Contacts of the helix formed by residues 107 - 124 (chain M) in PDB entry 6K4Y
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 THR 107 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M GLU 4.3 5.4 - - - +
106M ILE* 1.3 81.3 - - - +
108M SER* 1.3 60.8 + - - +
109M ASP* 3.8 8.1 + - - +
110M MET* 3.1 26.2 + - - +
111M GLU* 3.1 20.5 + - - +
156M ASN* 3.4 18.2 + - - +
196M ARG* 3.5 12.8 + - - +
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Residues in contact with SER 108 (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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106M ILE 4.0 0.6 + - - -
107M THR* 1.3 71.3 - - - +
109M ASP* 1.3 67.0 + - - +
111M GLU* 3.2 15.0 + - - +
112M GLU* 2.9 38.6 + - - +
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Residues in contact with ASP 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M THR* 3.3 9.1 + - - +
108M SER* 1.3 81.4 + - - +
110M MET* 1.3 58.2 + - - +
112M GLU* 4.0 16.0 - - - +
113M ASP* 2.9 43.4 + - - +
196M ARG* 4.2 7.4 - - - +
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Residues in contact with MET 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M ILE* 3.6 13.2 - - + -
107M THR* 3.1 21.8 + - - +
109M ASP* 1.3 76.4 - - - +
111M GLU* 1.3 59.6 + - - +
113M ASP* 3.8 0.5 - - - +
114M LYS* 2.9 28.2 + - - +
136M SER 3.7 5.4 - - - +
137M ASN* 3.7 13.7 - - - -
138M TYR* 3.5 27.6 - - + -
154M ILE* 3.3 40.5 - - + +
155M ASN 3.7 1.6 - - - -
156M ASN* 3.4 44.6 - - - +
196M ARG* 3.7 13.9 - - - +
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Residues in contact with GLU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M ILE* 3.3 15.4 - - + +
107M THR 3.1 14.5 + - - +
108M SER* 3.2 16.6 + - - +
110M MET* 1.3 75.2 - - - +
112M GLU* 1.3 60.5 + - + +
114M LYS* 3.2 21.1 + - - +
115M ASP* 2.9 34.8 + - - +
133M ILE* 5.5 0.5 - - - +
138M TYR* 2.5 29.3 + - - -
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Residues in contact with GLU 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M SER* 2.9 25.0 + - - +
109M ASP* 4.0 17.6 - - - +
111M GLU* 1.3 75.0 - - + +
113M ASP* 1.3 64.0 + - - +
115M ASP* 3.0 16.8 + - - +
116M LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M ASP* 2.9 27.0 + - - +
110M MET 4.1 0.7 - - - +
112M GLU* 1.3 76.7 - - - +
114M LYS* 1.3 60.3 + - - +
116M LEU* 5.4 0.5 - - - +
117M MET* 2.9 28.9 + - - +
154M ILE* 4.3 6.2 - - + +
196M ARG* 3.2 45.0 + - + +
197M SER* 4.3 4.4 - - - -
198M ALA* 3.7 15.2 + - - +
201M ILE* 3.4 28.2 - - + +
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Residues in contact with LYS 114 (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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110M MET 2.9 19.8 + - - +
111M GLU* 3.3 21.2 + - - +
113M ASP* 1.3 77.7 - - - +
115M ASP* 1.3 73.2 + - - +
117M MET* 4.0 13.2 - - + -
118M LEU* 2.9 56.6 + - + +
131M VAL* 5.2 3.4 - - + -
138M TYR* 3.8 38.6 - - + -
154M ILE* 4.3 1.5 - - + +
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Residues in contact with ASP 115 (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 GLU* 2.9 23.9 + - - +
112M GLU* 3.0 20.4 + - - +
114M LYS* 1.3 93.8 + - - +
116M LEU* 1.3 57.8 + - - +
118M LEU* 3.9 3.1 - - - +
119M LYS* 2.9 28.3 + - - +
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Residues in contact with LEU 116 (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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112M GLU 3.0 14.4 + - - +
113M ASP* 5.4 0.2 - - - +
115M ASP* 1.3 73.5 - - - +
117M MET* 1.3 59.6 + - - +
119M LYS* 3.4 28.2 - - + +
120M LEU* 2.9 42.3 + - + +
198M ALA* 3.7 43.3 - - + +
