Contacts of the helix formed by residues 98 - 111 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36S TRP* 4.0 26.7 - - + -
44S PHE* 3.6 29.3 - - + +
76S GLN* 3.0 20.7 + - - +
96S ASN* 2.8 3.8 - - + -
97S GLU* 1.3 79.0 - - - +
99S SER* 1.3 54.9 + - - +
101S LEU* 3.1 6.8 - - - +
102S HIS* 2.7 35.0 + - - +
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Residues in contact with SER 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S TRP* 4.7 9.1 + - - +
77S LYS 4.2 6.4 + - - -
79S ASN* 4.5 13.0 + - - +
92S LEU* 5.4 9.0 - - - -
94S CYS* 3.5 16.2 + - - +
96S ASN* 3.0 30.1 + - - +
98S ALA* 1.3 72.7 - - - +
100S VAL* 1.3 61.0 + - - +
102S HIS* 2.6 29.7 + - - +
103S ASN* 2.7 17.3 + - - +
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Residues in contact with VAL 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S MET* 3.2 33.7 - - + +
92S LEU* 5.5 4.2 - - + +
94S CYS 5.7 0.2 - - - +
95S LEU* 3.9 17.3 - - + -
96S ASN 2.9 24.0 + - - +
97S GLU 4.6 1.1 - - - +
99S SER* 1.3 78.8 - - - +
101S LEU* 1.3 57.7 + - - +
103S ASN* 4.8 0.4 - - - -
104S LEU* 2.9 31.4 + - - +
705S LEU* 3.5 25.4 - - + -
710S VAL* 4.6 8.3 - - + -
711S LEU* 3.3 30.5 - - + -
714S ILE* 5.1 1.8 - - + -
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Residues in contact with LEU 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S HIS 4.1 14.6 - - - +
43S GLY* 4.9 0.4 - - - -
44S PHE* 3.6 31.2 - - + -
97S GLU 3.0 16.8 + - - +
98S ALA 3.1 4.4 + - - +
99S SER 2.9 0.2 - - - -
100S VAL* 1.3 78.0 - - - +
102S HIS* 1.3 74.6 + - - +
104S LEU* 3.0 9.2 + - + +
105S ARG* 2.8 40.5 + - + +
696S LEU* 5.9 3.4 - - + -
698S ALA* 4.3 14.6 - - + +
701S VAL* 4.2 22.4 - - + -
702S LEU* 3.7 18.8 - - + -
705S LEU* 4.6 6.7 - - + -
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Residues in contact with HIS 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S TRP* 3.5 33.2 - + + -
78S MET* 5.8 2.0 - - + -
84S SER* 5.7 4.5 - - - -
98S ALA 2.7 14.0 + - - +
99S SER* 2.6 18.0 + - - +
101S LEU* 1.3 73.8 - - - +
103S ASN* 1.3 55.0 + - - +
105S ARG* 2.5 47.8 + - - +
106S GLU* 2.5 50.4 + - + +
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Residues in contact with ASN 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S PHE 3.6 7.8 - - - +
85S LYS* 3.7 4.5 + - - +
86S VAL* 3.1 46.5 + - - +
89S MET* 3.8 20.7 - - - -
92S LEU* 3.9 10.8 - - + +
99S SER 2.7 16.8 + - - +
100S VAL 4.1 0.2 - - - +
102S HIS* 1.3 74.6 + - - +
104S LEU* 1.3 60.1 + - - +
106S GLU* 3.2 5.8 + - - +
107S ARG* 2.7 64.6 + - - +
115S THR* 4.2 1.8 - - - +
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Residues in contact with LEU 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S MET* 3.2 22.9 - - + -
100S VAL 2.9 21.8 - - - +
101S LEU* 3.0 8.0 + - - +
103S ASN* 1.3 79.9 - - - +
105S ARG* 1.3 63.4 + - - +
107S ARG* 4.2 3.4 - - - +
108S TYR* 3.0 26.8 + - - +
115S THR* 3.9 26.9 - - + +
122S VAL* 4.5 12.8 - - + -
124S ILE* 3.9 27.1 - - + +
685S ILE* 5.5 0.2 - - + -
696S LEU* 5.1 0.9 - - - -
701S VAL* 5.2 9.2 - - + -
