Contacts of the strand formed by residues 247 - 254 (chain D) in PDB entry 1O19
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D PHE* 1.3 83.9 - - - +
248D MLY 1.3 66.5 + - - +
267D THR* 3.6 1.4 - - - -
268D TYR* 3.0 36.8 + - - -
269D LEU* 4.4 0.4 + - - +
463D ASP* 3.3 11.0 - - - -
464D ILE* 4.2 16.2 - - - -
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Residues in contact with MLY 248 (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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186D THR* 3.3 33.4 - - - -
189D THR* 4.8 13.2 - - - -
190D MLY 4.8 9.9 - - - -
193D ILE* 5.6 1.3 - - - -
226D ASN* 2.8 42.8 - - - -
229D LEU* 5.4 9.4 - - + +
230D GLU* 5.0 5.8 - - - -
234D ASN* 5.9 0.2 - - - -
244D SER* 4.6 7.0 - - - -
246D PHE* 4.0 25.4 - - + -
247D GLY* 1.3 77.7 - - - +
249D PHE* 1.3 64.6 + - - +
250D ILE* 3.8 32.8 - - + -
265D ILE* 4.5 14.1 - - + -
266D GLU 3.3 11.4 - - - +
267D THR* 4.9 0.4 - - - -
268D TYR* 4.1 6.0 - - - -
461D VAL 3.7 0.8 - - - +
462D LEU* 3.5 3.2 - - - +
463D ASP* 2.4 64.0 + - + +
464D ILE* 4.2 0.2 - - - +
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Residues in contact with PHE 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D SER* 5.5 1.8 - - - -
248D MLY 1.3 77.8 - - - +
250D ILE* 1.3 60.4 + - - +
251D ARG* 4.0 26.5 - - + -
264D ASP 3.0 12.6 - - - +
265D ILE 3.6 0.2 - - - -
266D GLU* 3.1 24.6 + - + +
268D TYR* 3.8 23.6 - - + +
458D PHE* 4.7 5.6 - + - -
460D GLY* 3.9 28.3 - - - -
461D VAL 3.5 6.1 - - - -
462D LEU* 3.6 28.7 - - + -
660D LEU* 3.9 19.3 - - + -
663D ASN* 4.2 21.1 - - + -
664D LEU* 4.0 24.7 - - + -
667D THR* 6.0 0.4 - - - -
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Residues in contact with ILE 250 (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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189D THR* 5.0 3.8 - - + -
193D ILE* 3.1 34.3 - - + -
222D ILE* 6.0 0.7 - - + -
226D ASN* 5.4 0.7 - - - +
248D MLY 3.8 39.3 - - + -
249D PHE* 1.3 76.3 - - - +
251D ARG* 1.3 71.2 + - - +
252D ILE* 4.3 13.5 - - + -
263D ALA* 4.3 6.3 - - + -
264D ASP 3.2 18.8 - - - +
265D ILE* 4.3 17.0 - - + -
459D ILE 3.5 2.8 - - - +
460D GLY* 3.3 4.3 - - - -
461D VAL* 3.1 37.8 + - + +
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Residues in contact with ARG 251 (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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249D PHE* 4.0 20.9 - - + -
250D ILE* 1.3 77.7 - - - +
252D ILE* 1.3 62.5 + - - +
253D HIS* 3.1 45.0 + - + -
263D ALA* 3.0 22.9 - - - -
264D ASP* 3.0 42.9 + - + -
458D PHE* 3.7 37.0 - - + -
459D ILE 4.0 2.0 - - - -
663D ASN* 3.6 35.3 + - - +
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Residues in contact with ILE 252 (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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193D ILE* 3.9 34.1 - - + -
196D PHE* 4.6 19.7 - - + -
222D ILE* 5.0 7.4 - - + -
250D ILE* 4.3 11.7 - - + -
251D ARG* 1.3 71.8 - - - +
253D HIS* 1.3 61.6 + - - +
254D PHE* 3.3 24.5 - - + -
260D LEU* 3.2 34.3 - - + -
262D SER 3.4 5.6 - - - +
263D ALA* 4.6 7.0 - - + -
458D PHE* 3.0 3.1 - - - -
459D ILE 2.7 44.7 + - - +
461D VAL* 4.6 9.9 - - + -
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Residues in contact with HIS 253 (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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251D ARG* 3.1 66.2 + - + -
252D ILE* 1.3 71.4 - - - +
254D PHE* 1.3 64.1 + - - +
260D LEU* 4.4 0.2 - - - -
261D ALA* 2.9 24.9 + - - +
262D SER* 2.4 39.3 + - - +
263D ALA 4.3 0.6 + - - -
264D ASP* 3.6 9.7 + - - -
455D ARG* 4.2 33.9 + - + -
457D TYR 3.5 6.1 - - - +
458D PHE* 3.6 19.4 - + + +
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Residues in contact with PHE 254 (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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163D TYR* 4.1 11.7 - + - -
166D MET* 3.0 40.2 - - + -
196D PHE* 3.6 31.4 - + + -
200D ALA* 4.3 7.9 - - + -
252D ILE* 3.3 36.3 - - + -
253D HIS* 1.3 76.9 - - - +
255D GLY* 1.3 66.7 + - - +
258D GLY* 3.9 20.9 - - - +
259D LYS 4.2 0.7 - - - -
260D LEU* 3.7 29.8 - - + -
261D ALA* 4.2 0.7 - - - -
455D ARG* 3.8 3.3 - - - -
456D GLN 3.4 12.1 + - - -
457D TYR* 2.7 18.7 + - + +
459D ILE* 3.3 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