Contacts of the helix formed by residues 112 - 128 (chain A) in PDB entry 3BYH
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 PRO 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.8 19.1 - - + -
110A LEU 4.3 0.2 - - - +
111A ASN* 1.3 90.0 - - - +
113A LYS* 1.3 65.6 + - - +
114A ALA* 3.4 2.2 - - + +
115A ASN* 3.0 31.9 + - - +
116A ARG* 3.3 5.9 + - - +
177A ARG* 1.3 88.8 - - - +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASN 3.5 2.0 + - - -
112A PRO* 1.3 69.8 - - - +
114A ALA* 1.3 64.0 + - + +
116A ARG* 3.2 20.5 + - - +
117A GLU* 3.2 19.3 + - - +
371A HIS* 3.5 33.2 - - + +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 3.4 2.1 - - + +
113A LYS* 1.3 77.0 - - + +
115A ASN* 1.3 62.8 + - - +
117A GLU* 3.7 12.2 - - - +
118A LYS* 2.8 28.5 + - - +
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.3 28.5 - - - +
76A VAL* 3.5 18.4 + - - +
79A TRP* 4.1 22.0 - - + +
111A ASN* 3.2 23.5 + - - +
112A PRO* 3.0 23.2 + - - +
114A ALA* 1.3 77.8 + - - +
116A ARG* 1.3 65.3 + - - +
118A LYS* 3.0 2.8 + - - +
119A MET* 2.9 29.0 + - + +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.0 52.2 + - - +
111A ASN* 3.5 23.8 - - - +
112A PRO 3.3 4.5 + - - +
113A LYS* 3.2 11.8 + - - +
115A ASN* 1.3 75.4 - - - +
117A GLU* 1.3 62.7 + - - +
119A MET* 3.4 14.2 + - + +
120A THR* 2.9 27.6 + - - -
134A VAL* 4.4 8.8 + - + +
370A VAL* 3.2 34.0 + - + +
371A HIS* 3.8 21.6 + - + +
374A CYS* 3.0 36.6 + - - +
375A PHE* 5.4 0.2 - - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 3.2 16.8 + - - +
114A ALA* 3.8 11.2 - - - +
115A ASN 3.2 0.2 - - - -
116A ARG* 1.3 74.8 - - - +
118A LYS* 1.3 64.6 + - - +
120A THR* 3.0 3.5 + - - -
121A GLN* 2.9 26.4 + - - +
367A PRO* 3.9 29.2 - - + +
368A SER* 4.2 13.5 + - - -
370A VAL* 4.0 8.1 - - - -
371A HIS* 2.8 30.5 + - + -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.4 54.0 - - + +
80A ASP* 5.7 0.6 + - - -
83A GLU* 4.5 6.5 + - - -
114A ALA 2.8 21.6 + - - +
115A ASN 3.0 4.0 + - - +
117A GLU* 1.3 71.2 - - - +
119A MET* 1.3 57.8 + - - +
121A GLN* 3.1 16.9 - - + +
122A ILE* 3.0 51.5 + - + +
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASN* 5.7 0.4 - - - -
76A VAL* 6.4 2.0 - - + -
79A TRP* 4.2 13.8 - - + -
86A TRP* 4.2 21.5 - - + -
105A LEU* 3.5 27.8 - - + -
106A THR 4.7 5.4 - - - +
107A GLU* 4.4 7.6 - - + -
111A ASN* 3.5 28.9 - - - +
115A ASN* 2.9 19.9 + - + +
116A ARG* 3.5 11.0 - - - +
118A LYS* 1.3 76.2 - - - +
120A THR* 1.4 60.0 + - - +
122A ILE* 4.6 3.6 - - - +
123A MET* 3.2 30.8 + - - +
132A MET* 3.9 1.0 - - + +
134A VAL* 3.9 25.4 - - + -
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Residues in contact with THR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ARG 2.9 15.0 + - - -
117A GLU 3.0 8.8 + - - -
119A MET* 1.4 73.9 - - - +