705S LEU* 3.4 37.2 - - + -
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Residues in contact with ARG 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S TRP* 4.7 7.3 - - - -
42S HIS* 3.3 37.0 + - - +
44S PHE* 4.4 8.5 + - - +
101S LEU* 2.8 29.8 + - + +
102S HIS* 2.5 46.5 + - - +
104S LEU* 1.3 70.9 - - - +
106S GLU* 1.3 70.6 + - - +
108S TYR* 3.1 4.5 - - - +
109S PHE* 3.0 48.1 + - + -
696S LEU* 3.9 24.0 - - + +
698S ALA* 4.3 11.4 - - - +
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Residues in contact with GLU 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84S SER* 5.1 8.5 - - - +
85S LYS* 3.8 24.0 - - + +
102S HIS* 2.5 64.4 + - + +
103S ASN* 3.6 8.5 - - - +
105S ARG* 1.3 78.5 + - - +
107S ARG* 1.3 69.7 + - - +
109S PHE* 2.6 22.9 + - - +
110S SER* 2.9 14.2 + - - -
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Residues in contact with ARG 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S LEU 5.1 3.0 + - - -
15S VAL* 4.3 4.8 - - - +
85S LYS* 3.3 22.4 + - + +
86S VAL 3.0 19.5 + - - -
87S GLU* 2.5 34.5 + - - -
103S ASN* 2.7 39.9 - - - +
104S LEU* 4.2 3.6 - - - +
106S GLU* 1.3 74.0 - - - +
108S TYR* 1.3 57.6 + - - +
110S SER* 3.2 1.6 + - - -
111S GLY 3.1 5.4 + - - -
112S LEU* 2.7 79.5 + - + +
114S TYR 3.1 25.5 + - - -
115S THR* 3.4 24.2 + - - +
151S PRO* 4.1 4.0 - - - +
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Residues in contact with TYR 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S LEU 3.0 22.9 + - - +
105S ARG* 3.1 5.8 - - - +
106S GLU 2.6 3.4 + - - -
107S ARG* 1.3 74.6 - - - +
109S PHE* 1.3 77.1 + + - +
111S GLY* 3.1 14.7 + - - -
112S LEU 3.3 7.6 + - - -
113S ILE* 4.1 13.6 - - + +
124S ILE* 3.7 24.0 - - + -
125S ASN 3.3 26.5 + - - -
126S PRO* 3.5 23.7 + - + -
687S PRO* 4.1 5.5 - - + +
692S ARG 5.0 0.2 + - - -
693S ALA* 4.7 0.7 - - - -
694S GLY* 3.7 15.6 + - - -
695S LYS 4.1 8.9 + - - -
696S LEU* 3.4 41.5 - - + -
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Residues in contact with PHE 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105S ARG* 3.0 40.3 + - + -
106S GLU* 2.6 14.8 + - - +
108S TYR* 1.3 88.7 - + - +
110S SER* 1.3 59.4 + - - +
111S GLY* 3.3 1.2 + - - -
694S GLY* 3.1 34.1 - - - -
696S LEU* 4.0 23.1 - - + -
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Residues in contact with SER 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S LYS 3.9 14.9 - - - +
12S PHE* 3.9 7.2 - - - -
85S LYS* 3.5 30.0 + - - +
106S GLU* 2.9 11.4 + - - -
107S ARG 3.6 8.5 - - - -
109S PHE* 1.3 76.4 - - - +
111S GLY* 1.3 58.1 + - - +
112S LEU* 3.6 15.7 - - - -
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Residues in contact with GLY 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S PHE* 3.2 35.3 - - - +
107S ARG 3.1 1.6 + - - -
108S TYR 3.1 7.7 + - - -
109S PHE 3.1 4.7 - - - -
110S SER* 1.3 80.0 - - - +
112S LEU* 1.3 61.8 + - - +
113S ILE* 5.1 0.7 - - - -
130S LEU* 3.1 28.8 - - - +
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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