Contacts of the helix formed by residues 113 - 127 (chain A) in PDB entry 1MZC
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLU* 2.6 38.2 + - - -
112A ARG* 1.3 77.2 - - - +
114A GLU* 1.3 59.9 + - - +
115A ARG* 3.2 7.3 - - - +
116A ALA* 3.2 16.1 + - - +
117A PHE* 3.0 22.5 + - - +
140A LEU* 3.8 1.8 - - - +
144A LEU* 3.4 15.1 - - - +
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Residues in contact with GLU 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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113A SER* 1.3 71.4 - - - +
115A ARG* 1.3 66.8 + - - +
117A PHE* 3.1 12.8 + - - +
118A LYS* 3.0 58.4 + - - +
144A LEU* 3.9 13.4 - - + +
146A LYS* 3.0 34.8 + - - +
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Residues in contact with ARG 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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66A TYR* 5.3 0.2 - - - -
71A GLU* 2.8 22.6 + - + -
72A TRP* 3.3 52.8 + - + +
74A ASP* 2.8 43.0 + - - -
75A ILE* 3.9 14.8 - - - +
109A ARG* 3.9 1.8 - - - +
111A GLU* 2.7 33.4 + - - +
113A SER* 3.2 12.0 - - - +
114A GLU* 1.3 79.2 - - - +
116A ALA* 1.3 66.3 + - - +
118A LYS* 3.4 11.0 + - - +
119A LEU 3.0 17.8 + - - -
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Residues in contact with ALA 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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72A TRP* 4.2 5.4 - - - -
106A VAL* 3.3 34.2 - - + +
111A GLU* 3.5 8.5 - - - +
113A SER* 3.2 18.7 + - - +
114A GLU 3.2 0.2 - - - -
115A ARG* 1.3 80.5 - - - +
117A PHE* 1.3 63.6 + - - +
119A LEU* 3.1 10.9 + - - +
120A THR* 3.1 25.6 + - - +
136A PHE* 4.4 1.3 - - + -
140A LEU* 3.8 9.9 - - + -
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Residues in contact with PHE 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 SER 3.0 13.2 + - - +
114A GLU* 3.1 24.2 + - - +
116A ALA* 1.3 76.9 - - - +
118A LYS* 1.3 64.1 + - + +
120A THR* 2.6 22.2 + - - -
137A ARG* 3.3 54.0 + - + -
140A LEU* 3.6 25.1 - - + +
141A LEU* 3.6 33.4 - - + -
144A LEU* 3.8 12.6 - - + -
146A LYS* 3.7 27.6 - - + -
151A GLU* 4.0 3.1 - - - -
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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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55A PHE* 4.2 51.1 - - + +
66A TYR* 4.2 7.6 + - + +
114A GLU* 3.0 46.2 + - + +
115A ARG* 3.8 10.8 - - - +
117A PHE* 1.3 78.4 - - + +
119A LEU* 1.3 63.5 + - - +
121A ARG* 3.2 25.2 + - - +
122A ASP* 3.6 6.2 + - - +
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Residues in contact with LEU 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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66A TYR* 3.4 40.4 - - + +
72A TRP* 3.8 23.1 - - + -
99A VAL* 3.8 23.1 - - + +
102A TYR* 3.8 8.5 - - + +
103A PHE* 3.7 36.1 - - + +
106A VAL* 4.2 9.2 - - + -
115A ARG 3.0 13.5 + - - +
116A ALA 3.3 9.9 - - - +
118A LYS* 1.3 76.1 - - - +
120A THR* 1.3 66.6 + - - +
122A ASP* 2.9 12.0 + - - +
123A ALA* 3.0 11.1 + - - +
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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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103A PHE* 4.4 9.2 - - + -
106A VAL* 6.2 0.2 - - + -
116A ALA 3.1 14.8 + - - +
117A PHE* 2.6 18.7 + - - -
119A LEU* 1.3 75.3 - - - +
121A ARG* 1.3 56.3 + - - +
123A ALA* 3.6 3.2 - - - +
124A ILE* 2.8 36.9 + - - +
133A VAL* 3.9 22.7 - - + +
136A PHE* 4.2 14.1 - - + -
137A ARG* 2.8 37.1 + - - +
140A LEU* 4.0 17.5 - - + -