121A GLN* 1.3 60.0 + - - +
123A MET* 3.6 0.5 + - - +
124A PHE* 2.9 50.8 + - + +
132A MET* 4.1 14.6 - - - -
357A ILE* 5.3 2.0 - - + -
362A TYR* 3.7 26.7 - - + -
367A PRO* 4.2 11.0 - - + +
369A ILE* 4.9 6.5 - - + -
370A VAL* 3.0 28.3 - - + +
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 2.9 12.7 + - - +
118A LYS* 3.1 25.4 - - + +
120A THR* 1.3 76.2 - - - +
122A ILE* 1.4 57.0 + - + +
124A PHE* 3.9 0.3 - - - +
125A GLU* 2.9 70.3 + - - +
362A TYR* 3.3 17.9 + - - -
367A PRO* 3.9 20.4 - - + +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.5 36.1 - - + -
83A GLU* 3.9 30.3 - - + +
86A TRP* 4.1 15.9 - - + -
118A LYS* 3.0 34.9 + - + +
119A MET* 4.4 3.4 - - - +
121A GLN* 1.4 74.2 - - + +
123A MET* 1.3 70.1 - - - +
126A THR* 2.8 39.1 + - - +
127A PHE* 2.9 32.0 + - + -
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Residues in contact with MET 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 3.5 41.5 - - + -
90A PHE* 4.0 16.4 - - + -
103A VAL* 3.8 22.4 - - - -
105A LEU* 3.8 14.4 - - + -
119A MET 3.2 21.1 + - - +
120A THR 3.9 1.8 - - - +
122A ILE* 1.3 82.0 - - + +
124A PHE* 1.3 57.9 + - - +
127A PHE* 3.1 37.0 + - + +
128A ASN 3.2 3.1 + - - -
129A THR* 2.7 26.9 + - - +
132A MET* 3.8 26.7 - - + -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A THR* 2.9 35.7 + - + +
123A MET* 1.3 77.6 - - - +
125A GLU* 1.3 58.5 + - - +
128A ASN* 3.0 26.5 - - - +
129A THR* 3.0 32.3 - - - +
131A ALA* 4.0 5.8 - - - -
132A MET* 3.6 24.5 - - + -
357A ILE* 3.6 28.9 - - + -
358A SER 4.0 6.1 - - - -
359A LYS* 3.7 37.2 + - + +
362A TYR* 3.3 44.2 - + + -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLN* 2.9 42.1 + - - +
124A PHE* 1.3 73.2 - - - +
126A THR* 1.4 66.5 + - - +
128A ASN* 4.4 4.7 + - - +
359A LYS* 4.7 6.3 - - - +
362A TYR* 2.8 31.4 + - + +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.9 23.0 + - - +
122A ILE* 2.8 35.7 + - + +
125A GLU* 1.4 77.5 - - - +
127A PHE* 1.3 78.2 + - + +
128A ASN* 5.3 0.4 - - - +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 4.0 11.4 - - + -
86A TRP* 3.9 17.0 - + + -
87A HIS* 3.7 41.7 - - + -
90A PHE* 4.2 6.3 - + + -
91A TYR* 4.1 23.2 + + - -
98A PRO* 3.3 32.8 - - + +
99A GLU* 3.8 6.6 - - - +
122A ILE* 2.9 33.5 + - + -
123A MET* 3.4 27.1 - - + +
126A THR* 1.3 88.4 - - + +
128A ASN* 1.3 73.6 + - - +
129A THR* 4.1 4.9 - - - +
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Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLU* 3.1 37.5 + - + +
123A MET 3.2 1.0 + - - -
124A PHE 3.0 19.5 + - - +
125A GLU 5.1 3.8 - - - +
126A THR 3.6 1.6 - - - -
127A PHE* 1.3 81.1 - - - +
129A THR* 1.3 62.9 - - - +
130A PRO 3.9 0.3 - - - -
359A LYS* 3.8 20.8 + - - +
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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