Contacts of the strand formed by residues 247 - 254 (chain G) in PDB entry 1O1F
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 GLY 247 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246G PHE* 1.3 84.4 - - - +
248G MLY 1.3 66.5 + - - +
267G THR* 3.6 1.6 - - - -
268G TYR* 3.0 36.6 + - - -
269G LEU* 5.4 0.4 - - - +
463G ASP 3.3 10.5 - - - -
464G ILE* 4.2 15.7 - - - -
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Residues in contact with MLY 248 (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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186G THR* 3.3 33.4 - - - -
189G THR* 4.8 13.2 - - - -
190G MLY 4.8 9.4 - - - -
193G ILE* 5.6 1.6 - - - -
226G ASN* 2.8 42.5 - - - -
229G LEU* 5.4 9.4 - - + +
230G GLU* 5.0 5.6 - - - -
234G ASN* 5.9 0.4 - - - -
244G SER* 4.6 6.5 - - - -
246G PHE* 4.0 26.5 - - + -
247G GLY* 1.3 77.9 - - - +
249G PHE* 1.3 64.3 + - - +
250G ILE* 3.8 32.3 - - + -
265G ILE* 4.5 15.7 - - + -
266G GLU 3.3 10.8 - - - +
268G TYR* 4.1 7.0 - - - -
461G VAL 3.7 1.0 - - - +
462G LEU* 3.5 3.7 - - - +
463G ASP* 2.4 65.2 + - + +
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Residues in contact with PHE 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G SER* 5.5 1.6 - - - -
248G MLY 1.3 77.7 - - - +
250G ILE* 1.3 61.4 + - - +
251G ARG* 4.0 26.5 - - + -
264G ASP 3.0 13.3 - - - +
266G GLU* 3.1 26.1 + - + +
268G TYR* 3.8 23.6 - - + +
458G PHE* 4.7 4.9 - + - -
460G GLY* 3.9 29.4 - - - -
461G VAL 3.5 6.3 - - - -
462G LEU* 3.6 29.2 - - + -
660G LEU* 3.9 17.9 - - + -
663G ASN* 4.2 21.5 - - + -
664G LEU* 4.0 24.0 - - + -
667G THR* 6.0 0.2 - - - -
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Residues in contact with ILE 250 (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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189G THR* 5.0 3.6 - - + -
193G ILE* 3.1 35.4 - - + -
222G ILE* 6.0 0.9 - - + -
226G ASN* 5.4 0.9 - - - +
248G MLY 3.8 39.3 - - + -
249G PHE* 1.3 76.5 - - - +
251G ARG* 1.3 71.7 + - - +
252G ILE* 3.6 14.7 + - + +
263G ALA* 4.3 5.8 - - + -
264G ASP 3.2 17.9 - - - +
265G ILE* 4.3 16.8 - - + -
459G ILE 3.5 2.6 - - - +
460G GLY* 3.3 5.0 - - - -
461G VAL* 3.1 37.5 + - + +
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Residues in contact with ARG 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G PHE* 4.0 21.1 - - + -
250G ILE* 1.3 78.4 - - - +
252G ILE* 1.3 62.1 + - - +
253G HIS* 3.1 44.9 + - + -
263G ALA* 3.0 22.7 - - - -
264G ASP* 3.0 43.0 + - + -
458G PHE* 3.7 35.5 - - + -
459G ILE 4.0 2.2 - - - -
663G ASN* 3.6 34.2 + - - +
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Residues in contact with ILE 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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193G ILE* 3.9 33.0 - - + -
196G PHE* 4.6 20.6 - - + -
222G ILE* 5.0 6.3 - - + -
250G ILE* 3.6 12.3 + - + -
251G ARG* 1.3 72.3 - - - +
253G HIS* 1.3 62.1 + - - +
254G PHE* 3.3 24.8 - - + -
260G LEU* 3.2 35.2 - - + -
262G SER 3.4 4.7 - - - +
263G ALA* 4.6 7.4 - - + -
458G PHE* 3.0 3.4 - - - -
459G ILE 2.7 43.7 + - - +
461G VAL* 4.6 10.5 - - + -
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Residues in contact with HIS 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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251G ARG* 3.1 66.8 + - + -
252G ILE* 1.3 70.8 - - - +
254G PHE* 1.3 64.0 + - - +
260G LEU* 4.4 0.2 - - - -
261G ALA* 2.9 24.8 + - - +
262G SER* 2.4 40.5 + - - +
263G ALA 4.3 0.4 + - - -
264G ASP* 3.6 9.7 + - - -
455G ARG* 4.2 32.4 + - + -
457G TYR* 3.5 5.6 - - - +
458G PHE* 3.6 21.1 - + + +
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Residues in contact with PHE 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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163G TYR* 4.1 11.7 - + - -
166G MET* 3.0 41.3 - - + -
196G PHE* 3.6 31.9 - + + -
200G ALA* 4.3 8.1 - - + -
252G ILE* 3.3 28.5 - - + -
253G HIS* 1.3 76.0 - - - +
255G GLY* 1.3 69.2 + - - +
258G GLY* 3.9 20.6 - - - +
259G LYS 4.2 0.9 - - - -
260G LEU* 3.7 31.0 - - + -
261G ALA* 4.2 0.4 - - - -
455G ARG* 3.8 3.5 - - - -
456G GLN 3.4 12.5 + - - -
457G TYR 2.7 18.2 + - - +
459G ILE* 3.3 26.0 - - + -
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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