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Residues in contact with ARG 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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55A PHE 5.7 8.3 - - - +
56A VAL 6.0 1.6 - - - -
57A SER* 6.5 0.7 - - - +
117A PHE 4.5 0.4 - - - +
118A LYS* 3.2 17.5 + - - +
119A LEU 3.0 0.8 - - - -
120A THR* 1.3 82.5 + - - +
122A ASP* 1.3 68.3 + - - +
124A ILE* 3.5 2.8 + - - +
125A GLU* 3.1 21.0 + - + +
137A ARG* 3.9 21.6 - - - +
154A TYR* 3.4 52.5 + - + +
158A ILE* 5.7 0.6 - - - +
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Residues in contact with ASP 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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56A VAL 3.9 15.7 - - - +
57A SER* 4.7 1.6 - - - -
58A LEU* 3.3 35.5 + - + +
63A TYR* 4.1 10.6 - - - -
66A TYR* 2.5 31.8 + - - +
69A ARG* 4.4 2.1 + - - -
99A VAL* 4.2 15.9 - - + -
118A LYS 3.6 5.3 + - - +
119A LEU 2.9 7.9 + - - +
121A ARG* 1.3 83.6 - - - +
123A ALA* 1.3 67.7 + - - +
125A GLU* 3.2 3.7 + - - +
126A LEU* 3.1 20.6 + - - +
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Residues in contact with ALA 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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99A VAL* 3.7 18.7 - - + +
100A TYR* 2.8 38.6 + - + +
103A PHE* 4.8 8.5 - - + -
119A LEU 3.0 12.5 + - - +
120A THR* 3.6 8.3 - - - +
122A ASP* 1.3 75.8 - - - +
124A ILE* 1.3 57.5 + - - +
126A LEU* 3.3 2.8 + - - +
127A ASN 3.0 18.0 + - - -
133A VAL* 3.8 18.4 - - + -
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Residues in contact with ILE 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 2.8 21.6 + - - +
121A ARG 3.7 4.5 - - - +
122A ASP 3.2 0.2 - - - -
123A ALA* 1.3 74.2 - - - +
125A GLU* 1.3 65.4 + - - +
127A ASN 3.0 6.7 - - - +
128A ALA* 2.8 40.5 + - + +
133A VAL* 3.7 17.5 - - + -
134A TRP* 3.5 47.6 - - + +
137A ARG* 3.7 26.9 - - + -
154A TYR* 3.6 23.1 - - - +
158A ILE* 5.1 8.3 - - + -
162A GLN* 6.0 0.4 - - - +
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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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57A SER* 3.7 9.2 + - - -
58A LEU* 3.0 37.9 + - + +
59A ASP* 3.3 21.9 - - - +
121A ARG* 3.1 15.3 + - + +
122A ASP* 3.2 11.4 + - - +
124A ILE* 1.3 78.6 - - - +
126A LEU* 1.3 62.8 + - - +
127A ASN 3.6 0.2 + - - -
128A ALA 4.8 0.9 + - - -
158A ILE* 6.4 1.3 - - + -
162A GLN* 4.9 10.3 + - - +
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Residues in contact with LEU 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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58A LEU* 3.3 27.8 - - + -
93A SER* 5.4 1.6 - - - +
95A LYS* 4.0 4.3 - - + +
96A PHE* 3.8 54.6 - - + +
99A VAL* 3.5 41.5 - - + -
100A TYR* 4.1 4.3 - - + -
122A ASP 3.1 11.3 + - - +
123A ALA 3.5 6.7 - - - +
125A GLU* 1.3 79.0 - - + +
127A ASN* 1.3 61.0 + - - +
594B GLU* 4.9 9.5 - - - +
595B CYS* 5.3 1.6 + - - -
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Residues in contact with ASN 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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96A PHE* 4.2 6.7 - - + -
100A TYR* 3.8 10.7 + - - +
123A ALA 3.0 9.9 + - - +
124A ILE* 3.0 7.3 + - - +
126A LEU* 1.3 80.4 - - - +
128A ALA* 1.3 58.5 + - - +
129A ALA* 3.1 24.4 + - - +
130A ASN* 3.1 35.8 + - - +
134A TRP* 5.1 0.3 + - - -
594B GLU 3.8 22.3 + - - +
595B CYS* 3.5 13.1 + - - +
597B ASP* 3.9 6.7 + - - +
598B ALA* 3.9 21.2 - - - +
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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