Contacts of the strand formed by residues 305 - 312 (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 ALA 305 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H ARG* 4.0 11.9 - - + -
253H GLN 3.4 29.6 - - - +
254H PRO* 3.7 6.1 - - + -
255H PRO* 4.2 5.6 - - - -
302H ASP 5.9 0.2 - - - +
303H ASP 3.2 4.6 + - - +
304H THR* 1.3 78.3 - - - +
306H ARG* 1.3 61.7 + - - +
307H TYR* 3.4 22.1 - - + -
331H SER* 4.7 1.1 - - - -
332H VAL 2.8 30.0 + - - +
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Residues in contact with ARG 306 (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* 3.1 5.0 - - - +
253H GLN* 2.7 38.9 + - + +
255H PRO* 5.5 0.4 - - - +
305H ALA* 1.3 73.4 - - - +
307H TYR* 1.3 61.0 + - - +
308H TYR* 3.5 35.8 - - + +
328H GLN* 2.7 27.2 + - - +
329H GLY* 2.7 30.2 + - - -
330H THR* 3.5 14.3 - - - +
331H SER* 4.1 26.1 - - - +
42L GLY* 6.3 2.0 - - - -
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Residues in contact with TYR 307 (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* 3.7 7.4 - - - +
232H LEU* 3.7 21.7 - - + +
234H ILE* 3.7 23.6 - - + -
250H TRP* 4.7 4.5 - + + -
251H VAL 3.6 3.1 - - - -
252H ARG* 2.8 36.9 + - + -
262H LEU* 3.8 22.9 - - + -
294H LEU* 4.5 8.7 - - + -
296H MET* 4.0 9.8 - - - +
299H LEU* 4.4 0.2 - - - +
303H ASP* 2.7 33.5 + - - +
305H ALA* 3.4 22.7 - - + -
306H ARG* 1.3 75.0 - - - +
308H TYR* 1.3 60.3 + - - +
329H GLY* 3.3 1.2 - - - -
330H THR* 2.8 37.7 + - - +
332H VAL* 3.6 20.2 - - + -
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Residues in contact with TYR 308 (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* 3.2 6.5 - - - +
250H TRP* 3.2 11.5 - - - -
251H VAL* 2.7 48.5 + - + +
253H GLN* 3.1 32.6 + - + -
259H LEU* 4.5 7.2 - - + -
306H ARG* 3.5 33.1 - - + -
307H TYR* 1.3 74.8 - - - +
309H CYS* 1.3 61.1 + - - +
310H VAL* 4.1 15.8 - - + +
326H TRP* 4.0 16.8 - + + -
327H GLY 3.4 21.5 - - - +
328H GLN* 3.5 18.8 - - - -
329H GLY* 3.6 8.3 - - - -
38L GLN* 3.1 14.4 + - - -
42L GLY* 3.9 11.8 + - - -
44L VAL* 4.3 9.0 - - + -
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Residues in contact with CYS 309 (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* 3.8 13.3 - - - +
219H LYS 4.2 2.2 - - - -
220H GLU* 2.9 25.4 + - - +
236H CYS* 2.1 53.6 - - + -
248H VAL* 4.1 4.3 - - + -
249H ASP 3.2 8.1 - - - +
250H TRP* 3.8 16.8 - - + -
308H TYR* 1.3 71.1 - - - +
310H VAL* 1.3 62.7 + - - +
327H GLY 2.9 25.3 + - - -
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Residues in contact with VAL 310 (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* 3.9 4.9 - - - -
248H VAL* 3.5 1.0 - - - -
249H ASP* 2.6 40.0 + - + +
251H VAL* 4.3 10.3 - - + -
308H TYR* 4.1 9.9 - - + +
309H CYS* 1.3 82.8 - - - +
311H ARG* 1.3 64.5 + - - +
323H LEU* 3.5 26.2 - - + -
325H TYR 3.2 17.5 - - - +
326H TRP* 3.4 56.3 - - + +
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Residues in contact with ARG 311 (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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216H VAL* 3.5 22.5 - - - +
218H LEU* 3.7 16.9 - - + +
241H PHE* 3.6 40.3 - - + +
246H TYR* 3.3 44.5 + - + -
247H GLY 3.5 14.1 - - - +
248H VAL* 4.4 0.2 - - - +
249H ASP* 4.1 0.2 - - - -
310H VAL* 1.3 76.0 - - - +
312H ASP* 1.3 62.4 + - - +
323H LEU* 3.4 6.1 - - - -
324H ASP* 2.8 62.2 + - - +
325H TYR* 2.8 34.8 + - + +
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Residues in contact with ASP 312 (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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632A ARG* 5.5 0.4 + - - -
246H TYR* 3.8 2.8 - - - +
247H GLY 2.8 37.9 + - - +
249H ASP* 2.4 33.1 + - - +
264H MET* 3.5 19.0 - - - +
311H ARG* 1.3 78.1 - - - +
313H PRO* 1.4 61.4 - - - +
314H ALA* 2.7 33.5 + - - +
321H TYR* 3.4 25.0 - - - +
322H ALA 3.1 16.6 - - - +
323H LEU* 4.4 1.1 - - + -
324H ASP* 4.0 0.9 - - - -
96L TRP* 6.1 0.2 - - - -
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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