Contacts of the helix formed by residues 84 - 100 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E VAL* 3.6 29.4 - - + +
42E SER* 5.9 2.0 - - - -
44E TRP* 4.0 18.8 - - + -
45E HIS* 3.4 34.4 + - + +
81E PHE* 2.9 14.6 + - + +
83E SER* 1.3 91.9 - - - +
85E LEU* 1.3 58.9 + - - +
86E VAL* 3.4 2.5 - - - -
87E ASP* 3.4 9.1 + - - +
88E ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TRP* 3.7 26.7 - - + -
117D TYR* 3.5 39.5 - - + +
121D PHE* 3.8 11.0 - - + -
125D LEU* 3.4 13.5 - - + -
44E TRP* 4.2 24.2 - - + -
60E LEU* 5.0 0.9 - - + -
63E ALA* 4.8 4.7 - - + -
67E ILE* 4.2 1.8 - - + -
81E PHE* 3.1 30.2 + - + +
82E GLU 3.9 1.0 + - - -
83E SER 3.8 1.0 - - - -
84E VAL* 1.3 75.6 - - - +
86E VAL* 1.3 61.4 + - - +
88E ALA* 4.1 1.8 - - + -
89E PHE* 2.8 42.8 + - + +
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D PHE* 3.9 13.5 - - + -
124D GLN* 3.7 48.0 - - + +
125D LEU* 3.6 19.7 - - + -
128D SER* 3.8 9.7 - - - -
82E GLU 5.3 2.2 - - - +
83E SER 5.1 7.2 - - - +
84E VAL 5.0 1.1 - - - -
85E LEU* 1.3 76.4 - - - +
87E ASP* 1.3 62.9 + - + +
90E SER* 2.9 32.8 + - - -
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Residues in contact with ASP 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E HIS* 2.6 33.9 + - + +
49E ARG* 2.9 28.6 + - - +
84E VAL* 3.4 9.3 + - - +
85E LEU 3.3 0.2 - - - -
86E VAL* 1.3 84.3 - - + +
88E ALA* 1.3 58.1 + - - +
90E SER* 3.7 6.0 - - - -
91E HIS* 2.9 28.6 + - - +
94E ARG* 4.9 4.7 + - - -
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Residues in contact with ALA 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E TRP* 3.8 20.4 - - + -
45E HIS* 4.2 2.9 + - + -
48E LEU* 3.6 27.4 - - + -
60E LEU* 4.1 5.8 - - + -
84E VAL 2.9 17.0 + - - +
85E LEU* 3.7 7.2 - - + +
87E ASP* 1.3 80.7 + - - +
89E PHE* 1.3 58.1 + - - +
91E HIS* 3.3 2.9 + - - +
92E VAL* 3.0 35.3 + - - +
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Residues in contact with PHE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.8 24.7 - - + +
107D LEU* 4.2 13.2 - - + -
108D LEU* 3.6 41.1 - - + -
111D TRP* 3.8 30.5 - + - -
125D LEU* 4.0 10.5 - - + -
128D SER* 3.4 18.4 - - - +
129D MET* 4.4 11.4 - - + -
60E LEU* 4.1 34.8 - - + -
85E LEU* 2.8 32.9 + - + +
88E ALA* 1.3 70.8 - - - +
90E SER* 1.3 62.0 + - - +
92E VAL* 3.9 0.7 - - - +
93E ALA* 2.9 32.8 + - - +
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Residues in contact with SER 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D SER* 3.6 27.8 + - - +
131D ASP* 4.8 7.3 - - - -
86E VAL 2.9 20.9 + - - -
87E ASP* 3.7 6.7 - - - -
89E PHE* 1.3 78.0 - - - +
91E HIS* 1.3 61.1 + - - +
93E ALA* 3.4 1.6 + - - +
94E ARG* 3.0 46.4 + - - +
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Residues in contact with HIS 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 4.3 13.0 - - + -
49E ARG* 3.7 46.2 + - + +
56E LYS* 2.9 39.1 + - + -
87E ASP* 2.9 19.8 + - - +
88E ALA* 3.6 5.4 - - - +
90E SER* 1.3 76.6 - - - +
92E VAL* 1.3 64.0 + - - +
94E ARG* 3.2 34.9 + - - +
95E GLU* 3.0 41.4 + - + +
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Residues in contact with VAL 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615C TYR* 4.0 20.1 - - + -
104D LEU* 3.8 24.0 - - + -
48E LEU* 4.1 23.6 - - + -
56E LYS* 4.2 10.1 - - + +
