Contacts of the strand formed by residues 295 - 301 (chain C) in PDB entry 3CB4
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 VAL 295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294C GLN* 1.3 97.2 - - + +
296C TYR* 1.3 70.3 + - - +
341C GLY* 3.3 2.8 - - - -
342C PHE* 2.7 41.7 + - + +
344C GLY* 4.3 19.7 - - - -
345C LEU* 4.8 0.7 - - + +
348C MET* 4.5 15.3 - - + -
368C PRO* 3.6 28.5 - - + -
369C THR 3.7 3.6 - - - +
370C VAL* 4.6 2.2 - - + -
451C VAL* 3.5 30.7 - - + -
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Residues in contact with TYR 296 (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 LYS* 5.5 2.1 - - - +
293C PRO* 2.9 37.4 + - + +
295C VAL* 1.3 77.3 - - - +
297C ALA* 1.3 60.1 + - - +
325C PHE* 3.7 28.8 - + - -
339C ARG* 3.3 31.0 - - + +
340C CYS 3.2 8.1 - - - +
341C GLY* 3.6 12.1 - - - -
342C PHE* 5.1 0.2 - - - -
368C PRO* 3.4 4.9 - - - +
369C THR* 2.8 51.8 + - + +
370C VAL 5.2 0.4 - - - -
371C VAL* 3.7 22.3 - - + +
385C ASP* 3.5 37.2 + - + +
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Residues in contact with ALA 297 (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 TYR* 1.3 76.7 - - - +
298C GLY* 1.3 61.3 + - - +
299C LEU* 3.8 3.5 + - + +
339C ARG* 3.7 5.6 - - - +
340C CYS* 2.9 34.6 + - - +
342C PHE* 4.1 8.7 - - + -
348C MET* 4.0 25.8 - - - -
365C THR* 4.4 7.0 - - - +
366C THR* 3.9 19.7 - - - +
367C ALA 4.4 1.1 - - - -
368C PRO* 4.5 2.7 - - + -
369C THR* 5.2 1.6 - - - -
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Residues in contact with GLY 298 (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 ALA* 1.3 71.5 - - - +
299C LEU* 1.3 62.0 + - - -
300C PHE* 3.7 12.5 - - - -
329C GLU* 4.3 10.1 - - - -
338C PHE 3.9 4.7 - - - -
339C ARG* 4.6 0.7 - - - -
364C ILE 3.6 1.2 - - - +
365C THR* 3.3 4.7 + - - -
366C THR* 2.8 53.5 + - - +
494C ALA 5.1 1.5 + - - -
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Residues in contact with LEU 299 (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 ALA* 3.8 2.4 + - + +
298C GLY* 1.3 74.3 - - - -
300C PHE* 1.3 63.1 + - - +
310C PHE* 3.5 23.4 - - + -
314C LEU* 5.7 0.2 - - + -
338C PHE 2.9 35.7 + - - +
340C CYS* 3.5 26.9 - - + -
342C PHE* 3.7 24.5 - - + -
348C MET* 6.4 0.2 - - - -
351C ILE* 5.7 0.7 - - + -
352C GLN* 4.3 16.4 - - + +
355C LEU* 4.8 11.9 - - + -
363C LEU* 3.9 25.4 - - + -
364C ILE 3.5 1.1 - - - -
365C THR* 3.6 27.8 - - - +
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Residues in contact with PHE 300 (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 GLY* 3.7 24.9 - - - -
299C LEU* 1.3 87.0 - - - +
301C PRO* 1.3 68.4 - - + +
310C PHE* 4.2 0.2 - - - -
329C GLU* 3.4 35.2 - - + -
331C SER* 3.6 12.8 - - - -
334C LEU* 3.7 37.9 - - + +
335C GLY 3.6 14.8 - - - -
336C PHE 4.0 0.9 - - - -
337C GLY* 3.5 14.4 - - - -
338C PHE 4.8 0.9 - - - -
363C LEU* 3.3 8.6 - - - +
364C ILE* 2.7 47.1 + - + +
366C THR* 4.4 2.0 - - + -
494C ALA* 3.7 31.2 - - + -
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Residues in contact with PRO 301 (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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300C PHE* 1.3 84.6 - - + +
302C VAL* 1.3 65.5 + - - +
303C SER 3.2 22.6 + - - +
304C SER* 5.2 2.5 - - - -
306C ASP* 4.0 15.0 - - + -
307C TYR* 4.3 17.5 - - + +
310C PHE* 3.7 24.2 - - + -
334C LEU 4.3 12.0 - - - +
336C PHE 3.3 23.8 - - - +
362C ASP 3.8 0.9 - - - +
363C LEU* 3.7 14.3 - - + -
364C ILE* 4.9 1.6 - - - +
552F LYS* 5.0 3.5 + - - +
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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