Contacts of the helix formed by residues 101 - 114 (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 LYS 101 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D ALA* 3.7 29.2 - - + +
96D ALA* 3.8 19.7 - - + -
97D ASP* 2.7 30.4 + - - +
97E ASP 4.5 15.5 + - - +
98E GLU 4.4 3.7 + - - +
99E GLY 3.2 0.2 - - - -
100E CYS* 1.3 77.5 - - + +
102E LYS* 1.3 65.6 + - - +
103E PRO* 3.3 2.2 - - - -
104E LEU* 2.9 28.1 + - + +
105E GLU* 3.0 13.6 + - - +
129E MET* 3.7 26.2 - - + +
130E GLU* 5.8 0.2 - - - +
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Residues in contact with LYS 102 (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* 3.6 15.3 - - - +
98E GLU* 3.9 42.9 + - - +
99E GLY* 3.2 11.1 + - - +
101E LYS* 1.3 76.6 - - - +
103E PRO* 1.4 65.4 - - + +
105E GLU* 2.8 32.0 + - - +
106E ARG* 2.8 73.8 + - + +
205E UNX 4.0 15.5 + - - +
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Residues in contact with PRO 103 (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* 5.1 4.0 - - - +
57D LEU* 3.6 34.7 - - + +
61D TYR* 4.1 12.1 + - - +
99E GLY 3.7 9.0 - - - +
100E CYS 4.0 7.4 - - - +
101E LYS 3.6 2.0 - - - -
102E LYS* 1.4 93.3 - - + +
104E LEU* 1.3 59.2 + - + +
106E ARG* 3.4 13.3 + - + +
107E LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 104 (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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57D LEU* 3.6 18.4 - - + -
60D LEU* 3.5 31.2 - - + -
89D PHE* 4.2 6.0 - - + +
92D VAL* 3.7 22.7 - - + +
93D ALA* 4.0 17.0 - - - +
96D ALA* 4.9 3.1 - - + -
100E CYS 5.3 0.9 - - - +
101E LYS* 2.9 26.7 + - + +
103E PRO* 1.3 74.4 - - + +
105E GLU* 1.3 66.7 + - - +
107E LEU* 3.2 6.8 + - + +
108E LEU* 3.1 27.5 + - - +
129E MET* 3.4 30.5 - - - -
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Residues in contact with GLU 105 (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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101E LYS* 3.0 11.9 + - + +
102E LYS* 2.8 41.2 + - - +
104E LEU* 1.3 76.8 - - - +
106E ARG* 1.3 62.9 + - - +
108E LEU* 3.2 6.2 + - - +
109E ASN* 3.1 43.9 + - - +
126E LYS* 5.6 6.1 - - - +
129E MET* 4.1 13.6 - - + +
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Residues in contact with ARG 106 (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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1611C BTN 3.8 44.6 - - - +
1612C SER* 2.7 44.1 + - - +
1613C PRO 5.1 0.2 + - - -
1614C SER* 4.1 5.1 + - - -
102E LYS* 2.8 50.8 + - + +
103E PRO* 3.8 11.3 - - + +
105E GLU* 1.3 78.0 - - + +
107E LEU* 1.3 62.3 + - - +
109E ASN* 3.3 14.6 + - - +
110E ILE* 3.1 29.3 + - + +
205E UNX 3.7 19.6 + - - -
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Residues in contact with LEU 107 (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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57D LEU* 5.1 2.7 - - + -
60D LEU* 4.0 31.2 - - + +
61D TYR* 4.1 15.5 - - + -
64D ASN* 3.8 16.2 - - + +
89D PHE* 4.0 22.7 - - + -
103E PRO 2.9 18.6 + - - +
104E LEU* 3.6 7.0 - - - +
105E GLU 3.2 0.4 - - - -
106E ARG* 1.3 77.4 - - - +
108E LEU* 1.3 61.7 + - - +
110E ILE* 3.3 10.0 + - + +
111E TRP* 3.1 46.8 + - + +
1624F PRO* 4.0 15.9 - - + -
