Contacts of the strand formed by residues 354 - 359 (chain C) in PDB entry 5TF6
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 GLY 354 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C LEU 3.2 13.5 - - - -
317C PHE* 4.2 0.7 - - - -
319C LEU* 4.3 8.2 - - - +
348C LEU* 3.9 4.0 - - - +
349C VAL* 2.7 39.5 + - - +
350C SER* 4.7 1.1 - - - +
352C PHE 3.2 0.2 + - - -
353C ASN* 1.3 79.4 - - - +
355C ALA* 1.3 57.9 + - - +
390C MET* 3.9 11.7 - - - -
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Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ILE 3.9 0.2 - - - +
315C CYS* 3.2 7.4 - - - +
316C LEU* 2.9 32.7 + - + +
319C LEU* 4.0 7.2 - - + +
328C ILE* 3.8 28.7 - - + -
346C ILE* 4.6 4.9 - - + -
347C LEU 3.2 13.7 - - - +
348C LEU* 4.1 6.5 - - + -
349C VAL* 4.1 2.9 - - - +
354C GLY* 1.3 77.0 - - - +
356C ILE* 1.3 64.0 + - - +
357C ILE* 4.9 4.5 - - + -
390C MET* 4.3 1.0 - - - -
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Residues in contact with ILE 356 (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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298C VAL* 4.9 5.6 - - + -
301C LEU* 4.7 18.2 - - + -
302C LEU* 4.4 16.6 - - + -
313C LEU* 4.0 17.3 - - + -
314C ILE 3.5 3.8 - - - +
315C CYS* 3.8 20.0 - - - -
345C LYS 3.8 0.5 - - - +
346C ILE* 3.4 5.2 - - - +
347C LEU* 2.7 43.8 + - + +
349C VAL* 3.7 23.3 - - + -
355C ALA* 1.3 73.6 - - - +
357C ILE* 1.3 68.4 + - - +
358C ILE* 3.8 26.5 - - + -
387C ILE* 4.6 12.8 - - + -
390C MET* 5.2 0.2 - - + -
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Residues in contact with ILE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LEU* 3.1 5.4 - - - +
314C ILE* 2.7 51.7 + - + +
316C LEU* 4.3 20.0 - - + -
328C ILE* 3.9 19.3 - - + -
332C LEU* 4.0 17.9 - - + -
343C ILE* 4.3 7.0 - - + -
345C LYS 3.7 2.0 - - - +
346C ILE* 3.8 29.2 - - + -
355C ALA* 4.9 3.1 - - + -
356C ILE* 1.3 79.9 - - - +
358C ILE* 1.3 63.0 + - - +
359C PHE* 3.5 38.4 + - + -
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Residues in contact with ILE 358 (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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297C GLU* 5.8 0.2 - - - +
301C LEU* 3.8 27.6 - - + -
309C GLU* 6.0 3.8 - - + +
312C THR* 3.7 15.0 - - - +
313C LEU* 4.2 7.2 - - + -
343C ILE* 3.7 2.4 - - - +
344C ARG* 2.7 66.1 + - + +
345C LYS* 2.8 41.4 + - + +
347C LEU* 4.2 11.2 - - + -
356C ILE* 3.8 12.3 - - + -
357C ILE* 1.3 76.0 - - - +
359C PHE* 1.3 65.6 + - - +
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Residues in contact with PHE 359 (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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312C THR* 2.8 32.4 + - - +
314C ILE* 3.8 22.4 - - + -
332C LEU* 5.0 1.8 - - + -
338C ILE* 4.4 10.1 - - + -
342C ASP 3.2 21.1 - - - +
343C ILE* 3.8 21.3 - - + -
344C ARG* 4.4 4.6 + - - +
357C ILE* 3.5 27.8 - - + -
358C ILE* 1.3 82.3 - - - +
360C ARG* 1.3 65.9 + - - +
361C ASP 3.5 13.0 - - - +
364C PHE* 3.6 28.7 - + + -
365C ALA* 4.0 16.2 - - + +
368C MET* 3.8 20.6 - - + -
372C LEU* 4.5 9.0 - - + -
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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