Contacts of the helix formed by residues 339 - 348 (chain B) in PDB entry 5FI4
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 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024A LYS* 6.2 4.3 - - - -
337B ASP 3.7 2.2 + - - -
338B ILE* 1.3 75.7 - - - +
340B ARG* 1.4 61.1 + - - +
341B GLU* 3.7 16.7 + - - +
342B GLU* 3.0 48.3 + - - +
343B VAL* 3.2 13.8 + - - +
358B ARG* 4.5 1.6 - - - +
361B SER* 5.5 1.3 - - - -
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 2.8 33.5 + - - +
541A SER* 3.8 1.6 - - - +
542A GLU* 3.4 51.5 + - - +
1020A ALA* 5.2 1.0 - - - +
1023A ARG* 3.9 26.0 - - - +
339B SER* 1.4 71.5 - - - +
341B GLU* 1.3 82.2 + - - +
343B VAL* 3.6 5.4 + - + +
344B ASN* 3.1 43.5 + - - +
358B ARG* 3.8 23.8 - - - +
361B SER* 4.5 3.1 + - - +
380B LEU* 4.7 11.7 - - + -
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A PHE 5.9 0.2 - - - -
1017A ASP* 3.7 36.9 - - + +
1020A ALA* 3.4 27.0 - - + +
1023A ARG* 5.4 0.7 + - - -
1024A LYS* 5.8 3.0 - - - -
339B SER* 3.1 13.4 - - - +
340B ARG* 1.3 117.5 + - - +
342B GLU* 1.4 62.5 + - + +
344B ASN* 3.5 10.5 - - - +
345B GLU* 3.3 20.1 + - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ASP 4.2 2.9 - - - +
338B ILE* 3.4 27.0 - - + +
339B SER* 3.0 40.7 + - - +
341B GLU* 1.4 73.6 - - + +
343B VAL* 1.4 63.7 + - - +
345B GLU* 3.2 9.8 + - - +
346B LYS* 3.2 24.9 + - + +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ILE* 3.5 17.2 - - + +
339B SER 3.2 15.6 + - - +
340B ARG* 3.6 6.7 - - - +
342B GLU* 1.4 74.4 - - - +
344B ASN* 1.4 52.7 + - - +
346B LYS* 3.1 9.1 + - - +
347B LEU* 2.8 39.0 + - + +
356B LEU* 3.9 20.0 - - + -
358B ARG* 3.4 30.7 - - - +
371B THR* 3.8 35.2 - - + +
378B ASN* 5.9 0.2 - - - +
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Residues in contact with ASN 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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1017A ASP* 3.8 22.8 + - - +
340B ARG* 3.1 37.8 + - - +
341B GLU* 3.5 15.3 - - - +
342B GLU 3.3 0.2 - - - -
343B VAL* 1.4 76.1 - - - +
345B GLU* 1.4 52.1 + - - +
347B LEU* 3.2 2.8 + - - +
348B ARG* 2.8 36.0 + - - +
371B THR* 6.0 0.7 - - - +
378B ASN* 3.3 28.2 + - - +
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Residues in contact with GLU 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 GLU 3.3 8.3 + - - +
342B GLU* 3.2 11.0 + - - +
344B ASN* 1.4 77.1 - - - +
346B LYS* 1.4 61.8 + - + +
348B ARG* 3.4 29.2 + - - +
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Residues in contact with LYS 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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335B TRP* 5.2 11.0 - - + -
338B ILE* 5.6 3.4 - - + -
342B GLU* 3.2 15.3 + - + +
343B VAL* 3.1 8.4 + - - +
345B GLU* 1.4 76.5 - - + +
347B LEU* 1.3 60.5 + - - +
348B ARG 3.7 1.2 + - - +
350B THR* 3.3 17.2 - - - +
356B LEU* 4.0 22.0 - - + -
428B VAL* 4.2 22.6 - - + +
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Residues in contact with LEU 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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343B VAL* 2.8 25.4 + - + +
344B ASN 3.5 0.7 - - - -
346B LYS* 1.3 71.6 - - - +
348B ARG* 1.4 62.6 + - - +
349B ASP 3.2 1.0 + - - -
350B THR* 2.7 25.8 + - - +
354B THR* 3.7 31.9 - - + +
355B PHE* 4.7 2.0 - - - +
356B LEU* 4.5 6.1 - - + -
371B THR* 3.8 38.8 - - + +
373B ARG* 3.4 25.2 + - + +
378B ASN* 3.5 29.4 - - - +
428B VAL* 3.9 16.4 - - + -
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Residues in contact with ARG 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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419A HIS 5.9 0.4 + - - -
453A GLU* 3.8 37.8 + - - +
454A ASP* 3.0 35.2 + - - +
455A LEU* 5.6 3.2 - - - +
344B ASN 2.8 13.1 + - - +
345B GLU* 3.4 25.1 + - - +
346B LYS 3.4 2.6 - - - +
347B LEU* 1.4 72.8 - - - +
349B ASP* 1.3 83.3 + - - +
350B THR* 3.2 8.1 + - - +
373B ARG* 4.9 2.7 - - - +
378B ASN* 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