Contacts of the helix formed by residues 114 - 128 (chain M) in PDB entry 4GUN
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 114 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108M ILE* 3.7 10.1 + - - +
109M VAL* 5.2 3.6 - - - +
112M TYR* 3.2 11.7 + - - +
113M GLY* 1.4 77.1 - - - +
115M VAL* 1.3 62.9 + - - +
116M SER* 3.6 11.2 + - - -
117M ASN* 3.1 24.1 + - - +
118M LEU 3.3 14.6 + - - -
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Residues in contact with VAL 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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97M HIS* 4.1 24.9 - - + +
98M PRO* 3.7 35.2 - - + +
100M THR* 5.5 8.3 - - + -
105M GLY* 6.3 0.4 - - - -
108M ILE* 3.8 20.2 - - + -
109M VAL* 6.2 1.6 - - + -
114M SER* 1.3 70.2 - - - +
116M SER* 1.3 54.8 + - - +
118M LEU* 3.3 4.3 + - + +
119M ILE* 2.8 36.4 + - + +
197M TRP* 3.7 35.7 - - + -
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Residues in contact with SER 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M HIS* 4.9 9.8 - - - -
114M SER* 3.8 11.2 - - - -
115M VAL* 1.3 74.4 - - - +
117M ASN* 1.3 58.7 + - - +
119M ILE* 3.4 11.0 + - - +
120M ASP* 3.1 37.9 + - - +
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Residues in contact with ASN 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M TYR* 3.0 32.9 + - - +
114M SER* 3.1 13.8 + - - +
116M SER* 1.3 74.8 - - - +
118M LEU* 1.4 58.1 + - - +
120M ASP* 3.2 14.0 + - - +
121M ILE* 3.0 47.4 + - - +
142O GLN 4.8 3.6 + - - -
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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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108M ILE* 4.0 33.9 - - + -
112M TYR* 3.6 46.3 - - + +
114M SER 3.3 10.1 + - - +
115M VAL* 3.3 9.8 + - + +
117M ASN* 1.4 74.9 - - - +
119M ILE* 1.4 59.0 + - - +
121M ILE* 3.3 2.5 + - + +
122M THR* 2.9 35.0 + - - +
137M ILE* 4.1 34.3 - - + -
147M LEU* 5.0 0.9 - - + -
149M VAL* 3.8 20.6 - - + -
197M TRP* 4.4 8.5 - - + -
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Residues in contact with ILE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M HIS* 4.0 24.7 - - + +
115M VAL* 2.8 25.0 + - + +
116M SER* 3.6 9.4 - - - +
117M ASN 3.3 0.2 - - - -
118M LEU* 1.4 70.9 - - - +
120M ASP* 1.4 55.7 + - - +
122M THR* 3.4 3.0 + - - -
123M ASN* 2.9 41.9 + - - +
192M TRP* 3.7 67.7 - - + +
197M TRP* 4.1 15.3 - - + +
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Residues in contact with ASP 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M SER* 3.1 27.2 + - - +
117M ASN* 3.2 17.4 + - - +
119M ILE* 1.4 77.3 - - - +
121M ILE* 1.3 64.8 + - + +
123M ASN* 3.4 10.0 + - - +
124M SER* 3.2 22.5 + - - -
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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
----------------------------------------------------------
112M TYR* 3.5 32.5 - - + -
117M ASN* 3.0 36.1 + - - +
118M LEU* 3.3 7.1 + - - +
120M ASP* 1.3 71.9 - - + +
122M THR* 1.3 65.2 + - - +
124M SER* 3.3 8.4 + - - -
125M LYS* 3.1 24.1 + - + +
149M VAL* 3.9 20.9 - - + -
142O GLN* 3.4 49.8 - - + +
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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
----------------------------------------------------------
118M LEU* 2.9 18.0 + - - +
119M ILE 3.7 4.3 - - - -
121M ILE* 1.3 76.6 - - - +
123M ASN* 1.4 56.1 + - - +
125M LYS* 3.2 2.9 + - - +
126M LEU* 2.9 38.3 + - + +
135M ALA* 4.4 9.9 - - + -
137M ILE* 3.8 16.7 - - + +
149M VAL* 3.6 33.7 - - + +
169M ILE* 5.0 3.6 - - + -
192M TRP* 3.6 28.7 - - + -
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Residues in contact with ASN 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M ILE* 2.9 23.7 + - - +
120M ASP* 3.8 9.9 + - - +
121M ILE 3.3 0.2 - - - -
122M THR* 1.4 75.4 - - - +
124M SER* 1.3 56.2 + - - +
126M LEU* 3.5 10.0 + - - +
127M ALA* 3.0 28.5 + - - +
188M PHE* 3.5 27.0 + - + +
189M LYS* 4.3 12.1 - - - +
192M TRP* 2.7 38.9 + - - +
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Residues in contact with SER 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M ASP 3.2 14.0 + - - -
121M ILE* 3.5 11.7 - - - -
122M THR 3.2 0.2 - - - -
123M ASN* 1.3 73.9 - - - +
125M LYS* 1.4 63.6 + - - +
127M ALA* 3.3 8.4 + - - +
128M GLY* 3.2 17.8 + - - -
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Residues in contact with LYS 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* 3.1 18.1 + - + +
122M THR 3.5 7.4 - - - +
124M SER* 1.4 73.9 - - - +
126M LEU* 1.3 62.4 + - - +
128M GLY* 3.2 12.7 + - - -
129M ILE* 3.5 13.9 + - - +
135M ALA* 5.0 1.6 - - + -
149M VAL* 3.3 45.6 + - + -
150M VAL* 4.3 4.2 - - - +
151M THR* 3.8 28.9 + - + +
142O GLN* 5.2 3.8 - - - +
162O HIS* 4.3 22.9 + - + +
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Residues in contact with LEU 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 THR* 2.9 34.2 + - + +
123M ASN* 3.5 23.1 - - - +
125M LYS* 1.3 75.1 - - - +
127M ALA* 1.4 60.5 + - - +
129M ILE* 3.3 18.3 + - + +
135M ALA* 3.5 22.9 - - + -
151M THR* 4.8 0.2 - - - +
169M ILE* 3.7 32.1 - - + +
171M ALA* 4.0 15.0 - - + -
184M ARG* 3.2 12.6 + - - -
188M PHE* 3.4 42.8 - - + -
191M ILE* 5.8 0.2 - - + -
192M TRP* 4.7 2.9 - - + +
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Residues in contact with ALA 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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123M ASN 3.0 17.0 + - - +
124M SER* 3.3 9.8 + - - +
126M LEU* 1.4 75.2 - - - +
128M GLY* 1.3 56.8 + - - +
129M ILE 4.2 0.2 - - - +
184M ARG* 2.8 20.6 + - - +
185M PRO* 6.0 6.3 - - + -
188M PHE* 3.8 9.4 - - + -
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Residues in contact with GLY 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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124M SER 3.2 8.5 + - - -
125M LYS 3.2 9.9 + - - -
127M ALA* 1.3 74.2 - - - +
129M ILE* 1.4 62.5 + - - +
130M GLN* 3.3 16.1 + - - +
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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