Contacts of the helix formed by residues 250 - 259 (chain G) in PDB entry 6IY6
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 PRO 250 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220G THR* 4.0 25.8 - - + +
222G LYS* 4.9 5.2 - - - +
249G SER* 1.4 86.6 - - - +
251G GLN* 1.3 67.7 + - + +
252G LEU 3.3 2.5 - - - -
253G TYR* 3.1 18.7 + - + +
254G LYS* 3.4 13.9 + - - +
267G SER* 4.7 5.4 - - - +
271G VAL* 4.2 26.0 - - + -
290G ASP* 3.8 29.2 - - - +
602G PO4 4.2 7.6 - - - +
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Residues in contact with GLN 251 (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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249G SER* 3.6 4.9 - - - -
250G PRO* 1.3 80.5 - - + +
252G LEU* 1.3 65.2 + - - +
254G LYS* 3.2 16.4 + - - +
255G GLN* 3.1 39.6 + - + +
292G GLU* 4.5 10.1 - - - +
402G TYR* 3.0 54.7 + - - -
431G ARG* 3.4 9.6 + - - -
602G PO4 3.3 28.2 + - - +
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Residues in contact with LEU 252 (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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249G SER* 4.6 6.1 + - - +
250G PRO 3.2 0.4 + - - -
251G GLN* 1.3 78.5 - - - +
253G TYR* 1.3 85.3 + - + +
255G GLN* 3.4 7.1 + - - +
256G MET* 3.1 54.2 + - + +
455G TYR* 4.5 33.8 - - + -
180H LEU* 4.4 16.4 - - + -
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Residues in contact with TYR 253 (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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218G ILE* 4.5 0.7 - - - -
220G THR* 3.8 18.2 - - + -
221G PRO* 3.5 31.6 - - + +
224G ILE* 2.8 40.3 - - + +
249G SER 3.7 21.5 - - - -
250G PRO 3.1 8.5 + - - +
252G LEU* 1.3 95.1 - - + +
254G LYS* 1.3 64.4 + - - +
256G MET* 3.4 7.2 + - - +
257G CYS* 3.1 30.4 + - - -
492H PHE* 3.6 43.8 - + + -
494H ARG* 4.9 7.3 + - - -
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Residues in contact with LYS 254 (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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218G ILE* 4.1 21.7 - - + +
220G THR* 4.8 0.7 - - + -
250G PRO 3.7 8.7 - - - +
251G GLN* 3.2 25.1 + - - +
253G TYR* 1.3 77.3 - - - +
255G GLN* 1.3 56.6 + - - +
257G CYS* 3.3 6.2 + - - +
258G ILE* 3.0 29.8 + - - +
265G VAL* 3.9 6.6 - - + +
266G PHE* 5.7 0.4 - - - -
267G SER* 4.1 9.9 - - - +
290G ASP* 3.3 30.8 + - + +
291G ILE 3.1 15.5 + - - +
292G GLU* 3.1 39.7 + - + +
602G PO4 2.7 29.4 + - - -
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Residues in contact with GLN 255 (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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251G GLN* 3.1 31.3 + - + +
252G LEU* 3.6 8.7 - - - +
253G TYR 3.3 0.2 - - - -
254G LYS* 1.3 74.0 - - - +
256G MET* 1.3 59.5 + - + +
258G ILE* 3.3 9.5 + - - +
259G CYS* 2.9 35.2 + - - -
292G GLU* 4.5 7.6 - - - -
402G TYR* 5.1 0.2 - - - +
431G ARG* 3.2 24.0 - - + +
432G ILE 4.8 1.2 + - - -
455G TYR* 2.5 31.1 + - + -
458G SER* 5.2 0.7 - - - -
459G PHE* 3.2 27.3 - - + -
466G HIS* 2.9 32.6 + - + +
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Residues in contact with MET 256 (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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252G LEU* 3.1 41.4 + - + +
253G TYR* 3.6 11.2 - - + +
254G LYS 3.3 0.2 - - - -
255G GLN* 1.3 74.1 - - + +
257G CYS* 1.3 57.9 + - - +
259G CYS* 3.3 4.7 + - - +
260G ALA* 2.9 28.5 + - - +
455G TYR* 6.2 2.0 - - + -
458G SER* 4.0 12.3 - - - +
180H LEU* 3.6 50.7 - - + +
183H ARG* 4.4 9.9 - - + -
184H VAL* 3.9 17.3 - - + +
187H LEU* 5.7 1.8 - - + -
492H PHE* 3.9 29.4 - - + -
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Residues in contact with CYS 257 (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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218G ILE* 3.8 20.2 - - - -
253G TYR 3.1 22.6 + - - -
254G LYS* 3.3 10.1 + - - +
256G MET* 1.3 72.5 - - - +
258G ILE* 1.3 59.0 + - - +
260G ALA* 3.0 18.4 + - - -
262G PHE* 3.0 39.7 + - + +
265G VAL* 4.0 13.7 - - + -
187H LEU* 5.2 1.6 - - - -
491H MET* 3.6 30.3 - - - -
492H PHE* 3.6 8.3 - - - -
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Residues in contact with ILE 258 (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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254G LYS 3.0 18.3 + - - +
255G GLN* 3.3 9.2 + - - +
257G CYS* 1.3 73.7 - - - +
259G CYS* 1.3 62.2 - - - +
260G ALA 3.2 1.0 + - - -
261G ASP* 3.2 14.4 + - - -
262G PHE 3.5 11.5 + - - +
263G GLU* 3.2 27.6 - - - +
265G VAL* 4.5 1.8 - - + -
292G GLU* 3.6 34.1 - - + +
293G MET 3.9 0.9 - - - -
294G ALA* 3.6 15.7 - - + +
464G PRO* 3.7 26.3 - - + +
466G HIS* 3.5 34.8 - - + +
65H ARG* 4.7 0.5 + - - -
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Residues in contact with CYS 259 (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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255G GLN 2.9 21.2 + - - +
256G MET 3.5 9.6 - - - +
258G ILE* 1.3 74.1 - - - +
260G ALA* 1.3 54.4 + - - +
261G ASP 3.4 1.6 - - - -
458G SER* 3.7 20.6 - - - +
459G PHE* 3.5 37.7 - - - -
462G GLY 5.2 0.7 - - - +
463G ALA* 4.5 7.9 - - - -
464G PRO* 4.2 10.8 - - - -
466G HIS* 4.9 3.1 - - - -
65H ARG* 3.2 5.6 + - - +
184H VAL* 3.5 15.6 - - + +
188H ARG* 2.7 34.7 + - - +
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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