Contacts of the strand formed by residues 314 - 319 (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 LEU 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B VAL* 3.9 28.3 - - + -
280B ILE* 3.8 21.1 - - + -
283B LEU* 4.1 9.0 - - + -
292B GLY 3.5 4.9 - - - +
294B ALA* 4.5 11.9 - - + -
310B ILE* 4.2 22.0 - - + -
312B GLN 4.1 2.5 - - - +
313B PRO* 1.3 74.9 - - - +
315B PHE* 1.3 62.2 + - - +
316B PHE* 3.7 30.8 - - + -
334B CYS* 4.2 6.1 - - + -
340B GLU 3.1 6.3 + - - -
341B ARG* 3.4 24.1 - - + +
342B LYS 3.2 22.9 + - - +
391B PHE* 3.7 3.9 - - - -
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Residues in contact with PHE 315 (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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292B GLY 3.1 9.0 + - - +
293B ILE* 3.3 14.0 - - + +
294B ALA 2.8 31.2 + - - -
314B LEU* 1.3 72.4 - - - +
316B PHE* 1.3 71.5 + - - +
317B ILE* 3.7 28.3 - - + -
342B LYS* 3.5 27.4 - - + -
343B MET 4.1 2.7 - - - -
344B ILE* 3.9 15.7 - - + -
387B ALA* 3.7 23.3 - - + -
391B PHE* 3.4 44.4 - + + -
409B ILE* 3.8 29.2 - - + -
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.9 22.9 - - + -
294B ALA* 3.4 22.7 - - + -
297B ALA* 4.8 1.1 - - + -
299B MET* 4.2 4.3 - - - -
314B LEU* 3.7 34.3 - - + -
315B PHE* 1.3 76.3 - - - +
317B ILE* 1.3 59.3 + - - +
318B ASN* 3.9 8.5 - - - +
331B MET* 3.6 57.7 - - + -
334B CYS* 4.3 3.6 - - + -
335B TYR* 4.4 11.7 - + - -
341B ARG* 4.8 1.6 - - + -
342B LYS 3.0 17.8 + - - -
343B MET* 3.2 26.1 - - + -
344B ILE 3.0 25.0 + - - +
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Residues in contact with ILE 317 (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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293B ILE* 4.0 3.8 - - + -
294B ALA 2.9 6.7 + - - -
295B LEU* 3.2 20.7 - - + -
296B ASP 2.6 30.1 + - - -
315B PHE* 3.7 36.5 + - + -
316B PHE* 1.3 73.7 - - - +
318B ASN* 1.3 56.5 + - - +
344B ILE* 3.7 18.6 - - + -
346B ILE* 4.1 13.9 - - + -
354B PHE* 3.6 23.9 - - + -
384B SER* 3.8 15.0 - - - +
387B ALA* 4.0 5.2 - - + -
388B SER* 3.5 25.1 - - - +
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Residues in contact with ASN 318 (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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294B ALA 4.6 0.2 - - - +
296B ASP* 3.5 12.2 + - - +
297B ALA 4.4 0.7 + - - -
316B PHE* 4.1 6.9 - - - +
317B ILE* 1.3 79.7 - - - +
319B SER* 1.3 65.2 + - - +
323B GLN* 3.6 22.0 + - + -
328B ILE* 4.3 7.5 - - - +
331B MET* 3.8 19.1 - - - +
343B MET* 3.6 31.7 - - - +
344B ILE 2.9 19.1 + - - +
345B THR* 3.8 12.7 + - - +
346B ILE* 3.0 27.0 + - - +
354B PHE* 3.7 11.2 - - - -
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Residues in contact with SER 319 (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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296B ASP* 2.8 31.3 + - - -
318B ASN* 1.3 76.1 - - - +
320B GLU* 1.3 62.8 + - - +
322B PHE* 3.0 23.9 + - - +
323B GLN* 3.8 16.1 - - - +
345B THR* 3.5 7.6 - - - +
349B SER* 2.8 16.8 - - - -
350B VAL 3.3 23.8 - - - -
351B HIS 3.4 3.3 + - - -
354B PHE* 3.8 5.4 - - - -
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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