Contacts of the helix formed by residues 289 - 302 (chain A) in PDB entry 1F44
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 HIS 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ALA* 4.0 12.3 - - + -
173A ARG* 3.7 35.1 - - + +
288A GLY* 1.3 78.0 + - - +
290A SER* 1.3 58.8 + - - +
291A ALA 3.4 1.8 - - - -
292A ARG* 3.3 25.2 + - + +
293A VAL* 3.0 29.4 + - + +
324A PHE* 4.0 18.4 - + - -
15M G 3.9 36.1 - - - -
16M C 4.3 3.0 + - - -
9N T 3.7 27.2 - - - +
10N A 3.1 17.0 + - - +
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA* 3.9 8.3 - - - +
135A LEU 2.4 27.3 + - - -
136A ALA* 3.7 1.2 - - - -
137A PHE* 2.8 32.9 + - - -
265A PHE* 4.2 2.2 - - - -
286A TRP* 3.3 9.0 - - - -
287A SER* 2.8 37.1 + - - -
288A GLY 3.4 0.2 - - - -
289A HIS* 1.3 78.6 - - - +
291A ALA* 1.3 58.2 + - - +
293A VAL* 3.6 1.5 + - - +
294A GLY 2.8 16.3 + - - -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 3.7 23.0 - - + +
167A ALA* 3.6 18.8 - - + +
168A TYR* 3.6 30.8 - - - +
265A PHE* 3.9 13.2 - - + -
288A GLY 4.9 0.4 + - - +
289A HIS 3.4 0.4 - - - -
290A SER* 1.3 76.2 - - - +
292A ARG* 1.3 60.0 + - - +
295A ALA* 2.7 34.3 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 4.5 1.4 + - - -
171A LEU* 2.7 59.0 + - + +
172A LEU* 4.9 3.7 - - - +
173A ARG* 4.8 10.3 - - - +
176A GLU* 5.6 1.4 + - - -
288A GLY 5.5 0.6 + - - +
289A HIS* 3.3 35.6 + - + +
291A ALA* 1.3 78.0 - - - +
293A VAL* 1.3 62.3 + - - +
296A ALA* 3.1 27.0 + - - +
313A GLY* 3.0 35.9 + - - -
314A GLY 5.1 0.8 - - - -
315A TRP* 3.3 28.5 - - + +
324A PHE* 3.7 13.1 - - + -
16M C 2.9 33.4 + - - -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.7 24.5 - - + +
134A ALA* 3.9 21.3 - - + +
136A ALA* 3.9 4.9 - - + -
289A HIS* 3.0 22.5 + - + +
290A SER 3.7 4.9 - - - +
292A ARG* 1.3 77.2 - - - +
294A GLY* 1.3 64.0 + - - +
296A ALA* 3.3 2.1 + - - +
297A ARG* 3.1 60.7 + - + +
324A PHE* 3.5 26.2 - - + +
15M G 4.5 1.6 - - - +
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Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 3.9 4.9 - - - -
137A PHE 3.1 22.7 - - - -
138A GLU* 3.5 19.3 - - - +
290A SER 2.8 13.0 + - - -
292A ARG 3.3 0.2 - - - -
293A VAL* 1.3 77.9 - - - +
295A ALA* 1.3 56.3 + - - +
297A ARG* 3.3 1.9 + - - +
298A ASP* 2.9 32.4 + - - -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR* 3.3 44.4 - - + +
171A LEU* 3.6 19.3 - - + -
291A ALA 2.7 21.2 + - - +
294A GLY* 1.3 72.6 - - - -
296A ALA* 1.3 56.9 + - - +
298A ASP* 3.2 2.8 + - - +
299A MET* 3.0 35.4 + - + +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 4.2 0.8 - - + +
292A ARG 3.1 19.5 + - - +
293A VAL 3.7 4.3 - - - +
295A ALA* 1.3 75.6 - - - +
297A ARG* 1.3 63.1 + - - +
299A MET* 3.4 13.8 + - - +
300A ALA 3.0 18.7 + - - -
315A TRP* 4.1 11.0 - - + -
324A PHE* 3.8 14.4 - - + -
325A ILE* 3.0 38.2 - - + +
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.2 26.7 + - - +
134A ALA 4.2 6.1 + - - -
136A ALA* 3.4 16.0 - - - +
138A GLU* 3.7 3.8 - - - +
293A VAL* 3.1 33.6 + - + +
294A GLY 3.6 7.2 - - - +
296A ALA* 1.3 76.2 - - - +
298A ASP* 1.3 57.6 + - - +
300A ALA* 3.3 2.1 + - - +
301A ARG* 2.8 45.2 + - - +
324A PHE 5.6 1.1 + - - +
325A ILE* 4.3 15.7 - - + -
327A ASN* 3.2 39.9 + - - +
328A LEU* 3.8 11.3 - - + +
329A ASP* 2.9 33.0 + - - +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLU* 3.6 6.4 - - - +
139A ARG* 2.8 26.0 + - - +
168A TYR* 2.5 34.1 + - - +
294A GLY 2.9 13.9 + - - +
295A ALA 3.2 6.7 + - - +
297A ARG* 1.3 76.8 - - - +
299A MET* 1.3 57.1 + - + +
301A ARG* 2.9 36.2 + - + +
302A ALA* 3.0 29.8 + - - +
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Residues in contact with MET 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.9 25.4 - - + -
295A ALA* 3.0 22.3 + - + +
296A ALA* 3.8 9.4 - - - +
298A ASP* 1.3 73.4 - - + +
300A ALA* 1.3 69.0 + - - +
302A ALA* 3.2 5.9 + - - -
304A VAL* 3.2 44.5 + - + +
308A GLU 4.7 1.3 - - - +
309A ILE* 3.8 32.8 - - + +
312A ALA* 3.4 34.1 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA 3.0 17.0 + - - +
297A ARG 3.7 3.8 - - - +
299A MET* 1.3 76.6 - - - +
301A ARG* 1.3 62.2 + - - +
303A GLY* 3.1 14.7 + - - -
304A VAL 4.9 2.1 - - - +
309A ILE* 3.9 13.9 - - + +
322A MET* 6.3 1.6 - - + -
325A ILE* 3.8 24.7 - - + -
328A LEU* 4.4 16.1 - - + +
332A THR* 4.5 4.5 - - - +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 3.2 22.1 + - - -
297A ARG* 2.8 26.6 + - - +
298A ASP* 2.9 38.0 + - + +
299A MET 3.2 0.2 - - - -
300A ALA* 1.3 72.4 - - - +
302A ALA* 1.3 61.1 + - + +
303A GLY 3.2 3.2 + - - -
328A LEU* 3.8 10.3 - - + +
329A ASP* 2.8 30.3 + - - -
330A SER* 2.9 41.7 + - - +
332A THR* 3.5 23.7 - - + +
337A ARG* 5.5 2.3 + - - -
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ASP 3.0 17.6 + - - +
299A MET* 3.2 5.5 + - - +
301A ARG* 1.3 76.9 - - + +
303A GLY* 1.3 62.5 + - - +
304A VAL* 3.2 12.5 + - + +
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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