Contacts of the helix formed by residues 111 - 128 (chain M) in PDB entry 5IYB
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 ASP 111 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M SER* 5.2 5.8 - - - +
77M ASP* 3.8 26.1 - - - +
78M GLY* 5.4 3.5 + - - -
108M SER* 3.2 22.0 + - - +
109M SER 3.0 0.4 - - - -
110M SER* 1.3 103.0 + - - +
112M ARG* 1.3 58.2 + - - +
113M ALA 3.0 6.5 - - - -
114M MET* 2.9 42.9 + - + +
115M MET* 3.3 14.5 + - + +
146M TYR* 5.1 6.9 - - - -
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Residues in contact with ARG 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M THR* 5.5 10.0 - - + +
108M SER* 2.9 36.1 + - - +
109M SER* 2.9 21.2 + - - +
111M ASP* 1.3 78.7 - - - +
113M ALA* 1.3 56.5 + - - +
115M MET* 4.1 22.6 + - - +
116M ASN* 3.3 21.2 + - - +
62Y C 5.5 0.4 - - - +
63Y G 3.2 71.5 + - - +
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Residues in contact with ALA 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M SER 4.4 1.4 + - - -
110M SER 5.1 2.0 + - - +
111M ASP 3.0 1.0 - - - -
112M ARG* 1.3 78.9 - - - +
114M MET* 1.3 58.8 + - - +
115M MET 3.5 0.2 - - - -
116M ASN* 3.6 13.4 - - + +
117M ALA* 2.9 24.1 + - - +
142M PHE* 5.1 0.5 - - - -
146M TYR* 5.9 8.1 - - + +
156M ASN* 3.6 20.3 + - - +
23X G 4.7 16.6 - - - +
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Residues in contact with MET 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU 3.1 24.0 - - - +
76M SER* 4.0 13.5 - - - -
77M ASP* 4.3 8.5 - - + +
111M ASP* 2.9 35.3 + - + +
113M ALA* 1.3 70.7 - - - +
115M MET* 1.3 63.4 + - + +
116M ASN 3.2 0.2 - - - -
117M ALA* 3.3 8.5 + - - +
118M PHE* 3.2 45.0 + - + -
142M PHE* 4.7 11.4 - - + -
143M LYS* 4.6 25.4 - - + -
146M TYR* 4.3 33.0 + - + -
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Residues in contact with MET 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU 5.6 2.2 - - - +
76M SER* 5.3 13.0 - - - +
108M SER* 5.6 3.4 - - - +
111M ASP* 3.3 9.2 + - + +
112M ARG* 4.2 32.5 - - - +
114M MET* 1.3 77.7 - - + +
116M ASN* 1.3 57.3 + - - +
118M PHE* 3.4 17.5 + - + +
119M LYS* 3.1 24.9 + - - +
62Y C 3.4 55.6 - - + +
63Y G 4.9 9.9 - - - +
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Residues in contact with ASN 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M ARG 3.3 18.3 + - - +
113M ALA* 3.6 15.8 + - - +
115M MET* 1.3 77.8 - - - +
117M ALA* 1.3 62.6 + - - +
119M LYS* 3.5 12.6 + - - +
120M GLU* 3.2 33.3 + - - +
156M ASN* 5.1 5.8 - - - +
157M ASP* 5.6 3.0 + - - -
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Residues in contact with ALA 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M ALA 2.9 11.7 + - - +
114M MET 3.3 10.7 + - - +
116M ASN* 1.3 74.4 - - - +
118M PHE* 1.3 55.1 + - + +
120M GLU* 3.1 9.0 + - - +
121M ILE* 2.8 39.9 + - + +
142M PHE* 3.4 44.0 - - + -
156M ASN* 4.3 7.2 - - - +
160M ALA* 4.9 4.3 - - + +
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Residues in contact with PHE 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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75M LEU* 3.6 51.1 - - + -
114M MET* 3.2 37.1 + - + -
115M MET* 3.6 17.3 - - + +
117M ALA* 1.3 76.5 - - - +
119M LYS* 1.3 62.0 + - - +
121M ILE* 3.9 12.1 - - + +
122M THR* 3.2 31.4 + - + +
139M ASN* 3.0 47.8 - - + +
142M PHE* 4.7 9.0 - + - -
143M LYS* 5.5 2.7 - - + -
62Y C 5.7 1.3 + - - -
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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
----------------------------------------------------------
414B GLU* 4.1 21.4 + - - -
436B LYS* 5.5 4.3 - - - +
438B ARG* 3.1 25.6 - - - +
439B ILE* 5.0 5.7 - - - +
115M MET 3.1 13.1 + - - +
116M ASN* 3.6 19.7 - - - +
117M ALA 3.2 0.4 - - - -
118M PHE* 1.3 78.0 - - - +
120M GLU* 1.3 66.6 + - - +
122M THR* 3.4 8.9 + - - -
123M THR* 2.8 25.2 + - - +
62Y C 2.7 49.8 + - - +
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Residues in contact with GLU 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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436B LYS* 6.0 1.4 - - - -
116M ASN* 3.2 24.0 + - - +
117M ALA* 3.1 9.7 + - - +
119M LYS* 1.3 83.6 - - - +
121M ILE* 1.3 62.6 + - - +
123M THR* 3.3 10.6 + - - +
124M MET* 3.0 40.8 + - + +
