Contacts of the helix formed by residues 180 - 190 (chain D) in PDB entry 2GTP
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 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D PHE* 3.4 36.6 - - - -
176D ARG 3.3 3.1 + - - -
177D PHE* 2.5 24.3 + - - -
178D LEU 3.5 0.6 - - - -
179D LYS* 1.3 79.4 - - - +
181D ASP* 1.3 65.5 + - - +
182D ILE* 3.9 4.8 + - - +
183D TYR* 3.4 10.6 + - - +
184D LEU* 2.9 26.4 + - - +
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Residues in contact with ASP 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LYS 4.2 0.2 + - - -
180D SER* 1.3 72.3 - - - +
182D ILE* 1.3 60.2 - - + +
184D LEU* 4.6 5.0 - - - +
185D ASN* 2.7 58.8 + - - +
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 3.8 33.7 - - + +
88D SER* 4.5 11.4 - - - +
89D PHE* 3.9 38.1 - - + +
92D SER* 4.2 11.0 - - - +
177D PHE* 4.5 3.8 - - + -
180D SER* 3.3 6.0 + - - +
181D ASP* 1.3 82.8 - - + +
183D TYR* 1.3 63.0 + - - +
185D ASN* 4.0 3.8 - - - +
186D LEU* 3.1 22.8 + - + +
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Residues in contact with TYR 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 2.6 50.0 + - + +
67D MET* 3.5 13.5 + - - -
69D TRP* 3.9 18.2 - + + -
70D SER* 3.9 10.1 + - - -
85D VAL* 5.3 1.6 - - + -
177D PHE* 3.4 50.0 - + + +
178D LEU* 3.6 34.8 - - + -
180D SER* 3.4 3.4 + - - +
181D ASP 3.3 0.4 - - - -
182D ILE* 1.3 80.8 - - - +
184D LEU* 1.3 65.3 + - + +
186D LEU* 3.2 7.6 + - + +
187D LEU* 2.9 42.7 + - + +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LEU 4.4 15.7 - - - +
179D LYS* 4.1 17.0 - - - +
180D SER 2.9 23.5 + - - +
181D ASP* 4.1 4.3 - - - +
183D TYR* 1.3 79.5 - - + +
185D ASN* 1.3 61.1 + - - +
187D LEU* 3.4 15.6 + - + +
188D ASN* 2.8 41.9 + - - +
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Residues in contact with ASN 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ASP* 2.7 53.0 + - - +
182D ILE* 4.0 3.5 - - - +
184D LEU* 1.3 70.2 - - - +
186D LEU* 1.3 63.7 + - - +
188D ASN* 4.9 2.9 - - - -
189D ASP* 3.1 28.1 + - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 4.6 9.0 - - + -
66D VAL* 4.0 15.3 - - + -
69D TRP* 4.0 28.5 - - + -
85D VAL* 4.2 22.7 - - + -
182D ILE* 3.1 19.3 + - + +
183D TYR* 3.2 6.3 + - + +
185D ASN* 1.3 78.0 - - - +
187D LEU* 1.3 66.1 + - - +
189D ASP* 3.4 4.1 + - - -
190D LEU* 3.0 35.4 - - + +
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 4.5 6.3 - - + +
66D VAL* 3.4 31.5 - - + +
67D MET* 3.9 24.5 - - + +
183D TYR* 2.9 31.5 + - + +
184D LEU* 3.7 16.4 - - + +
186D LEU* 1.3 79.4 - - - +
188D ASN* 1.3 68.3 + - - +
190D LEU* 3.4 13.3 + - - +
191D GLN* 3.3 37.7 - - - +
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 2.8 29.6 + - - +
185D ASN* 4.6 2.7 - - - +
187D LEU* 1.3 82.0 - - - +
189D ASP* 1.3 61.2 + - - +
190D LEU 3.2 0.7 + - - -
191D GLN* 3.5 29.4 + - - +
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D ASN 3.1 20.7 + - - +
186D LEU* 4.0 4.3 - - - +
187D LEU 3.4 0.2 - - - -
188D ASN* 1.3 76.6 - - - +
190D LEU* 1.3 66.9 + - + +
191D GLN 3.4 2.1 + - - -
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 4.7 11.9 - - + +
62D SER 3.3 28.9 - - - +
63D ALA* 4.1 20.0 - - + +
66D VAL* 4.3 13.5 - - + -
186D LEU* 3.0 29.4 - - + +
187D LEU 3.4 6.8 + - - +
188D ASN 3.2 1.0 - - - -
189D ASP* 1.3 85.7 - - + +
191D GLN* 1.3 62.0 + - - +
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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
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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