Contacts of the helix formed by residues 270 - 278 (chain B) in PDB entry 6G4O
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
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Residue Dist Surf HB Arom Phob DC
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44B ARG* 4.8 3.8 - - - +
92B GLU* 5.4 1.0 + - - -
267B ARG 6.0 0.2 + - - -
268B GLU 4.0 11.2 - - - +
269B LYS* 1.3 80.9 + - - +
271B PRO* 1.3 85.7 - - + +
272B GLN* 3.4 3.8 - - + +
273B GLU* 2.9 39.2 + - + +
274B LEU* 3.4 6.4 + - - +
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Residues in contact with PRO 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.5 9.2 - - - +
68B GLN* 3.6 37.7 - - + +
92B GLU* 3.5 22.4 - - + +
153B PHE* 3.6 21.3 - - + -
270B LYS* 1.3 97.4 - - + +
272B GLN* 1.3 65.1 + - - +
274B LEU* 3.0 15.6 + - + +
275B ILE* 3.1 16.8 + - - +
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN* 4.3 9.9 + - - -
69B GLN 4.5 5.8 + - - +
70B TYR* 5.1 1.2 - - - -
71B VAL* 5.5 4.3 + - - +
90B MET* 5.0 9.5 - - - +
270B LYS* 3.4 3.4 - - + +
271B PRO* 1.3 78.9 - - - +
273B GLU* 1.3 53.4 + - + +
275B ILE* 3.5 35.0 - - - +
276B ASP* 2.6 58.5 + - - +
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Residues in contact with GLU 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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252B LEU* 3.7 16.2 - - + +
269B LYS* 3.6 27.6 + - + +
270B LYS* 2.9 43.9 + - + +
272B GLN* 1.3 77.8 - - + +
274B LEU* 1.3 63.6 + - - +
276B ASP* 3.6 13.6 + - - +
277B VAL* 3.6 14.2 - - - +
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Residues in contact with LEU 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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44B ARG* 3.9 23.6 - - - +
45B PHE* 4.5 11.9 - - + -
152B ALA* 4.8 10.3 - - + -
153B PHE* 3.9 24.2 - - + -
248B LEU* 3.5 33.1 - - + +
252B LEU* 3.9 6.1 - - + -
266B LEU* 3.6 27.6 - - + +
269B LYS* 4.6 4.3 - - + +
270B LYS 3.4 15.0 + - - +
271B PRO* 3.0 4.1 + - + +
273B GLU* 1.3 73.4 - - - +
275B ILE* 1.3 57.3 + - + +
276B ASP 3.0 1.1 - - - -
277B VAL* 2.7 34.0 + - - +
278B GLU* 3.0 13.3 + - - -
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Residues in contact with ILE 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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68B GLN* 3.8 11.0 - - + -
69B GLN* 3.4 33.7 - - - +
70B TYR* 3.5 36.2 - - + +
153B PHE* 3.8 15.9 - - + -
271B PRO 3.1 15.4 + - - +
272B GLN* 3.5 36.1 - - - +
274B LEU* 1.3 73.6 - - - +
276B ASP* 1.3 61.4 + - - +
277B VAL 3.3 0.7 + - - -
278B GLU* 3.6 25.7 + - - +
279B TRP* 4.6 8.0 + - - -
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Residues in contact with ASP 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 GLN* 2.6 48.5 + - - +
273B GLU* 3.8 10.9 - - - +
274B LEU 2.8 0.6 + - - -
275B ILE* 1.3 76.9 - - - +
277B VAL* 1.3 62.1 + - + +
279B TRP* 5.3 3.5 + - - -
280B ASN* 4.5 5.7 + - - +
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Residues in contact with VAL 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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248B LEU* 3.6 18.2 - - + -
251B ASN* 3.9 27.1 - - + +
252B LEU* 4.0 19.5 - - + -
273B GLU 3.6 12.8 - - - +
274B LEU 2.7 18.0 + - - +
276B ASP* 1.3 78.5 - - + +
278B GLU* 1.3 65.4 + - - +
279B TRP 3.1 3.4 - - - -
280B ASN* 2.8 40.2 + - - +
281B VAL* 4.0 6.2 + - - +
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Residues in contact with GLU 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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69B GLN* 5.7 0.5 - - - -
70B TYR* 4.3 10.6 + - - +
121B TYR* 3.7 26.9 - - - +
151B GLY* 4.1 16.3 - - - -
152B ALA* 5.2 3.6 - - + +
248B LEU* 4.0 10.8 - - + -
274B LEU 3.0 12.9 + - - +
275B ILE* 3.6 28.6 + - - +
277B VAL* 1.3 77.2 - - - +
279B TRP* 1.3 81.7 + - + +
281B VAL* 3.3 9.2 - - - +
291B SER* 2.5 36.1 + - - +
292B PHE* 4.0 20.1 + - + -
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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