Contacts of the helix formed by residues 98 - 111 (chain V) in PDB entry 1I84
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 ALA 98 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36V TRP* 4.0 27.5 - - + -
44V PHE* 3.6 29.3 - - + +
76V GLN* 3.0 20.9 + - - +
96V ASN* 2.8 4.2 - - + -
97V GLU* 1.3 79.4 - - - +
99V SER* 1.3 53.3 + - - +
101V LEU* 3.1 6.6 - - - +
102V HIS* 2.7 34.7 + - - +
105V ARG* 5.7 0.2 + - - -
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Residues in contact with SER 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V TRP* 4.7 9.2 + - - +
77V LYS 4.2 6.4 + - - -
79V ASN* 4.5 14.2 + - - -
92V LEU* 5.4 9.2 - - - -
94V CYS* 3.5 15.7 + - - +
96V ASN* 3.0 30.1 + - - +
98V ALA* 1.3 72.4 - - - +
100V VAL* 1.3 60.9 + - - +
102V HIS* 2.6 30.1 + - - +
103V ASN* 2.7 16.8 + - - +
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Residues in contact with VAL 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89V MET* 3.2 33.2 - - + +
92V LEU* 5.5 4.9 - - + +
95V LEU* 3.9 17.0 - - + -
96V ASN 2.9 24.2 - - - +
97V GLU* 4.6 1.6 - - - +
99V SER* 1.3 78.3 - - - +
101V LEU* 1.3 57.7 + - - +
103V ASN* 4.8 0.2 - - - -
104V LEU* 2.9 30.7 + - - +
705V LEU* 3.5 24.7 - - + -
710V VAL* 4.6 9.2 - - + -
711V LEU* 3.3 30.1 - - + -
714V ILE* 5.1 1.6 - - + -
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Residues in contact with LEU 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V HIS 4.1 15.7 - - - +
43V GLY* 4.9 0.2 - - - -
44V PHE* 3.6 30.1 - - + -
97V GLU 3.0 16.6 + - - +
98V ALA 3.1 4.7 + - - +
100V VAL* 1.3 77.4 - - - +
102V HIS* 1.3 73.9 + - - +
104V LEU* 3.0 9.5 + - + +
105V ARG* 2.8 41.7 + - + +
696V LEU* 5.9 2.9 - - + -
698V ALA* 4.3 13.7 - - + +
701V VAL* 4.2 23.1 - - + -
702V LEU* 3.7 18.8 - - + -
705V LEU* 4.6 6.7 - - - -
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Residues in contact with HIS 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V TRP* 3.5 33.2 - + + -
78V MET* 5.8 2.5 - - + -
84V SER* 5.7 4.7 - - - -
98V ALA 2.7 14.2 + - - +
99V SER* 2.6 17.8 + - - +
101V LEU* 1.3 73.1 - - - +
103V ASN* 1.3 55.2 + - - +
105V ARG* 2.5 47.2 + - - +
106V GLU* 2.5 50.4 + - + +
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Residues in contact with ASN 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83V PHE 3.6 7.4 - - - +
84V SER* 5.0 0.2 - - - -
85V LYS* 3.7 4.7 + - - +
86V VAL* 3.1 46.0 + - - +
89V MET* 3.8 20.5 - - - -
92V LEU* 3.9 10.2 - - + +
99V SER 2.7 16.6 + - - +
100V VAL* 4.1 0.7 - - - +
102V HIS* 1.3 74.0 + - - +
104V LEU* 1.3 59.4 + - - +
106V GLU* 3.2 6.3 + - - +
107V ARG* 2.7 65.2 + - - +
115V THR* 4.2 1.4 - - - +
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Residues in contact with LEU 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89V MET* 3.2 23.1 - - + -
100V VAL* 2.9 20.9 - - + +
101V LEU* 3.0 8.4 + - - +
103V ASN* 1.3 79.9 - - - +
105V ARG* 1.3 62.1 + - - +
107V ARG* 4.2 3.8 - - - +
108V TYR* 3.0 27.1 + - - +
115V THR* 3.9 26.2 - - + +
122V VAL* 4.5 12.1 - - + -
124V ILE* 3.9 28.2 - - + +
685V ILE* 5.5 0.2 - - + -
