Contacts of the helix formed by residues 186 - 198 (chain G) in PDB entry 1GN2
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 ASN 186 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81G LYS 3.1 21.1 + - - +
82G ASN 2.8 18.7 + - - +
83G LEU 4.1 1.4 + - - -
84G SER* 3.4 31.5 - - - -
87G GLY* 4.7 3.6 - - - -
184G VAL 3.3 0.2 + - - -
185G VAL* 1.3 74.0 - - - +
187G TRP* 1.3 53.9 + - - +
188G ALA* 3.1 19.7 + - - +
189G ASP* 2.9 30.4 + - - +
190G VAL* 3.6 5.1 + - - +
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Residues in contact with TRP 187 (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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87G GLY* 5.5 1.0 - - - -
88G GLY* 3.6 23.5 + - - -
89G ASP 3.5 13.7 + - - -
90G LYS 4.1 8.5 - - - +
91G PRO* 3.7 37.9 - - + -
95G LEU* 4.1 3.1 - - + -
99G ILE* 4.1 9.0 - - + -
106G PHE* 3.5 34.1 - + - -
109G PHE* 4.3 6.7 - + - -
128G LEU* 5.8 0.7 - - + -
157G LEU* 4.2 13.5 - - + -
182G TRP* 3.8 23.8 + + - -
185G VAL* 3.5 25.0 + - + +
186G ASN* 1.3 68.9 + - - +
188G ALA* 1.3 62.2 + - - +
189G ASP 3.1 0.4 - - - -
190G VAL* 4.0 31.0 - - + -
191G GLN* 3.0 33.1 + - - +
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Residues in contact with ALA 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G ASN* 2.9 12.9 + - - +
187G TRP* 1.3 78.2 - - - +
189G ASP* 1.3 57.8 + - - +
191G GLN* 4.0 8.6 - - - +
192G SER* 3.2 26.2 + - - -
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Residues in contact with ASP 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G LYS* 3.7 22.8 - - - +
82G ASN* 2.8 21.1 + - - +
186G ASN* 2.9 28.0 + - - +
188G ALA* 1.3 79.6 - - - +
190G VAL* 1.3 63.4 - - - +
192G SER* 2.9 9.6 + - - -
193G ARG* 2.7 63.5 + - - +
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Residues in contact with VAL 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ASN* 4.3 6.5 - - + +
95G LEU* 3.4 22.4 - - + -
128G LEU* 4.7 7.6 - - + -
156G LEU* 4.1 26.7 - - + +
157G LEU* 4.0 31.9 - - + -
185G VAL* 4.6 0.7 - - + -
186G ASN 3.6 13.9 + - - +
187G TRP* 4.1 24.5 - - + +
189G ASP* 1.3 73.9 + - - +
191G GLN* 1.3 53.5 + - - +
193G ARG* 3.0 11.5 + - - +
194G TYR* 2.8 34.0 + - - +
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Residues in contact with GLN 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G PRO* 3.6 4.7 - - - +
92G THR* 2.6 54.0 + - - +
95G LEU* 3.1 38.6 - - + +
187G TRP* 3.0 21.0 + - - +
188G ALA* 4.0 7.9 - - - +
190G VAL* 1.3 79.1 - - - +
192G SER* 1.3 64.2 + - - +
194G TYR* 3.3 5.0 + - - +
195G ALA* 3.1 23.1 + - - +
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Residues in contact with SER 192 (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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188G ALA 3.2 14.6 + - - -
189G ASP* 2.9 16.2 + - - -
191G GLN* 1.3 82.4 - - - +
193G ARG* 1.3 60.7 + - - +
195G ALA* 3.2 9.2 + - - +
196G ALA* 3.1 21.3 + - - +
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Residues in contact with ARG 193 (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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77G THR* 5.1 1.4 + - - +
78G ILE* 3.9 37.3 - - - +
81G LYS* 3.8 20.8 - - - +
82G ASN* 3.8 2.0 - - - +
154G VAL* 5.3 2.3 - - + +
155G PRO 4.0 10.1 + - - +
156G LEU* 3.3 37.5 - - + +
189G ASP* 2.7 49.6 + - - +
190G VAL 3.4 4.5 - - - +
192G SER* 1.3 76.0 + - - +
194G TYR* 1.3 60.7 + - - +
196G ALA* 3.4 6.6 + - - +
197G ALA* 2.9 30.0 + - - +
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Residues in contact with TYR 194 (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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94G GLU* 4.2 23.8 + - + -
95G LEU* 3.6 32.5 - - + -
98G ALA* 3.4 30.2 - - + +
130G TRP* 4.2 19.3 - + - -
137G LEU* 4.3 7.6 - - + -
156G LEU* 3.8 24.6 - - + +
190G VAL 2.8 15.2 + - - +
191G GLN 3.6 5.6 - - - +
193G ARG* 1.3 78.7 - - - +
195G ALA* 1.3 53.0 + - + +
197G ALA* 3.2 2.4 + - + +
198G THR* 2.7 70.7 + - + +
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Residues in contact with ALA 195 (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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191G GLN 3.1 12.2 + - - +
192G SER* 3.2 13.0 + - - +
194G TYR* 1.3 81.4 - - + +
196G ALA* 1.3 60.9 + - - +
198G THR* 3.5 7.5 + - - -
199G SER* 3.4 21.8 + - - -
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Residues in contact with ALA 196 (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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192G SER* 3.1 10.8 + - - +
193G ARG* 3.9 8.7 - - - +
195G ALA* 1.3 78.1 - - - +
197G ALA* 1.3 66.0 + - - +
199G SER* 3.2 19.1 + - - +
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Residues in contact with ALA 197 (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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130G TRP* 3.7 40.5 + - + -
132G THR* 5.2 3.1 - - - +
154G VAL* 4.2 23.1 - - + -
156G LEU* 4.2 3.8 - - + -
193G ARG 2.9 18.8 + - - +
194G TYR* 3.5 5.4 - - - +
196G ALA* 1.3 80.1 - - - +
198G THR* 1.3 58.7 + - + +
199G SER 3.1 6.5 + - - -
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Residues in contact with THR 198 (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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130G TRP* 3.7 31.4 - - + +
194G TYR* 2.7 67.0 + - + +
195G ALA* 3.6 9.8 + - - -
196G ALA 3.3 0.2 - - - -
197G ALA* 1.3 71.0 - - - +
199G SER* 1.3 60.8 + - - +
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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