Contacts of the strand formed by residues 314 - 319 (chain C) in PDB entry 3F98
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279C VAL* 3.9 18.6 - - + -
280C ILE* 3.9 21.8 - - + -
283C LEU* 4.2 11.2 - - + -
292C GLY 3.4 18.4 - - - +
294C ALA* 4.5 6.1 - - + +
310C ILE* 5.2 2.2 - - + -
312C GLN 4.2 1.6 - - - +
313C PRO* 1.3 77.3 - - - +
315C PHE* 1.3 69.8 + - - +
316C PHE* 3.6 33.1 - - + -
334C CYS* 4.3 13.9 - - + -
340C GLU 3.1 5.9 + - - +
341C ARG* 3.3 29.1 - - + +
342C LYS 3.2 21.5 + - - +
391C PHE* 3.7 4.4 - - - -
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Residues in contact with PHE 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C GLY 3.1 8.4 + - - +
293C ILE* 3.4 11.2 - - + +
294C ALA* 2.8 33.4 + - - +
314C LEU* 1.3 74.4 - - - +
316C PHE* 1.3 72.1 + - - +
317C ILE* 3.6 30.7 - - + -
342C LYS* 3.4 26.7 - - + -
344C ILE* 3.8 24.5 - - + -
387C ALA* 3.7 27.1 - - + -
391C PHE* 3.6 40.8 - + + -
409C ILE* 3.9 20.6 - - + -
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Residues in contact with PHE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ILE* 3.9 18.8 - - + -
294C ALA* 3.5 18.4 - - + -
297C ALA* 4.5 0.4 - - + -
299C MET* 4.4 3.6 - - - -
314C LEU* 3.6 30.7 - - + -
315C PHE* 1.3 75.9 - - - +
317C ILE* 1.3 61.6 + - - +
318C ASN* 4.0 8.1 - - - +
331C MET* 3.8 40.6 - - + -
334C CYS* 3.9 19.3 - - + -
335C TYR* 4.1 20.9 - + - -
341C ARG* 4.4 4.0 - - + -
342C LYS 2.8 18.6 + - - +
343C MET* 3.2 25.9 - - + -
344C ILE 3.0 24.4 + - - +
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ILE* 4.0 4.7 - - + -
294C ALA 2.9 8.3 + - - -
295C LEU* 3.4 17.6 - - + -
296C ASP 2.7 29.6 + - - -
315C PHE* 3.6 34.5 - - + -
316C PHE* 1.3 73.2 - - - +
318C ASN* 1.3 56.1 + - - +
344C ILE* 3.6 16.8 - - + -
346C ILE* 3.8 17.0 - - + -
354C PHE* 3.5 13.4 - - + -
384C SER* 3.8 31.2 - - - +
387C ALA* 4.3 2.7 - - + -
388C SER* 3.5 25.1 - - - +
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Residues in contact with ASN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ASP* 3.4 9.0 + - - +
297C ALA 4.6 0.5 + - - -
316C PHE* 4.0 7.5 - - - +
317C ILE* 1.3 80.4 + - - +
319C SER* 1.3 59.8 + - - +
323C GLN* 3.8 10.2 + - - +
328C ILE* 3.8 5.9 - - - +
331C MET* 3.5 34.9 - - - +
343C MET* 3.7 20.1 - - - +
344C ILE 2.9 13.7 + - - +
345C THR* 3.9 1.1 - - - +
346C ILE* 2.8 31.0 + - - +
354C PHE* 4.2 3.8 - - - -
585C FMT 3.1 30.8 + - - +
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Residues in contact with SER 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ASP* 2.6 32.4 + - - -
318C ASN* 1.3 73.7 - - - +
320C GLU* 1.3 62.8 + - - +
322C PHE* 3.1 22.7 + - - +
323C GLN* 3.8 4.3 - - - +
345C THR* 3.7 1.8 - - - -
349C SER* 3.0 25.1 - - - -
350C VAL 3.5 15.7 - - - -
351C HIS 3.6 2.1 + - - -
354C PHE* 4.1 5.7 - - - -
585C FMT 2.8 22.2 - - - +
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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