57E LEU* 4.4 10.1 - - - +
60E LEU* 3.8 24.9 - - + -
88E ALA 3.0 17.6 + - - +
89E PHE 4.1 1.6 - - - +
91E HIS* 1.3 77.2 - - + +
93E ALA* 1.3 58.3 + - - +
95E GLU* 3.2 8.5 + - + +
96E ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LYS* 4.1 5.3 - - - +
104D LEU* 3.8 17.4 - - + +
128D SER 4.4 1.1 - - - +
129D MET* 3.8 34.1 - - - +
89E PHE 2.9 19.4 + - - +
90E SER 3.8 3.4 - - - +
92E VAL* 1.3 76.5 - - - +
94E ARG* 1.3 58.1 + - - +
96E ALA* 3.3 4.9 + - - +
97E ASP* 3.0 37.2 + - - +
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Residues in contact with ARG 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ARG* 3.0 35.4 - - - +
87E ASP* 4.9 4.2 + - - -
90E SER* 3.0 34.9 + - - +
91E HIS* 3.3 30.2 + - - +
93E ALA* 1.3 73.4 - - - +
95E GLU* 1.3 66.6 + - + +
97E ASP* 3.4 10.3 + - - +
98E GLU* 3.2 21.1 + - - +
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615C TYR* 3.7 15.8 + - + +
53E SER* 2.8 29.6 + - - -
56E LYS* 3.7 32.4 - - + -
91E HIS* 3.0 32.2 + - + +
92E VAL* 3.6 7.9 - - + +
94E ARG* 1.3 76.5 + - + +
96E ALA* 1.3 52.5 + - - +
98E GLU* 3.3 22.2 + - - +
99E GLY* 2.8 31.7 + - - -
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615C TYR* 3.5 40.8 - - + +
100D CYS* 3.3 17.0 - - - -
101D LYS* 4.1 12.8 - - + -
104D LEU* 5.2 0.2 - - + -
92E VAL 2.9 13.4 + - - +
93E ALA* 3.5 9.2 - - - +
94E ARG 3.2 0.2 - - - -
95E GLU* 1.3 73.1 - - - +
97E ASP* 1.3 66.1 + - - +
98E GLU 3.1 1.6 - - - -
99E GLY 3.0 0.3 + - - -
100E CYS 2.9 24.4 + - - -
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Residues in contact with ASP 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D CYS* 4.6 4.6 - - - -
101D LYS* 3.2 34.1 + - - +
129D MET 4.6 1.4 - - - +
130D GLU 5.3 3.3 - - - +
93E ALA* 3.0 20.3 + - - +
94E ARG* 3.7 8.0 - - - +
96E ALA* 1.3 75.5 - - - +
98E GLU* 1.3 60.7 + - - +
100E CYS* 4.7 1.6 + - - +
101E LYS* 4.5 16.1 + - - +
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Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E SER* 5.3 0.7 + - - -
94E ARG 3.2 12.0 + - - +
95E GLU* 3.5 26.3 - - - +
96E ALA 3.1 0.8 - - - -
97E ASP* 1.3 79.7 - - - +
99E GLY* 1.3 60.5 + - - +
100E CYS 3.9 0.2 + - - -
101E LYS* 4.4 1.2 + - - +
102E LYS* 3.9 43.7 + - - +
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Residues in contact with GLY 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1614C SER* 4.0 16.1 - - - -
1615C TYR 3.8 20.1 - - - +
95E GLU 2.8 19.3 + - - -
96E ALA 3.0 0.9 + - - -
98E GLU* 1.3 75.0 - - - +
100E CYS* 1.3 65.9 + - - +
101E LYS 3.2 3.6 + - - -
102E LYS* 3.2 16.2 + - - +
103E PRO* 3.7 5.4 - - - +
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Residues in contact with CYS 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615C TYR* 3.6 21.5 + - - -
1617C PRO* 4.2 11.7 - - + -
96D ALA* 4.3 19.6 - - + +
97D ASP* 5.7 1.3 - - - +
100D CYS* 2.0 59.7 - - + -
96E ALA 2.9 11.8 + - - +
97E ASP 4.7 1.3 + - - +
98E GLU 3.7 0.2 - - - -
99E GLY* 1.3 73.2 - - - +
101E LYS* 1.3 63.7 + - + +
102E LYS 3.8 0.3 + - - -
103E PRO* 4.0 7.8 - - - +
104E LEU* 5.3 1.7 - - - +
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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
------------------------------------------------------------
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