Contacts of the helix formed by residues 120 - 132 (chain I) in PDB entry 4Z2M
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 MET 120 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116I ARG* 3.3 32.1 - - - +
118I THR* 4.2 6.7 - - + +
119I ILE* 1.3 77.0 - - - +
121I PRO* 1.3 68.3 - - + +
122I LYS* 4.1 17.3 - - + +
123I ASP* 2.5 36.1 + - - +
124I ILE* 3.5 3.3 + - - +
47J SER* 3.4 26.9 - - - +
49J LEU* 4.2 14.1 - - + -
50J ILE* 3.6 6.7 - - - +
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Residues in contact with PRO 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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120I MET* 1.3 87.6 - - + +
122I LYS* 1.3 61.2 + - - +
124I ILE* 3.4 2.8 + - + +
125I GLN* 3.0 48.3 + - - +
47J SER* 4.4 2.5 - - - +
49J LEU* 3.7 46.2 - - + +
50J ILE* 3.9 8.5 - - + -
53J GLU* 3.7 26.7 - - + +
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Residues in contact with LYS 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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113G HIS* 4.0 34.1 + - + +
115G LYS* 5.6 9.7 - - - +
116I ARG* 4.7 13.0 - - - +
120I MET* 4.1 16.4 - - + +
121I PRO* 1.3 77.9 - - - +
123I ASP* 1.3 55.4 + - - +
125I GLN* 3.5 11.2 + - - +
126I LEU* 3.0 27.9 + - - +
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Residues in contact with ASP 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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113G HIS* 3.0 16.7 + - - -
107I THR* 3.5 24.2 - - + +
110I CYS* 3.4 5.3 - - - -
111I ALA* 3.1 17.6 + - - -
116I ARG* 2.7 38.3 + - - -
119I ILE* 3.2 3.5 - - - -
120I MET* 2.5 39.3 + - - +
122I LYS* 1.3 71.3 - - - +
124I ILE* 1.3 65.3 + - - +
126I LEU* 3.2 4.0 + - - +
127I ALA* 3.0 22.3 + - - +
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Residues in contact with ILE 124 (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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103I LEU* 4.1 26.9 - - + -
104I PHE* 4.5 10.3 - - + -
107I THR* 3.4 27.4 - - + +
120I MET 3.5 6.5 + - - +
121I PRO 3.4 5.3 + - - +
123I ASP* 1.3 74.3 - - - +
125I GLN* 1.3 59.9 + - + +
127I ALA* 3.0 3.3 + - - +
128I ARG* 2.8 33.3 + - - +
50J ILE* 4.1 18.6 - - + -
53J GLU* 3.8 26.7 - - + +
54J THR* 4.3 16.8 - - + +
57J VAL* 4.1 19.1 - - + -
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Residues in contact with GLN 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 PRO* 3.0 29.6 + - - +
122I LYS* 3.6 8.9 - - - +
124I ILE* 1.3 76.3 - - + +
126I LEU* 1.3 56.4 + - - +
128I ARG* 4.0 7.5 - - - +
129I ARG* 2.9 44.9 + - - +
134I ARG 5.3 0.7 - - - +
53J GLU* 3.0 33.3 + - - +
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Residues in contact with LEU 126 (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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109G LEU* 4.0 27.8 - - + +
110G CYS* 4.5 12.8 - - - -
113G HIS* 3.5 40.6 - - + +
126G LEU* 5.1 2.2 - - + -
110I CYS* 3.6 22.7 - - - -
122I LYS 3.0 14.7 + - - +
123I ASP 3.2 7.4 + - - +
125I GLN* 1.3 76.5 - - - +
127I ALA* 1.3 62.4 + - - +
129I ARG* 3.3 8.5 + - + +
130I ILE* 3.0 43.8 + - + +
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Residues in contact with ALA 127 (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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130G ILE* 3.9 7.2 - - - +
103I LEU* 4.0 11.9 - - + -
106I ASP* 3.7 31.2 - - + +
107I THR* 4.0 10.5 - - - +
110I CYS* 4.4 5.4 - - - -
123I ASP 3.0 13.7 + - - +
124I ILE 3.0 7.4 + - - +
126I LEU* 1.3 76.7 - - - +
128I ARG* 1.3 57.7 + - - +
130I ILE* 3.4 2.3 + - - +
131I ARG* 2.9 35.7 + - - +
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Residues in contact with ARG 128 (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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99I TYR* 3.8 5.0 + - - -
103I LEU* 4.1 10.8 - - + -
124I ILE* 2.8 22.5 + - - +
125I GLN* 4.0 7.1 - - - +
127I ALA* 1.3 75.0 - - - +
129I ARG* 1.3 66.9 + - - +
131I ARG* 3.1 6.8 + - - +
132I GLY 3.0 18.0 + - - -
133I GLU* 3.0 56.3 + - + +
134I ARG* 3.0 42.3 - - - +
57J VAL* 3.6 41.7 - - - +
60J VAL* 4.1 28.1 - - - +
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Residues in contact with ARG 129 (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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106G ASP* 5.0 1.3 - - - +
109G LEU* 3.5 43.2 - - + +
125I GLN* 2.9 33.0 + - - +
126I LEU* 3.5 10.6 - - - +
128I ARG* 1.3 76.0 - - - +
130I ILE* 1.3 58.2 + - - +
132I GLY* 2.9 21.1 + - - -
134I ARG 4.0 10.9 + - - +
135I ALA* 3.5 31.6 + - - -
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Residues in contact with ILE 130 (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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106G ASP* 3.9 38.4 - - + +
109G LEU* 4.4 4.9 - - + -
110G CYS* 3.7 29.6 - - - -
127G ALA* 3.9 9.9 - - - +
130G ILE* 3.8 28.0 - - + -
131G ARG* 3.7 31.6 + - + +
126I LEU* 3.0 29.1 + - + +
127I ALA 3.9 3.1 - - - +
129I ARG* 1.3 74.7 - - - +
131I ARG* 1.3 61.0 + - - +
132I GLY* 3.1 1.3 + - - -
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Residues in contact with ARG 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B LYS* 4.0 6.3 - - - +
130G ILE* 3.7 18.4 - - + +
131G ARG* 5.8 2.7 - - - +
99I TYR* 3.2 27.9 + - - -
102I GLY* 3.6 17.0 + - - -
103I LEU* 3.8 23.8 - - - +
106I ASP* 2.8 35.3 + - - +
127I ALA 2.9 27.2 + - - +
128I ARG 3.1 5.3 + - - +
130I ILE* 1.3 75.6 - - - +
132I GLY* 1.3 62.0 + - - +
133I GLU* 2.9 37.8 + - + +
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Residues in contact with GLY 132 (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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129I ARG 2.9 16.2 + - - -
130I ILE 3.1 2.3 - - - -
131I ARG* 1.3 79.0 - - - +
133I GLU* 1.3 60.7 + - - +
134I ARG 5.3 0.9 - - - -
135I ALA* 5.5 1.8 - - - -
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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