Contacts of the helix formed by residues 112 - 125 (chain I) in PDB entry 4XZG
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 LYS 112 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66I HIS* 4.1 34.6 + - + +
68I VAL* 3.5 38.2 - - + +
110I HIS* 3.8 2.2 + - - -
111I LEU* 1.3 77.8 - - - +
113I LYS* 1.3 58.9 + - - +
114I GLU* 3.3 19.7 + - - +
115I LEU* 3.4 12.0 + - + +
116I ALA* 2.9 24.3 + - - +
143I THR* 5.6 2.6 - - - +
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Residues in contact with LYS 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I TYR 4.8 11.5 + - - +
94I ASP* 4.0 28.2 + - + +
96I ASN* 5.8 0.2 + - - -
111I LEU 3.6 1.0 + - - -
112I LYS* 1.3 70.2 - - - +
114I GLU* 1.3 77.5 + - + +
116I ALA* 3.7 3.2 - - - +
117I GLY* 3.1 18.5 + - - -
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Residues in contact with GLU 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I LYS* 3.6 26.0 - - - +
113I LYS* 1.3 84.2 - - + +
115I LEU* 1.3 63.5 + - - +
117I GLY* 3.1 4.7 + - - -
118I ALA* 3.1 16.3 + - - +
167I HIS* 4.2 11.1 - - - +
169I PHE* 3.8 21.7 - - + -
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Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 3.6 29.2 - - + -
65I GLY* 4.7 10.8 - - - -
66I HIS 5.0 4.3 - - - +
111I LEU* 4.0 27.4 - - + -
112I LYS* 3.4 13.2 + - + +
114I GLU* 1.3 76.6 + - - +
116I ALA* 1.3 67.1 + - - +
118I ALA* 3.1 5.1 + - + +
119I LEU* 3.0 42.8 + - + +
148I MET* 3.7 25.1 - - + -
169I PHE* 3.7 28.9 - - + -
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Residues in contact with ALA 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I ASP* 4.5 5.4 - - - +
96I ASN* 3.4 23.7 - - - +
97I ALA* 4.6 0.9 - - - -
98I ILE* 3.9 18.8 - - + +
111I LEU* 4.2 12.5 - - + +
112I LYS 2.9 19.3 + - - +
113I LYS* 3.7 7.4 - - - +
114I GLU 3.2 0.2 - - - -
115I LEU* 1.3 77.0 - - - +
117I GLY* 1.3 57.7 + - - +
119I LEU 3.0 0.2 + - - -
120I ALA* 2.9 34.7 + - - +
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Residues in contact with GLY 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I ASN* 3.8 22.8 + - - +
113I LYS 3.1 14.5 + - - -
114I GLU* 3.1 5.6 + - - -
116I ALA* 1.3 76.5 - - - +
118I ALA* 1.3 60.2 + - - +
120I ALA* 4.2 6.6 + - - +
121I TYR* 4.5 1.4 + - - +
163I GLN* 3.6 7.6 + - - -
167I HIS* 3.5 24.1 + - - -
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Residues in contact with ALA 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I GLU 3.1 5.2 + - - +
115I LEU* 3.1 10.6 + - + +
117I GLY* 1.3 77.0 - - - +
119I LEU* 1.3 63.0 + - + +
120I ALA 3.7 0.2 + - - -
122I ILE* 3.6 6.2 + - - +
163I GLN* 3.3 26.9 + - - +
164I LEU* 4.0 20.9 - - + -
167I HIS* 3.7 30.1 - - + +
169I PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I LEU* 4.4 4.0 - - + -
98I ILE* 3.5 15.0 - - + -
111I LEU* 3.6 26.7 - - + -
115I LEU* 3.0 28.8 + - + +
116I ALA 3.0 0.4 + - - -
118I ALA* 1.3 80.8 - - + +
120I ALA* 1.3 60.4 + - - +
121I TYR 3.3 2.2 - - - -
122I ILE* 2.9 8.7 + - + +
123I MET* 2.8 33.3 + - + +
130I ILE* 4.2 19.3 - - + -
148I MET* 4.3 15.7 - - - -
150I PHE* 3.8 27.6 - - + -
164I LEU* 3.9 14.8 - - + -
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Residues in contact with ALA 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I ARG* 3.8 27.5 + - - +
96I ASN* 3.5 33.9 - - + +
98I ILE* 4.0 1.5 - - - +
116I ALA 2.9 16.7 + - - +
117I GLY 4.4 2.9 - - - +
118I ALA 3.5 0.4 - - - -
119I LEU* 1.3 76.9 - - - +
121I TYR* 1.3 63.4 + - - +
124I ASP* 2.9 32.1 + - - +
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Residues in contact with TYR 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I GLY 4.5 1.6 + - - +
118I ALA 4.1 0.8 + - - -
119I LEU 3.3 0.4 - - - -
120I ALA* 1.3 77.5 - - - +
122I ILE* 1.3 64.6 + - - +
124I ASP* 4.6 2.9 - - - -
125I ASN* 2.8 55.3 + - - +
127I LEU* 3.8 24.2 - - + +
159I ALA* 5.5 2.9 - - + -
163I GLN* 3.4 47.6 - - + +
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Residues in contact with ILE 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I ALA 3.6 18.2 - - - +
119I LEU* 2.9 14.9 + - + +
121I TYR* 1.3 76.5 - - - +
123I MET* 1.3 60.0 + - - +
126I LYS* 3.3 1.9 + - - -
127I LEU* 2.9 44.2 + - + -
128I ALA* 3.8 31.4 + - + +
130I ILE* 4.3 14.6 - - + -
150I PHE* 4.6 2.5 - - + -
160I VAL* 3.7 26.5 - - + +
163I GLN* 3.8 19.5 - - + -
164I LEU* 3.9 22.2 - - + -
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Residues in contact with MET 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I LEU* 3.6 37.0 - - + +
87I ARG* 3.9 26.0 - - + +
98I ILE* 4.0 33.4 - - - -
119I LEU* 2.8 20.7 + - - +
120I ALA 4.0 1.3 - - - +
122I ILE* 1.3 71.2 - - - +
124I ASP* 1.3 66.0 + - - +
126I LYS* 3.2 17.1 + - - +
128I ALA 4.9 5.8 - - - +
130I ILE* 3.8 28.3 - - + -
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Residues in contact with ASP 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I ARG* 2.8 47.2 + - - +
89I PRO* 5.5 2.2 - - - +
120I ALA* 2.9 24.0 + - - +
121I TYR* 4.0 4.0 - - - +
123I MET* 1.3 72.3 - - - +
125I ASN* 1.3 65.7 + - - +
126I LYS* 3.2 7.8 + - - +
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Residues in contact with ASN 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I TYR* 2.8 65.2 + - + +
124I ASP* 1.3 84.1 - - - +
126I LYS* 1.3 71.8 + - - +
127I LEU* 2.9 25.4 + - + +
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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