201M ILE* 3.8 17.8 - - + +
202M GLU* 4.3 15.5 - - + +
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Residues in contact with MET 117 (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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113M ASP 2.9 21.2 + - - +
114M LYS* 3.6 12.3 - - + +
115M ASP 3.3 0.2 - - - -
116M LEU* 1.3 77.2 - - - +
118M LEU* 1.3 79.1 + - + +
120M LEU 3.3 1.2 + - - -
121M LEU* 2.9 44.7 + - + +
131M VAL* 5.4 1.6 - - + -
138M TYR* 4.6 9.6 - - + -
139M LEU 5.4 0.2 - - - -
140M ALA* 3.7 26.2 - - + +
152M PHE* 3.8 10.5 - - + +
154M ILE* 3.6 32.3 - - + -
160M MET* 5.2 6.7 - - + +
201M ILE* 4.0 14.5 - - + +
205M ILE* 3.8 6.6 - - + +
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Residues in contact with LEU 118 (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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114M LYS* 2.9 51.5 + - + +
115M ASP* 4.2 3.4 - - - +
117M MET* 1.3 90.5 - - + +
119M LYS* 1.3 59.1 + - - +
121M LEU* 4.5 4.5 - - + +
122M ASP* 2.8 36.2 + - + +
128M LEU* 5.8 7.2 - - + -
131M VAL* 4.4 28.0 - - + -
140M ALA* 5.5 1.6 - - + -
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Residues in contact with LYS 119 (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 ASP 2.9 19.9 + - - +
116M LEU* 3.4 28.5 - - + +
117M MET 3.2 0.2 - - - -
118M LEU* 1.3 77.9 - - - +
120M LEU* 1.3 64.2 + - + +
122M ASP* 3.9 3.0 - - - +
123M LYS* 2.9 31.6 + - + +
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Residues in contact with LEU 120 (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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116M LEU* 2.9 30.2 + - + +
119M LYS* 1.3 83.9 - - + +
121M LEU* 1.3 59.6 + - - +
123M LYS* 3.7 31.4 - - + +
124M ASN* 3.0 37.4 + - - +
201M ILE* 3.7 23.8 - - + +
202M GLU* 3.7 34.1 - - + -
205M ILE* 3.3 20.9 - - + +
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Residues in contact with LEU 121 (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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117M MET* 2.9 29.1 + - + +
118M LEU* 4.6 3.1 - - + +
120M LEU* 1.3 76.3 - - - +
122M ASP* 1.3 62.9 + - - +
123M LYS 3.2 0.2 - - - -
124M ASN* 4.5 0.4 - - - +
125M GLY 3.6 2.6 + - - -
126M PHE* 3.1 53.8 + - + +
128M LEU* 4.2 17.0 - - + -
140M ALA* 3.8 24.0 - - + -
142M LEU* 6.1 0.2 - - + -
152M PHE* 3.6 41.5 - - + -
205M ILE* 3.8 27.1 - - + -
208M ALA* 5.9 0.7 - - + -
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Residues in contact with ASP 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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118M LEU* 2.8 23.4 + - + +
119M LYS* 4.2 2.9 - - - +
121M LEU* 1.3 75.4 - - - +
123M LYS* 1.3 65.2 + - - +
125M GLY* 3.9 6.6 + - - -
126M PHE 5.0 1.8 - - - -
128M LEU* 5.0 5.4 - - + +
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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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119M LYS* 2.9 24.2 + - + +
120M LEU* 3.7 29.8 - - + +
121M LEU 3.2 0.2 - - - -
122M ASP* 1.3 80.3 + - - +
124M ASN* 1.3 69.1 + - - +
125M GLY 3.1 5.7 + - - -
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Residues in contact with ASN 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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120M LEU* 3.0 26.6 + - - +
121M LEU 3.6 0.6 + - - +
122M ASP 3.5 0.2 - - - -
123M LYS* 1.3 91.2 - - - +
125M GLY* 1.3 60.9 + - - +
126M PHE* 3.2 22.2 + - + -
205M ILE* 3.3 14.3 + - - +
206M THR* 5.2 1.0 - - - +
209M SER* 2.9 33.7 + - - +
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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