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Residues in contact with LEU 108 (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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89D PHE* 3.8 23.3 - - + -
104E LEU 3.1 9.6 + - - +
105E GLU* 3.7 6.5 - - - +
107E LEU* 1.3 74.6 - - - +
109E ASN* 1.3 59.6 + - - +
111E TRP* 3.1 12.2 + - + +
112E GLN* 2.8 29.3 + - - +
122E ILE* 4.2 9.0 - - + +
125E LEU* 3.7 33.9 - - + +
126E LYS* 3.6 49.4 - - + +
129E MET* 3.7 24.9 - - + -
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Residues in contact with ASN 109 (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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105E GLU* 3.1 34.6 + - - +
106E ARG* 3.3 17.4 + - - +
108E LEU* 1.3 75.0 - - - +
110E ILE* 1.3 57.1 + - + +
112E GLN* 3.4 15.3 - - - +
113E GLU* 2.8 42.2 + - + +
126E LYS* 3.3 19.2 + - - -
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Residues in contact with ILE 110 (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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1611C BTN 3.5 31.9 - - + -
64D ASN* 4.8 0.7 - - - +
68D GLN* 4.0 7.4 - - - +
106E ARG* 3.1 16.8 + - + +
107E LEU* 3.5 11.2 - - - +
109E ASN* 1.3 77.5 - - + +
111E TRP* 1.3 61.8 + - + +
113E GLU* 3.4 11.8 + - - +
114E ARG* 2.9 50.3 + - - +
1624F PRO* 3.6 38.1 - - + +
1625F THR* 3.7 19.1 - - + -
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Residues in contact with TRP 111 (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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60D LEU* 4.8 2.7 - - + -
63D ALA* 5.4 0.7 - - + -
64D ASN* 2.7 50.6 + - + +
67D ILE* 4.3 10.3 - - + -
68D GLN* 4.3 2.0 - - - +
85D LEU* 4.0 26.9 - - + -
89D PHE* 3.8 30.7 - + - -
107E LEU* 3.1 28.8 + - + +
108E LEU* 3.1 15.2 + - + +
110E ILE* 1.3 75.1 - - + +
112E GLN* 1.3 64.2 + - - +
115E SER* 3.2 2.6 + - - -
116E VAL* 2.9 58.1 + - + +
117E TYR* 3.9 16.4 + + - +
122E ILE* 3.7 11.9 - - + -
125E LEU* 3.8 25.6 - - + -
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Residues in contact with GLN 112 (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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108E LEU 2.8 17.0 + - - +
109E ASN* 3.4 19.6 - - - +
111E TRP* 1.3 74.4 - - - +
113E GLU* 1.3 70.5 + - + +
115E SER* 3.0 17.7 + - - +
117E TYR 5.4 0.4 - - - -
119E GLY* 6.2 2.2 - - - -
122E ILE* 4.2 25.0 - - + +
126E LYS* 4.2 12.4 + - - +
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Residues in contact with GLU 113 (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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109E ASN* 2.8 35.5 + - + +
110E ILE* 3.6 11.7 - - - +
112E GLN* 1.3 78.2 - - + +
114E ARG* 1.3 62.1 + - + +
115E SER* 3.3 6.6 + - - -
1630F SER 4.4 3.7 - - - +
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Residues in contact with ARG 114 (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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68D GLN* 2.9 30.3 + - - +
110E ILE* 2.9 29.4 + - - +
113E GLU* 1.3 78.6 - - + +
115E SER* 1.3 70.8 + - - +
116E VAL* 3.1 11.9 + - + -
1625F THR* 3.0 50.1 + - - +
1627F PRO* 3.0 22.2 + - - +
1629F TYR* 3.4 26.8 + - + +
1630F SER* 3.5 14.3 - - - +
1631F NH2 3.1 18.2 + - - +
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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