Contacts of the helix formed by residues 101 - 112 (chain H) in PDB entry 3HR4
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 101 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H ASP* 5.3 1.1 + - - -
99H TYR 3.7 1.8 + - - -
100H ILE* 1.3 78.1 - - - +
102H ALA* 1.3 64.5 + - - +
103H ALA* 2.8 13.0 + - - +
104H GLU* 2.7 48.5 + - - +
105H LEU* 3.3 8.3 + - - +
135H GLN* 4.2 20.1 - - - +
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ILE 3.7 1.4 + - - -
101H SER* 1.3 72.8 - - - +
103H ALA* 1.3 55.9 + - - +
105H LEU* 3.7 1.8 + - - +
106H ARG* 3.1 22.2 + - - +
121H VAL* 3.1 27.8 - - + +
122H ASP* 4.1 13.2 - - - +
125H ILE* 3.5 31.9 - - + +
134H GLY 4.5 6.5 + - - +
135H GLN* 5.2 0.4 - - - +
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Residues in contact with ALA 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H SER* 2.8 11.4 + - - +
102H ALA* 1.3 75.8 - - - +
104H GLU* 1.3 55.1 + - + +
105H LEU 3.1 1.1 - - - -
106H ARG* 2.8 26.0 + - - +
107H HIS* 2.6 36.2 + - - +
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Residues in contact with GLU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H PHE* 3.7 17.4 - - - +
93H ASP* 4.0 1.3 - - - -
94H LYS* 3.2 23.4 + - + +
95H ASP* 3.1 17.6 + - - +
99H TYR 3.1 2.1 - - - +
100H ILE* 3.1 9.6 - - + -
101H SER* 2.7 44.3 + - - +
103H ALA* 1.3 75.7 - - + +
105H LEU* 1.3 61.0 + - - +
107H HIS* 3.3 9.6 - - - +
108H VAL* 3.1 29.3 + - - +
203H CA 2.3 31.6 - - - -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515G LEU* 4.9 13.2 - - + -
518G LEU* 4.2 17.3 - - + -
92H PHE* 4.6 11.0 - - + -
100H ILE* 4.2 13.5 - - + +
101H SER 3.3 7.3 + - - +
102H ALA* 3.7 9.0 - - - +
103H ALA 3.1 0.4 - - - -
104H GLU* 1.3 76.4 - - - +
106H ARG* 1.3 65.7 + - - +
108H VAL* 3.1 6.2 + - - +
109H MET* 2.8 29.2 + - + +
121H VAL* 3.6 17.7 - - + +
124H MET* 3.2 43.1 - - + -
125H ILE* 3.7 17.0 - - + +
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Residues in contact with ARG 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H ALA* 3.1 15.5 + - - +
103H ALA* 2.8 31.3 + - - +
105H LEU* 1.3 79.7 - - - +
107H HIS* 1.3 62.9 + - - +
109H MET* 3.3 6.9 + - - +
110H THR* 3.0 38.3 + - + +
116H LEU* 4.2 13.9 - - + +
118H ASP* 2.7 41.3 + - - +
121H VAL* 3.4 37.0 - - + +
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Residues in contact with HIS 107 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94H LYS* 4.1 32.3 - - + +
103H ALA 2.6 15.6 + - - +
104H GLU* 3.3 15.0 + - - +
106H ARG* 1.3 71.3 - - - +
108H VAL* 1.3 66.2 + - - +
110H THR* 2.5 26.0 + - - -
111H ASN* 3.3 30.4 + - - -
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518G LEU* 4.7 9.9 - - + -
522G VAL* 6.5 1.6 - - + -
38H SER 5.6 1.3 - - - +
39H LEU* 5.2 11.7 - - + -
91H VAL* 4.1 19.5 - - + +
92H PHE* 3.7 38.4 - - + +
104H GLU 3.3 13.7 - - - +
105H LEU* 3.1 6.8 + - + +
107H HIS* 1.3 83.3 - - + +
109H MET* 1.3 65.2 + - - +
110H THR 3.3 0.2 + - - -
111H ASN* 3.3 18.8 + - - +
112H LEU* 3.7 21.4 + - + +
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Residues in contact with MET 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513G ILE* 3.6 31.0 - - + -
518G LEU* 3.6 28.9 - - - -
105H LEU* 2.8 32.7 + - + +
106H ARG* 3.4 12.1 - - + +
108H VAL* 1.3 75.5 - - - +
110H THR* 1.3 58.7 + - + +
112H LEU* 3.4 14.6 + - - +
114H GLU* 2.7 30.9 + - + +
116H LEU* 3.1 40.6 - - + -
124H MET* 3.4 20.6 - - + -
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Residues in contact with THR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ARG* 3.0 25.6 + - + +
107H HIS* 2.5 28.6 + - - -
109H MET* 1.3 70.3 - - + +
111H ASN* 1.3 64.5 + - - -
112H LEU 2.9 4.4 + - - -
113H GLY* 3.0 16.3 + - - -
114H GLU 3.4 6.3 - - - -
115H LYS* 4.2 24.7 - - + -
116H LEU 4.7 4.3 - - - +
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Residues in contact with ASN 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H SER* 3.9 40.4 + - - +
107H HIS* 3.3 44.7 + - - -
108H VAL* 3.3 11.7 + - - +
110H THR* 1.3 80.8 + - - +
112H LEU* 1.3 59.1 + - + +
113H GLY 3.3 4.0 + - - -
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Residues in contact with LEU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518G LEU* 4.2 23.8 - - + -
521G ALA* 6.3 1.1 - - + -
18H LEU* 5.6 14.4 - - + +
21H LYS* 3.7 21.9 + - - +
35H VAL* 4.2 26.5 - - + -
38H SER* 3.6 28.3 - - - +
39H LEU* 4.3 15.9 - - + -
108H VAL* 3.8 16.6 - - + +
109H MET* 3.4 9.5 + - - +
110H THR 2.9 2.2 + - - -
111H ASN* 1.3 77.0 - - + +
113H GLY* 1.3 53.7 + - - -
114H GLU* 2.9 15.4 + - + +
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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