127M ARG* 6.0 0.3 + - - -
157M ASP* 4.2 27.9 - - + +
160M ALA* 5.2 5.2 - - + -
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Residues in contact with ILE 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 ALA 2.8 24.6 + - - +
118M PHE* 3.9 14.1 - - + +
119M LYS 3.5 0.2 - - - -
120M GLU* 1.3 72.9 - - - +
122M THR* 1.3 59.4 + - - +
124M MET* 3.9 9.5 - - + +
125M ALA* 2.9 27.4 + - + +
135M VAL* 3.7 23.6 - - + -
138M THR* 4.0 32.3 - - + -
139M ASN* 3.5 20.6 - - - +
142M PHE* 4.5 21.3 - - + -
160M ALA* 4.2 16.8 - - + +
164M LEU* 4.9 8.7 - - + +
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Residues in contact with THR 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ARG* 3.8 26.7 + - - -
118M PHE* 3.2 17.0 + - + +
119M LYS* 3.4 7.8 + - - -
121M ILE* 1.3 75.8 - - + +
123M THR* 1.3 60.4 + - - +
125M ALA* 3.2 7.0 + - - +
126M ASP* 2.8 31.2 + - - +
132M ARG* 4.5 19.5 - - - +
135M VAL* 3.8 21.5 - - + -
139M ASN* 5.9 1.8 - - - +
62Y C 5.3 3.3 + - - +
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Residues in contact with THR 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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436B LYS* 4.1 33.2 - - + +
437B THR* 5.3 1.0 + - - +
438B ARG* 4.5 13.3 + - - +
119M LYS* 2.8 17.1 + - - +
120M GLU* 3.3 14.9 + - - +
121M ILE 3.3 0.2 - - - -
122M THR* 1.3 80.4 + - - +
124M MET* 1.3 64.0 + - - +
126M ASP* 3.3 13.4 + - - +
127M ARG* 3.3 46.9 + - - +
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Residues in contact with MET 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 GLU* 3.0 36.8 + - + +
121M ILE* 3.9 8.7 - - + +
123M THR* 1.3 77.5 - - - +
125M ALA* 1.3 65.7 + - - +
127M ARG* 3.0 28.6 + - - +
128M ILE* 3.6 9.4 + - - +
157M ASP* 4.9 2.2 - - + +
160M ALA* 4.5 7.6 - - + +
161M SER* 3.5 40.4 - - - +
164M LEU* 4.2 17.0 - - + -
180M ILE* 5.7 0.7 - - - -
183M VAL* 4.0 28.3 - - + +
184M SER* 3.7 19.7 - - - -
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Residues in contact with ALA 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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121M ILE* 2.9 20.3 + - + +
122M THR* 3.2 6.0 + - - +
124M MET* 1.3 76.0 - - - +
126M ASP* 1.3 58.7 + - - +
128M ILE* 3.2 11.0 + - - +
129M ASN 2.8 22.3 + - - -
130M LEU* 3.4 23.3 + - + +
135M VAL* 3.8 29.2 - - + -
164M LEU* 4.6 6.4 - - + +
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Residues in contact with ASP 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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148B PHE* 4.3 7.8 - - - -
151B LYS* 3.4 27.3 + - - -
437B THR* 2.4 36.8 + - - +
438B ARG* 3.8 17.4 + - + -
441B SER* 5.1 1.5 + - - -
122M THR 2.8 19.1 + - - +
123M THR* 3.8 5.6 - - - +
124M MET 3.3 0.4 - - - -
125M ALA* 1.3 73.6 - - - +
127M ARG* 1.3 62.5 + - - +
129M ASN* 3.0 23.2 + - - +
130M LEU 6.0 0.2 - - - -
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Residues in contact with ARG 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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148B PHE* 5.6 8.2 - - + -
432B GLU* 3.6 14.2 + - - -
433B LEU* 2.6 40.5 + - - +
435B ILE 3.0 20.8 + - - -
436B LYS* 4.5 2.4 - - - +
437B THR* 5.1 11.8 - - + +
120M GLU* 6.0 0.2 + - - -
123M THR* 3.3 38.2 + - - +
124M MET* 3.0 18.9 + - - +
126M ASP* 1.3 76.2 - - - +
128M ILE* 1.3 60.9 + - - +
129M ASN* 5.2 0.4 - - - +
183M VAL* 3.4 42.7 + - + +
151T THR* 4.9 4.0 + - - -
152T ASN* 4.0 21.1 + - - +
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Residues in contact with ILE 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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99B TRP* 5.5 0.7 - - - -
103B GLY* 5.1 10.2 - - - -
124M MET 3.8 9.0 - - - +
125M ALA 3.4 10.3 - - - +
127M ARG* 1.3 77.6 - - - +
129M ASN* 1.3 71.1 + - - +
130M LEU* 3.3 36.3 + - + +
164M LEU* 4.7 13.5 - - + -
168M CYS* 5.1 1.1 - - - -
175M ARG* 4.5 16.6 + - + +
179M GLU* 5.0 16.2 - - + +
180M ILE* 4.8 13.5 - - + -
183M VAL* 3.6 25.8 - - + -
152T ASN* 5.4 2.0 - - - +
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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
------------------------------------------------------------
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