Contacts of the helix formed by residues 114 - 128 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ILE* 3.7 14.6 + - - +
109G VAL* 5.2 3.4 - - - +
112G TYR* 3.1 8.3 + - - +
113G GLY* 1.3 78.0 - - - +
115G VAL* 1.4 62.6 + - - +
116G SER* 3.7 11.3 - - - -
117G ASN* 3.3 20.8 + - - +
118G LEU 3.3 14.7 + - - -
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Residues in contact with VAL 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G HIS* 3.9 21.5 - - + +
98G PRO* 3.7 35.2 - - + +
100G THR* 5.6 7.6 - - + -
105G GLY* 6.2 0.9 - - - -
108G ILE* 3.7 22.9 - - + -
109G VAL* 6.2 1.3 - - + -
114G SER* 1.4 71.0 - - - +
116G SER* 1.3 57.4 + - - +
118G LEU* 3.2 4.5 + - + +
119G ILE* 3.0 36.6 + - + +
197G TRP* 3.7 34.5 - - + -
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Residues in contact with SER 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G HIS* 4.6 10.8 - - - -
114G SER* 3.7 11.7 - - - -
115G VAL* 1.3 78.1 - - - +
117G ASN* 1.3 57.0 + - - +
119G ILE* 3.4 10.8 + - - +
120G ASP* 3.1 35.9 + - - +
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Residues in contact with ASN 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E GLN 4.9 4.0 + - - -
112G TYR* 3.1 31.4 + - - +
114G SER* 3.3 12.9 + - - +
115G VAL 3.4 0.2 - - - -
116G SER* 1.3 75.4 + - - +
118G LEU* 1.4 64.3 + - - +
120G ASP* 3.3 14.1 + - - +
121G ILE* 3.1 42.5 + - - +
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Residues in contact with LEU 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ILE* 3.9 34.3 - - + -
112G TYR* 3.6 44.3 - - + +
114G SER 3.3 12.1 + - - +
115G VAL* 3.2 11.7 + - + +
117G ASN* 1.4 77.3 - - - +
119G ILE* 1.4 49.4 + - - +
121G ILE* 3.3 3.1 + - + +
122G THR* 2.8 39.9 + - - +
137G ILE* 4.0 35.2 - - + -
147G LEU* 4.9 0.7 - - + -
149G VAL* 3.8 20.9 - - + -
197G TRP* 4.5 7.6 - - + -
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Residues in contact with ILE 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G HIS* 4.2 21.8 - - + +
115G VAL* 3.0 21.7 + - + +
116G SER* 3.6 8.5 - - - +
117G ASN 3.3 0.2 - - - -
118G LEU* 1.4 73.5 - - + +
120G ASP* 1.4 57.9 + - - +
122G THR* 3.3 6.3 + - - -
123G ASN* 2.8 42.3 + - - +
192G TRP* 3.6 63.7 - - + +
197G TRP* 4.1 17.3 - - + +
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Residues in contact with ASP 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G SER* 3.1 28.3 + - - +
117G ASN* 3.6 18.3 - - - +
118G LEU 3.3 0.4 - - - -
119G ILE* 1.4 80.0 - - - +
121G ILE* 1.3 56.6 + - + +
123G ASN* 3.4 9.3 + - - +
124G SER* 3.1 31.5 + - - -
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Residues in contact with ILE 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLN* 3.4 50.0 - - + +
112G TYR* 3.6 29.2 - - + -
117G ASN* 3.1 33.9 + - - +
118G LEU* 3.6 6.5 - - - +
120G ASP* 1.3 72.1 - - + +
122G THR* 1.3 66.2 + - - +
124G SER* 3.3 7.7 + - - -
125G LYS* 3.1 24.8 + - + +
149G VAL* 3.8 19.1 - - + -
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Residues in contact with THR 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G LEU 2.8 19.7 + - - -
119G ILE 3.7 4.0 - - - -
121G ILE* 1.3 75.3 - - - +
123G ASN* 1.4 56.3 + - - +
125G LYS* 3.2 4.3 + - - +
126G LEU* 2.9 37.1 + - + +
135G ALA* 4.5 10.5 - - + -
137G ILE* 3.9 16.4 - - + +
149G VAL* 3.7 33.2 - - + +
167G ILE* 5.9 0.2 - - + -
169G ILE* 5.1 4.3 - - + -
192G TRP* 3.6 29.2 - - + -
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Residues in contact with ASN 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ILE* 2.8 31.6 + - - +
120G ASP* 3.7 9.6 + - - +
122G THR* 1.4 71.7 - - - +
124G SER* 1.4 56.1 + - - +
126G LEU* 3.5 14.7 + - - +
127G ALA* 3.0 28.8 + - - +
188G PHE* 3.5 20.2 + - + +
189G LYS* 4.5 11.1 - - - +
192G TRP* 2.7 34.5 + - - +
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Residues in contact with SER 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G ASP 3.1 14.2 + - - -
121G ILE* 3.6 11.0 - - - -
122G THR 3.3 0.8 - - - -
123G ASN* 1.4 72.2 - - - +
125G LYS* 1.4 64.3 + - - +
127G ALA* 3.5 7.3 + - - +
128G GLY* 3.2 17.7 + - - -
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Residues in contact with LYS 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLN* 5.4 3.4 - - - +
162E HIS* 4.7 22.4 + - + -
121G ILE* 3.1 21.2 + - + +
122G THR 3.5 6.5 - - - +
124G SER* 1.4 74.2 - - - +
126G LEU* 1.4 64.2 + - - +
128G GLY* 3.2 12.1 + - - -
129G ILE* 3.4 14.9 + - - +
135G ALA* 5.0 1.3 - - + -
149G VAL* 3.4 45.2 + - + +
150G VAL* 4.1 5.4 - - - +
151G THR* 3.8 33.0 + - + +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G THR* 2.9 27.7 + - + +
123G ASN* 3.6 26.9 - - - +
124G SER 3.4 0.2 - - - -
125G LYS* 1.4 75.6 - - - +
127G ALA* 1.3 60.1 + - - +
129G ILE* 3.2 30.6 + - + +
135G ALA* 3.5 24.2 - - + +
169G ILE* 3.8 28.7 - - + +
171G ALA* 4.1 4.9 - - + -
184G ARG* 3.4 8.3 + - - -
188G PHE* 3.4 49.0 - - + -
191G ILE* 5.5 0.2 - - + -
192G TRP* 4.6 3.6 - - + +
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Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ASN 3.0 17.0 + - - +
124G SER* 3.7 8.5 - - - +
125G LYS 3.4 0.2 - - - -
126G LEU* 1.3 75.2 - - - +
128G GLY* 1.3 57.3 + - - +
129G ILE 4.0 0.3 - - - +
184G ARG* 2.7 22.8 + - - +
185G PRO* 6.1 5.8 - - + -
188G PHE* 3.8 9.3 - - + -
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Residues in contact with GLY 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G SER 3.2 7.9 + - - -
125G LYS* 3.2 10.2 + - - -
127G ALA* 1.3 75.6 - - - +
129G ILE* 1.4 63.1 + - - +
130G GLN* 3.3 14.6 + - - +
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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