Contacts of the helix formed by residues 340 - 349 (chain B) in PDB entry 5FFO
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 SER 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B THR* 3.9 10.0 + - - -
137B GLU* 3.5 9.4 + - - +
138B LEU* 3.3 57.7 + - - +
141B ARG* 3.8 7.7 + - - +
336B LEU* 4.5 4.3 - - - -
337B GLN 3.8 15.7 - - - +
338B LYS 3.2 5.9 + - - -
339B ASP* 1.3 69.9 - - - +
341B GLY* 1.3 58.5 + - - +
342B ASN* 3.0 8.1 + - - +
343B ILE* 3.3 13.8 + - - +
344B LEU* 3.8 3.2 + - - +
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 3.3 26.9 - - - +
339B ASP* 2.9 6.2 + - - -
340B SER* 1.3 75.4 - - - +
342B ASN* 1.3 63.7 + - - +
343B ILE 3.3 0.2 - - - -
344B LEU* 3.1 18.2 + - - +
345B GLN* 3.1 27.6 + - - +
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Residues in contact with ASN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 4.0 20.3 + - + +
337B GLN* 2.7 52.0 + - + +
339B ASP* 3.6 7.3 + - - +
340B SER* 3.0 1.5 - - - -
341B GLY* 1.3 76.2 - - - +
343B ILE* 1.3 62.6 + - + +
345B GLN* 3.1 32.5 + - - +
346B LEU* 3.5 8.6 + - - +
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 3.7 32.3 - - + -
142B LEU* 6.3 1.3 - - + -
250B VAL* 5.1 7.2 - - + -
310B ILE* 4.5 9.9 - - + -
312B ALA* 3.7 30.7 - - + -
335B LEU 3.5 19.7 - - - +
336B LEU* 3.7 22.7 - - + -
340B SER* 3.3 9.8 + - - +
341B GLY 3.3 0.4 - - - -
342B ASN* 1.3 72.2 - - + +
344B LEU* 1.3 67.5 + - + +
346B LEU* 3.1 37.4 + - + +
347B ILE* 3.4 16.1 - - + +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.1 9.0 - - + -
141B ARG* 3.6 41.1 - - + +
142B LEU* 3.9 38.1 - - + -
145B GLU* 4.0 22.9 - - + -
340B SER 3.9 9.2 - - - +
341B GLY* 3.1 12.5 + - - +
343B ILE* 1.3 79.4 - - + +
345B GLN* 1.3 62.1 + - - +
347B ILE* 3.1 11.2 + - + +
348B ILE* 3.1 38.0 + - + +
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Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B GLY 3.1 18.7 + - - +
342B ASN* 3.1 21.0 + - - +
344B LEU* 1.3 77.1 - - - +
346B LEU* 1.3 53.0 + - - +
348B ILE* 4.2 9.0 - - + +
349B SER* 2.5 36.1 + - - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ILE* 4.1 18.4 - - + -
332B THR* 4.7 11.0 - - - +
333B VAL 3.4 26.7 - - - +
334B GLY* 3.7 16.2 - - - -
342B ASN 3.5 5.8 + - - +
343B ILE* 3.1 31.4 + - + +
345B GLN* 1.3 77.7 - - - +
347B ILE* 1.3 59.8 + - + +
349B SER* 3.1 8.9 + - - +
350B ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 5.9 0.7 - - + -
118B LEU* 4.9 7.0 - - + -
142B LEU* 4.0 26.7 - - + -
146B MET* 4.7 20.2 - - + -
248B LEU* 3.7 27.8 - - + -
250B VAL* 4.4 15.9 - - + -
310B ILE* 4.1 17.7 - - + -
343B ILE* 3.4 19.1 - - + +
344B LEU* 3.1 13.1 + - + +
346B LEU* 1.3 75.1 - - - +
348B ILE* 1.3 59.6 + - + +
350B ALA* 2.9 21.4 + - - +
351B TYR* 3.1 13.0 + - - +
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Residues in contact with ILE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 5.3 16.6 - - + +
149B LEU* 4.0 24.3 - - + +
344B LEU* 3.1 27.6 + - + +
345B GLN* 4.2 7.9 - - + +
347B ILE* 1.3 75.8 - - + +
349B SER* 1.3 58.7 + - - +
350B ALA 3.1 2.5 + - - -
351B TYR* 3.4 20.6 + - - +
352B GLU* 4.4 2.1 + - - +
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLN 2.5 26.0 + - - -
346B LEU* 3.1 9.2 + - - +
348B ILE* 1.3 75.6 - - - +
350B ALA* 1.3 56.3 + - - +
351B TYR 3.5 0.4 - - - -
352B GLU* 3.1 37.5 - - - +
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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