIS* 3.4 4.1 + - - +
92D VAL* 2.9 35.1 + - - +
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Residues in contact with PHE 89 (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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60D LEU* 3.9 29.4 - - + -
85D LEU* 2.9 30.7 + - + +
88D ALA* 1.3 69.1 - - - +
90D SER* 1.3 57.2 + - - +
92D VAL* 4.4 4.7 - - - -
93D ALA* 2.7 37.7 + - - +
104E LEU* 4.2 14.6 - - + -
107E LEU* 4.0 22.9 - - + -
108E LEU* 3.8 33.4 - - + -
111E TRP* 3.8 27.8 - + - -
125E LEU* 4.0 11.7 - - + +
128E SER* 3.5 17.3 - - - +
129E MET* 3.9 23.2 - - + +
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Residues in contact with SER 90 (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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86D VAL* 3.0 22.8 + - - -
87D ASP* 3.7 7.2 - - - -
88D ALA 3.3 0.2 - - - -
89D PHE* 1.3 77.8 - - - +
91D HIS* 1.3 56.3 + - - +
93D ALA* 3.8 1.4 - - - +
94D ARG* 2.9 34.7 + - - +
128E SER* 3.4 28.0 + - - +
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Residues in contact with HIS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D HIS* 5.9 0.7 - - - +
48D LEU* 4.4 6.7 - - + -
49D ARG* 3.6 45.5 + - + +
56D LYS* 2.9 36.1 + - + -
87D ASP 3.1 17.7 + - - +
88D ALA* 3.6 4.0 - - - +
90D SER* 1.3 75.3 + - - +
92D VAL* 1.3 73.1 + - + +
94D ARG* 3.2 10.2 + - - +
95D GLU* 3.0 51.2 + - + +
202D UNX 4.0 18.8 - - - -
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.8 28.7 - - + -
56D LYS* 4.1 22.6 - - + +
57D LEU* 5.1 1.3 - - + +
60D LEU* 3.8 21.3 - - + -
88D ALA 2.9 21.6 + - - +
89D PHE* 3.9 2.9 - - - +
91D HIS* 1.3 81.6 - - + +
93D ALA* 1.3 64.1 + - - +
95D GLU* 3.3 2.8 + - - +
96D ALA* 3.0 22.9 + - + +
104E LEU* 3.7 32.1 - - + -
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Residues in contact with ALA 93 (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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89D PHE 2.7 22.2 + - - +
90D SER 3.8 2.5 - - - +
92D VAL* 1.3 75.7 - - - +
94D ARG* 1.3 55.9 - - - +
96D ALA* 3.2 2.8 + - - +
97D ASP* 2.9 36.3 + - - -
101E LYS* 3.7 17.4 - - + +
104E LEU* 4.0 6.0 - - - +
128E SER 4.7 0.2 - - - +
129E MET* 3.7 39.7 - - + +
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Residues in contact with ARG 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D SER* 2.9 23.7 + - - +
91D HIS* 3.2 10.3 + - - +
93D ALA* 1.3 76.9 - - - +
95D GLU* 1.3 60.6 + - + +
97D ASP* 3.2 11.1 + - - +
98D GLU* 2.9 30.1 + - + +
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Residues in contact with GLU 95 (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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49D ARG 5.4 0.5 - - - +
53D SER* 4.6 16.4 - - - -
56D LYS* 3.8 32.0 + - + -
91D HIS* 3.0 39.6 + - + +
92D VAL 3.7 4.0 - - - +
94D ARG* 1.3 76.8 - - + +
96D ALA* 1.3 67.0 + - - +
98D GLU* 3.2 27.2 + - - +
99D GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 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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92D VAL* 3.0 14.7 + - + +
93D ALA* 3.2 8.9 + - - +
95D GLU* 1.3 75.1 - - - +
97D ASP* 1.3 58.8 + - - +
99D GLY* 3.8 0.7 - - - -
100D CYS* 3.0 33.9 + - - +
100E CYS* 4.3 16.8 - - + +
101E LYS* 3.8 20.6 - - + -
104E LEU* 4.9 4.3 - - + -
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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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93D ALA 2.9 19.5 + - - +
94D ARG* 3.2 11.6 + - - +
96D ALA* 1.3 78.4 - - - +
98D GLU* 1.3 62.5 + - - +
99D GLY 3.5 0.2 + - - -
100D CYS* 3.6 14.7 + - - +
101D LYS 4.9 0.9 + - - -
100E CYS* 5.7 1.2 - - - +
101E LYS* 2.7 37.3 + - - +
129E MET 4.1 7.8 - - - +
130E GLU 5.4 1.9 - - - +
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Residues in contact with GLU 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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53D SER* 5.5 3.6 - - - -
94D ARG* 2.9 18.8 + - + +
95D GLU* 3.2 32.2 - - - +
97D ASP* 1.3 79.3 - - - +
99D GLY* 1.3 63.7 + - - +
101D LYS 5.0 0.9 + - - -
102D LYS* 3.3 26.3 - - + +
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Residues in contact with GLY 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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1617C PRO* 3.7 14.9 - - - +
95D GLU 3.0 13.7 + - - -
96D ALA 3.8 0.7 - - - -
98D GLU* 1.3 89.2 - - - +
100D CYS* 1.3 67.3 + - - +
101D LYS 3.4 1.8 - - - -
102D LYS* 3.3 22.4 + - - +
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Residues in contact with CYS 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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1615C TYR* 2.7 34.8 + - - -
1617C PRO* 3.4 7.0 - - - +
96D ALA 3.0 15.1 + - - +
97D ASP* 3.6 11.4 + - - +
98D GLU 3.4 2.2 - - - -
99D GLY* 1.3 77.7 - - - +
101D LYS* 1.3 60.0 + - + +
96E ALA* 3.3 27.4 - - - -
97E ASP* 4.2 4.3 - - - +
100E CYS* 2.0 51.4 - - + -
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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