Contacts of the helix formed by residues 109 - 120 (chain D) in PDB entry 2ISZ
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 SER 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C GLU* 2.6 31.9 + - - -
103C ARG* 3.7 10.1 - - - +
78D LYS* 4.0 1.1 - - - +
107D VAL 3.5 1.4 + - - -
108D MET* 1.3 77.2 - - - +
110D GLU* 1.3 63.2 + - - +
111D ASP* 3.5 13.7 + - - +
112D VAL* 3.2 17.5 + - - +
113D GLU* 3.1 20.1 + - - +
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Residues in contact with GLU 110 (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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74D ALA* 5.1 4.2 - - - +
77D ARG* 3.3 18.7 + - - +
78D LYS* 3.6 8.0 - - - +
109D SER* 1.3 70.6 - - - +
111D ASP* 1.3 66.0 + - - +
113D GLU* 3.0 22.6 + - - +
114D ARG* 2.9 54.8 + - - +
137D GLU 5.6 0.7 - - - +
138D LEU* 4.0 8.3 - - + +
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Residues in contact with ASP 111 (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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92C LEU* 4.0 17.2 - - + +
96C GLU* 3.7 27.2 - - + +
109D SER* 3.1 13.6 + - - +
110D GLU* 1.3 78.0 - - - +
112D VAL* 1.3 61.2 + - - +
114D ARG* 3.0 27.6 + - - +
115D ARG* 3.5 23.7 + - - +
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Residues in contact with VAL 112 (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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86C LEU* 3.6 23.8 - - + -
90C ILE* 4.6 7.9 - - + -
92C LEU* 4.1 13.2 - - + -
100C GLU* 3.6 28.0 - - + +
104C TRP* 4.2 15.5 - - + -
108D MET* 3.8 21.5 - - + -
109D SER* 3.2 12.5 + - - +
111D ASP* 1.3 77.8 - - - +
113D GLU* 1.3 66.6 + - - +
115D ARG* 3.2 6.5 + - - +
116D LEU* 2.9 33.3 + - + +
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Residues in contact with GLU 113 (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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77D ARG* 2.6 48.6 + - - +
78D LYS* 2.5 47.3 + - + +
81D LEU* 3.7 10.0 - - + +
108D MET* 3.5 24.7 - - + -
109D SER 3.1 9.7 + - - +
110D GLU* 3.0 13.2 + - - +
112D VAL* 1.3 77.8 - - - +
114D ARG* 1.3 57.0 + - - +
116D LEU* 3.3 4.7 + - - +
117D VAL* 3.0 31.2 + - - +
138D LEU* 3.8 13.0 - - + -
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Residues in contact with ARG 114 (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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110D GLU* 2.9 30.5 + - - +
111D ASP* 3.0 38.2 + - - +
113D GLU* 1.3 74.6 - - - +
115D ARG* 1.3 64.2 + - + +
117D VAL* 3.5 6.4 + - - +
118D LYS* 3.3 28.7 + - + +
138D LEU* 2.8 56.4 + - + +
139D GLY* 3.3 25.1 - - - +
140D VAL* 5.1 1.3 - - + -
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Residues in contact with ARG 115 (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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89C VAL 4.9 0.6 + - - -
90C ILE* 2.6 47.6 + - + +
91C GLY* 3.5 27.8 + - - +
92C LEU* 4.4 10.1 - - + +
93C PRO* 5.2 4.3 - - + -
111D ASP 3.5 13.8 + - - +
112D VAL* 3.2 5.9 + - - +
114D ARG* 1.3 78.0 - - + +
116D LEU* 1.3 59.3 + - - +
118D LYS* 3.3 33.1 + - - +
119D VAL* 2.8 54.6 + - - +
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Residues in contact with LEU 116 (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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90C ILE* 4.1 18.4 - - + -
81D LEU* 3.9 27.4 - - + +
85D LEU* 3.6 40.4 - - + -
108D MET* 3.9 29.4 - - + -
112D VAL* 2.9 26.2 + - + +
113D GLU* 3.6 6.1 - - - +
115D ARG* 1.3 74.2 - - - +
117D VAL* 1.3 60.9 + - - +
119D VAL* 4.4 6.3 - - + +
120D LEU* 3.0 47.5 + - + +
123D PRO* 4.2 0.3 - - - +
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Residues in contact with VAL 117 (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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81D LEU* 4.2 10.8 - - + -
113D GLU 3.0 15.5 + - - +
114D ARG* 3.7 9.4 - - - +
115D ARG 3.3 0.2 - - - -
116D LEU* 1.3 77.8 - - - +
118D LYS* 1.3 60.5 + - + +
121D ASN 3.8 0.2 + - - -
122D ASN* 2.8 51.4 + - + +
123D PRO* 3.9 8.3 - - + +
135D LEU* 4.0 19.3 - - + -
138D LEU* 3.9 20.2 - - + -
140D VAL* 3.8 26.0 - - + -
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Residues in contact with LYS 118 (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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114D ARG* 3.3 17.8 + - - +
115D ARG* 3.3 39.4 - - - +
117D VAL* 1.3 80.8 - - + +
119D VAL* 1.3 64.1 + - + +
121D ASN* 3.1 17.3 + - - +
122D ASN* 4.9 4.8 + - - +
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Residues in contact with VAL 119 (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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89C VAL* 3.8 29.8 - - + +
90C ILE* 3.6 13.0 - - - +
85D LEU* 6.3 0.4 - - + -
89D VAL* 5.4 3.8 - - + -
115D ARG* 2.8 50.4 + - - +
116D LEU* 4.5 7.9 - - + +
118D LYS* 1.3 74.4 - - - +
120D LEU* 1.3 66.4 + - + +
121D ASN* 3.2 10.1 + - - -
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Residues in contact with LEU 120 (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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81D LEU* 4.1 8.1 - - + +
84D ARG* 3.6 29.8 - - + -
85D LEU* 4.0 14.4 - - + +
88D ASP* 4.4 19.7 - - + +
89D VAL* 3.8 29.2 - - + -
116D LEU* 3.0 35.0 + - + +
118D LYS 3.3 0.2 - - - -
119D VAL* 1.3 83.7 - - + +
121D ASN* 1.3 71.5 + - - +
122D ASN 3.4 1.8 - - - -
123D PRO* 3.6 21.3 - - + +
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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