696V LEU* 5.1 1.1 - - - -
701V VAL* 5.2 8.7 - - + -
705V LEU* 3.4 37.7 - - + -
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Residues in contact with ARG 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V TRP* 4.7 7.5 - - - -
42V HIS* 3.3 37.8 + - - +
44V PHE* 4.4 8.1 + - - +
45V GLU* 6.0 0.2 - - - +
101V LEU* 2.8 29.9 + - + +
102V HIS* 2.5 46.1 + - - +
104V LEU* 1.3 71.3 - - - +
106V GLU* 1.3 70.9 + - - +
108V TYR* 3.1 4.9 - - - +
109V PHE* 3.0 47.4 + - + -
696V LEU* 3.9 22.9 - - + -
698V ALA* 4.3 11.8 - - - +
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Residues in contact with GLU 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V SER* 5.1 8.5 - - - +
85V LYS* 3.8 24.9 - - + +
102V HIS* 2.5 63.6 + - + +
103V ASN* 3.6 9.0 - - - +
105V ARG* 1.3 80.5 + - - +
107V ARG* 1.3 69.6 + - - +
109V PHE* 2.6 22.2 + - - +
110V SER* 2.9 13.7 + - - +
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Residues in contact with ARG 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V LEU 5.1 3.2 + - - -
15V VAL* 4.3 4.6 - - - +
85V LYS* 3.3 23.1 + - + +
86V VAL 3.0 20.4 + - - -
87V GLU* 2.5 35.0 + - - -
103V ASN* 2.7 38.6 - - - +
104V LEU* 4.2 4.0 - - - +
106V GLU* 1.3 74.0 - - - +
108V TYR* 1.3 57.2 + - - +
110V SER* 3.2 1.6 + - - -
111V GLY 3.1 5.5 + - - -
112V LEU* 2.7 80.1 + - + +
114V TYR 3.1 25.7 + - - -
115V THR* 3.4 25.1 + - - +
151V PRO* 4.1 2.4 - - - +
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Residues in contact with TYR 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104V LEU 3.0 21.6 + - - +
105V ARG* 3.1 5.6 - - - +
106V GLU 2.6 5.1 + - - -
107V ARG* 1.3 74.1 - - - +
109V PHE* 1.3 79.1 + + - +
111V GLY* 3.1 14.9 + - - -
112V LEU 3.3 7.0 + - - -
113V ILE* 4.1 13.6 - - + +
124V ILE* 3.7 24.2 - - + -
125V ASN 3.3 27.5 + - - -
126V PRO* 3.5 22.7 + - + -
687V PRO* 4.1 5.0 - - + +
693V ALA* 4.8 0.5 - - - -
694V GLY* 3.7 16.0 + - - -
695V LYS 4.1 10.0 + - - -
696V LEU* 3.4 40.8 - - + -
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Residues in contact with PHE 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105V ARG* 3.0 39.5 + - + -
106V GLU* 2.6 15.3 + - - +
108V TYR* 1.3 88.1 - + - +
110V SER* 1.3 59.4 + - - +
111V GLY* 3.3 1.2 + - - -
694V GLY* 3.1 33.7 - - - -
696V LEU* 4.0 22.9 - - + -
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Residues in contact with SER 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V LYS 3.9 15.2 - - - +
12V PHE* 3.9 7.4 - - - -
85V LYS* 3.5 29.4 + - - +
106V GLU* 2.9 11.3 + - - -
107V ARG 3.6 8.5 - - - -
109V PHE* 1.3 77.0 - - - +
111V GLY* 1.3 58.2 + - - +
112V LEU* 4.0 15.7 - - - -
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Residues in contact with GLY 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V PHE* 3.2 33.2 - - - +
107V ARG 3.1 1.6 + - - -
108V TYR 3.1 7.3 + - - -
109V PHE 3.1 5.3 - - - -
110V SER* 1.3 80.4 - - - +
112V LEU* 1.3 62.1 + - - +
113V ILE* 5.1 0.9 - - - -
130V LEU* 3.1 30.4 - - - +
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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