Contacts of the strand formed by residues 247 - 253 (chain H) in PDB entry 1FNS
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246H TYR* 1.3 76.3 - - - +
248H VAL* 1.3 68.8 + - - +
264H MET* 4.1 1.1 - - - -
265H ILE 3.1 13.7 - - - -
266H TRP* 4.4 0.4 - - - -
311H ARG* 3.5 5.2 - - - +
312H ASP* 2.8 41.4 + - - +
314H ALA* 3.5 17.8 - - - +
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Residues in contact with VAL 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H LEU* 4.4 11.2 - - + -
236H CYS* 4.5 1.1 - - - -
238H VAL* 4.6 0.9 - - + -
241H PHE* 4.4 13.9 - - + -
243H LEU* 3.5 31.4 - - + -
247H GLY* 1.3 80.0 - - - +
249H ASP* 1.3 74.5 + - - +
250H TRP* 4.5 4.4 - - - +
264H MET* 3.2 1.7 - - - -
265H ILE* 2.9 37.0 + - + +
283H ILE* 4.9 0.2 - - - +
292H VAL* 4.0 28.5 - - + -
309H CYS* 4.1 17.3 - - + -
310H VAL 3.5 8.1 - - - +
311H ARG* 4.6 0.4 - - - -
312H ASP* 4.2 0.2 + - - -
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Residues in contact with ASP 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H VAL* 1.3 76.5 - - - +
250H TRP* 1.3 66.4 + - - +
251H VAL* 4.9 0.7 - - + -
261H TRP* 2.9 27.1 + - + +
263H GLY 3.2 9.9 - - - +
264H MET* 3.3 14.3 - - - +
309H CYS* 3.2 5.9 - - - -
310H VAL* 2.6 40.9 + - + +
312H ASP* 2.4 35.0 - - - +
323H LEU* 3.4 23.3 - - + +
96L TRP* 4.5 4.7 + - - -
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Residues in contact with TRP 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H GLU* 4.1 10.3 - - + -
234H ILE* 3.5 44.9 - - + -
236H CYS* 3.6 31.2 - - + -
248H VAL* 4.5 2.3 - - - +
249H ASP* 1.3 78.2 + - - +
251H VAL* 1.3 59.4 + - - +
261H TRP* 4.2 1.0 - - - -
262H LEU* 2.9 42.7 + - + +
263H GLY 3.0 9.7 + - - +
281H LEU* 5.8 0.4 - - + -
283H ILE* 3.8 30.9 - - + +
292H VAL* 3.7 29.9 - - + +
294H LEU* 3.5 39.9 - - + +
307H TYR* 4.7 6.3 - + + -
308H TYR 3.2 22.0 - - - -
309H CYS* 3.8 10.8 - - + -
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Residues in contact with VAL 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ASP* 4.9 1.6 - - + -
250H TRP* 1.3 81.5 - - - +
252H ARG* 1.3 63.7 + - - +
259H LEU* 4.1 24.0 - - + -
260H GLU 3.4 12.6 - - - +
261H TRP* 4.1 22.2 - - + -
262H LEU* 4.3 2.6 - - - +
307H TYR* 3.6 1.9 - - - +
308H TYR* 2.7 37.2 + - + +
310H VAL* 4.3 9.9 - - + -
323H LEU* 4.4 9.0 - - + -
326H TRP* 3.8 38.8 - - + -
98L PHE* 4.4 2.7 - - + -
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Residues in contact with ARG 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H VAL* 1.3 78.1 - - - +
253H GLN* 1.3 61.9 + - - +
254H PRO* 4.2 7.3 - - + +
258H GLY 3.8 0.3 - - - +
259H LEU* 3.6 3.0 - - - -
260H GLU* 2.7 67.9 + - + +
262H LEU* 3.7 11.6 - - + +
277H LEU* 3.8 19.7 - - - +
280H ARG* 4.7 1.2 - - - +
296H MET* 3.7 9.9 - - - +
302H ASP 4.5 7.4 + - - -
303H ASP* 2.7 36.7 + - - +
305H ALA* 4.0 13.7 - - + +
306H ARG 3.1 11.2 - - - +
307H TYR* 2.8 44.0 + - + -
308H TYR* 4.6 0.9 - - - -
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Residues in contact with GLN 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H ARG* 1.3 75.7 - - - +
254H PRO* 1.3 71.3 - - - +
255H PRO* 3.5 1.1 - - + +
256H GLY 5.7 0.4 - - - +
257H LYS 3.0 29.3 + - - +
258H GLY 3.2 6.9 + - - +
259H LEU* 3.8 17.4 - - + +
305H ALA* 3.4 2.9 - - - -
306H ARG* 2.7 36.1 + - + +
308H TYR* 3.1 14.4 + - + -
38L GLN* 3.0 42.2 + - - -
87L TYR* 3.4 13.1 + - - -
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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