Contacts of the helix formed by residues 121 - 132 (chain M) in PDB entry 6Y5D
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 121 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108M THR* 4.4 0.2 - - - +
117M ARG* 3.7 20.6 - - - +
119M THR* 4.4 6.1 - - + +
120M ILE* 1.3 77.9 - - - +
122M PRO* 1.3 69.4 - - + +
123M LYS* 3.1 27.4 - - + +
124M ASP* 2.8 40.4 + - - +
125M ILE* 3.5 3.6 + - - +
48N SER* 3.9 15.9 - - - +
50N LEU* 5.8 4.9 - - + -
51N ILE* 3.3 8.7 - - - +
74U G 5.3 0.4 - - - +
75U C 3.8 23.3 - - - +
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Residues in contact with PRO 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M MET* 1.3 92.8 - - + +
123M LYS* 1.3 60.7 + - + +
125M ILE* 3.2 6.7 + - + +
126M GLN* 3.1 31.0 + - - +
48N SER* 4.1 5.2 - - - +
50N LEU* 3.4 49.4 - - + +
51N ILE* 3.4 12.9 - - + +
54N GLU* 3.8 25.7 - - + +
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Residues in contact with LYS 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ALA* 6.0 0.4 - - - +
117M ARG* 3.5 27.8 - - - +
121M MET* 4.1 31.3 - - + +
122M PRO* 1.3 77.9 - - + +
124M ASP* 1.3 63.0 + - - +
126M GLN* 3.7 16.3 - - - +
127M LEU* 2.9 30.1 + - - +
114Q HIS* 3.8 26.7 + - + +
116Q LYS* 5.7 6.9 - - - +
75U C 5.4 3.8 + - - -
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Residues in contact with ASP 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M THR* 3.5 26.7 - - + +
111M ALA* 3.3 5.5 - - + +
112M ALA* 3.1 21.2 + - - -
117M ARG* 3.0 23.1 + - - -
120M ILE* 3.9 0.2 - - - -
121M MET* 2.8 34.1 + - - +
123M LYS* 1.3 75.2 - - - +
125M ILE* 1.3 66.0 + - - +
127M LEU* 4.0 1.5 - - - +
128M ALA* 3.1 24.9 + - - +
114Q HIS* 2.5 32.8 + - - -
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Residues in contact with ILE 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M LEU* 3.9 27.3 - - + +
105M PHE* 4.4 9.0 - - + -
108M THR* 3.4 27.4 - - + +
121M MET 3.5 2.2 + - - +
122M PRO 3.2 7.3 + - - +
123M LYS 3.2 0.4 - - - -
124M ASP* 1.3 78.7 - - - +
126M GLN* 1.3 64.0 + - + +
128M ALA* 3.3 3.5 + - - +
129M ARG* 3.1 25.9 + - - +
51N ILE* 3.8 26.5 - - + -
54N GLU* 4.1 20.0 - - + +
55N THR* 3.9 22.0 - - - +
58N VAL* 4.3 17.7 - - + -
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Residues in contact with GLN 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M PRO* 3.1 14.3 + - - +
123M LYS* 3.7 16.4 - - - +
124M ASP 3.3 0.2 - - - -
125M ILE* 1.3 78.8 - - + +
127M LEU* 1.3 62.0 + - - +
129M ARG* 3.4 11.2 + - - +
130M ARG* 3.0 24.1 + - - +
54N GLU* 2.9 36.9 + - - +
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Residues in contact with LEU 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ALA* 4.2 10.1 - - + -
123M LYS 2.9 17.9 + - - +
124M ASP* 4.0 3.6 - - - +
126M GLN* 1.3 77.8 - - - +
128M ALA* 1.3 58.0 + - - +
130M ARG* 3.1 6.3 + - + +
131M ILE* 2.8 56.4 + - + +
110Q LEU* 3.7 38.1 - - + +
111Q ALA* 4.7 5.2 - - - -
114Q HIS* 3.5 43.7 - - + +
127Q LEU* 5.1 3.1 - - + -
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Residues in contact with ALA 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M LEU* 4.5 5.2 - - + -
107M ASP* 3.6 39.9 - - + +
108M THR* 4.0 4.5 - - - +
111M ALA* 5.2 0.6 - - + +
124M ASP 3.1 18.5 + - - +
125M ILE 3.7 3.8 - - - +
127M LEU* 1.3 76.7 - - - +
129M ARG* 1.3 64.3 + - - +
131M ILE 3.3 0.2 + - - -
132M ARG* 3.1 29.7 + - - +
131Q ILE* 3.6 15.4 - - + +
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Residues in contact with ARG 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100M TYR* 4.1 3.2 + - - +
104M LEU* 3.6 17.9 - - + +
125M ILE* 3.1 22.1 + - - +
126M GLN* 3.7 10.6 - - - +
128M ALA* 1.3 76.1 - - - +
130M ARG* 1.3 62.9 + - - +
132M ARG* 3.1 17.5 + - - +
133M GLY 3.2 0.3 + - - -
134M GLU* 2.7 71.1 + - + +
54N GLU* 5.9 0.6 + - - -
57N GLY 5.6 0.8 + - - -
58N VAL* 4.0 39.0 - - - +
61N VAL* 5.3 11.3 - - - +
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Residues in contact with ARG 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M GLN 3.0 14.6 + - - +
127M LEU* 3.5 7.4 - - + +
129M ARG* 1.3 80.9 - - - +
131M ILE* 1.3 63.3 + - - +
133M GLY* 2.9 17.0 + - - -
134M GLU 3.9 16.4 + - - +
111O ASN* 6.1 1.4 - - - +
106Q GLU* 4.8 16.1 + - - +
107Q ASP* 4.3 10.5 + - - +
110Q LEU* 4.1 25.5 - - + +
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Residues in contact with ILE 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M LEU* 2.8 52.8 + - + +
128M ALA 3.7 4.3 - - - +
130M ARG* 1.3 73.2 - - - +
132M ARG* 1.3 60.5 + - - +
133M GLY* 3.3 1.4 + - - -
107Q ASP* 3.3 45.1 - - + +
110Q LEU* 4.9 2.0 - - + -
111Q ALA* 5.2 1.3 - - + -
127Q LEU* 4.9 5.6 - - + -
128Q ALA* 3.6 22.9 - - + +
131Q ILE* 3.8 26.9 - - + -
132Q ARG* 3.5 32.9 + - + +
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Residues in contact with ARG 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100M TYR* 4.5 18.3 + - - -
103M GLY* 3.8 7.5 + - - -
104M LEU* 3.5 36.5 - - - +
107M ASP* 2.9 28.5 + - - -
128M ALA 3.1 19.2 + - - +
129M ARG* 3.1 10.7 + - - +
131M ILE* 1.3 77.0 - - - +
133M GLY* 1.3 58.1 + - - +
134M GLU* 3.6 16.9 + - + +
96N ARG* 4.9 7.9 - - - +
131Q ILE* 3.5 25.5 + - + +
132Q ARG* 4.3 8.7 - - - +
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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