Contacts of the helix formed by residues 270 - 278 (chain B) 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 LYS 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLU* 3.1 30.1 + - - +
44B SER 4.5 4.3 - - - -
150B ASP* 2.5 32.6 + - - +
226B ALA* 3.8 16.2 - - + +
227B LEU* 4.1 1.5 - - - +
228B SER* 3.3 24.4 + - - +
229B ASP* 5.0 1.2 + - - -
242B ARG* 6.0 0.2 - - - +
269B ASN* 1.3 88.0 + - - +
271B LYS* 1.3 60.2 + - - +
272B ASP* 3.2 7.4 - - - -
273B LEU* 3.2 9.5 + - + +
274B PHE* 2.9 27.4 + - - +
324B THR 3.2 2.4 + - - -
403B GDP 3.2 65.1 + - + +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 3.8 20.0 - - + -
268B LEU 4.5 1.8 - - - +
269B ASN 3.2 1.4 - - - -
270B LYS* 1.3 78.5 - - - +
272B ASP* 1.3 62.2 + - + +
274B PHE* 3.4 2.6 - - - +
275B GLU* 2.8 31.6 + - - +
296B TYR* 3.6 24.0 - - + +
323B PHE* 3.3 26.5 + - + +
324B THR 3.3 20.4 + - - +
325B CYS* 4.3 10.5 - - + +
328B ASP* 6.0 0.7 - - - -
331B ASN* 2.8 35.8 - - - +
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ARG* 4.2 10.4 + - - -
270B LYS 3.6 4.9 - - - -
271B LYS* 1.3 79.1 - - + +
273B LEU* 1.3 67.7 + - - +
275B GLU* 3.3 18.0 + - - +
276B GLU* 3.4 15.2 + - - +
325B CYS* 3.4 26.0 - - + -
403B GDP 3.1 37.6 + - - -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP* 3.8 40.8 - - + +
176B ARG* 5.1 3.8 - - - +
228B SER* 3.6 18.6 - - - +
270B LYS* 3.2 16.1 + - + +
272B ASP* 1.3 80.7 + - - +
274B PHE* 1.3 65.1 + - - +
276B GLU* 3.2 7.2 + - + +
277B LYS* 3.0 24.1 + - - +
403B GDP 3.3 43.3 - - + +
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 3.5 37.5 - - + -
228B SER* 4.0 4.4 - - - +
230B TYR* 3.7 24.5 - + - -
270B LYS 2.9 16.7 + - - +
271B LYS* 3.4 5.6 - - - +
273B LEU* 1.3 78.6 - - - +
275B GLU* 1.3 61.2 + - - +
277B LYS* 3.1 4.2 + - - +
278B ILE* 3.0 32.8 + - + +
283B LEU* 5.1 0.2 - - + -
296B TYR* 3.6 35.7 - + - -
299B ALA* 3.9 19.7 - - + -
300B ALA* 3.9 18.8 - - + -
303B ILE* 3.6 31.0 - - + -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LYS 2.8 20.8 + - - +
272B ASP* 3.7 10.4 - - - +
273B LEU 3.3 0.4 - - - -
274B PHE* 1.3 73.7 - - - +
276B GLU* 1.3 63.0 + - + +
278B ILE* 3.8 12.3 - - - +
279B LYS* 3.5 21.9 + - - +
296B TYR* 3.7 37.2 - - + +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ASP 3.4 8.5 + - - +
273B LEU* 3.2 9.4 + - + +
274B PHE 3.2 0.6 - - - -
275B GLU* 1.3 83.6 - - + +
277B LYS* 1.3 60.0 + - - +
279B LYS* 3.3 37.6 + - - +
280B LYS* 3.9 17.8 - - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER* 5.8 2.3 + - - -
144B ARG* 6.2 0.7 - - - -
150B ASP* 5.3 3.8 + - - -
228B SER* 2.6 40.3 + - - +
230B TYR* 3.3 18.1 + - + +
231B ASP* 3.1 32.0 + - - +
232B LEU* 4.0 17.2 - - - +
273B LEU* 3.0 18.1 + - - +
274B PHE* 3.1 4.7 + - - +
276B GLU* 1.3 75.4 - - - +
278B ILE* 1.3 60.0 + - - +
279B LYS 3.2 2.5 - - - -
280B LYS* 3.0 9.2 + - + +
281B SER* 2.9 29.2 + - - -
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Residues in contact with ILE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B TYR* 3.3 24.6 + - + +
274B PHE* 3.0 29.4 + - + +
275B GLU 3.8 10.8 - - - +
277B LYS* 1.3 76.6 - - - +
279B LYS* 1.3 66.6 + - + +
280B LYS 3.5 0.2 + - - -
281B SER 3.8 10.7 + - - +
283B LEU* 4.1 16.6 - - + +
294B ASN* 3.5 38.2 - - - +
295B THR* 4.0 2.0 - - - +
296B TYR* 3.8 27.1 - - + +
299B ALA* 3.9 26.2 - - + -
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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