Contacts of the strand formed by residues 341 - 346 (chain B) in PDB entry 3F9C
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 ARG 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B TYR 5.0 1.0 + - - -
310B ILE* 2.6 43.0 + - - +
312B GLN 2.9 20.8 + - - -
314B LEU* 3.4 24.5 - - + +
316B PHE* 4.8 6.3 - - + -
334B CYS* 2.5 29.9 + - - +
335B TYR* 3.3 48.7 - - + +
336B SER 4.5 0.7 - - - +
339B LYS* 3.4 34.7 + - - +
340B GLU* 1.3 100.7 + - - +
342B LYS* 1.3 78.3 + - - +
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Residues in contact with LYS 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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314B LEU 3.2 8.9 + - - +
315B PHE* 3.5 24.0 - - + -
316B PHE* 3.0 24.4 + - - -
335B TYR* 3.7 7.1 + - - -
340B GLU* 3.6 28.0 + - - +
341B ARG* 1.3 81.0 + - - +
343B MET* 1.3 62.4 + - - +
391B PHE* 4.5 7.5 - - + -
409B ILE* 3.3 28.0 - - + +
410B GLU* 3.1 37.0 + - - +
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Residues in contact with MET 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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315B PHE* 4.0 0.4 - - - -
316B PHE* 3.2 17.0 - - + -
318B ASN* 3.6 22.7 - - - +
328B ILE* 4.4 10.8 - - + -
331B MET* 3.5 43.5 - - + -
332B LYS* 4.9 6.5 - - + +
335B TYR* 3.4 24.4 + - + +
342B LYS* 1.3 77.9 - - - +
344B ILE* 1.3 69.6 + - - +
409B ILE 4.4 2.0 + - - +
410B GLU 5.0 0.7 - - - +
418B PRO* 3.8 1.7 - - - +
419B GLY* 2.8 49.9 + - - -
420B THR* 3.9 11.9 - - + -
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Residues in contact with ILE 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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315B PHE* 3.9 15.9 - - + -
316B PHE 3.0 7.5 + - - +
317B ILE* 3.9 28.5 - - + -
318B ASN* 2.9 35.6 + - - +
343B MET* 1.3 79.7 - - - +
345B THR* 1.3 60.3 + - - +
346B ILE* 5.0 1.6 - - + -
384B SER* 5.8 0.4 - - - +
387B ALA* 3.9 15.5 - - + -
408B LEU 3.7 19.7 - - - +
409B ILE 3.5 19.7 - - - +
410B GLU 4.1 1.1 - - - -
411B GLY* 3.7 14.6 - - - +
416B LEU* 4.1 19.5 - - + -
417B ILE 3.3 13.2 - - - +
419B GLY 3.7 2.9 - - - -
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Residues in contact with THR 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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318B ASN* 3.5 14.0 + - - +
319B SER 3.5 10.3 - - - +
320B GLU* 3.4 34.3 - - + -
323B GLN* 5.6 1.0 - - + +
344B ILE* 1.3 73.8 + - - +
346B ILE* 1.3 64.3 + - - +
416B LEU* 3.4 7.5 - - - +
417B ILE* 2.9 45.4 + - + +
419B GLY 2.9 21.5 + - - -
420B THR* 3.7 11.2 + - - +
421B ASN* 4.1 12.8 - - - +
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Residues in contact with ILE 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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317B ILE* 4.1 13.9 - - + -
318B ASN 3.0 14.5 + - - +
320B GLU* 3.2 13.9 + - - +
344B ILE* 5.5 0.2 - - + -
345B THR* 1.3 71.2 - - - +
347B ARG* 1.3 63.9 + - - +
349B SER* 2.8 37.1 + - - +
354B PHE* 4.5 7.9 - - + -
375B ILE* 3.5 24.7 - - + -
380B ALA* 3.4 30.3 - - + +
383B LEU* 3.9 12.8 - - + -
384B SER* 3.6 26.5 - - - +
415B ASN 3.5 3.6 - - - -
416B LEU* 3.9 14.4 - - + -
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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