Contacts of the strand formed by residues 341 - 350 (chain C) in PDB entry 4YCV
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 GLU 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C PHE* 6.2 0.4 - - + -
327C LYS* 3.5 42.7 + - + +
328C VAL 3.4 4.0 - - - +
329C PHE* 3.9 26.8 - - + -
339C ASN* 2.7 25.6 + - - +
340C PRO* 1.3 74.1 - - + +
342C PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 342 (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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327C LYS* 4.4 3.6 - - - +
328C VAL* 2.9 49.2 + - + +
330C ARG* 3.5 52.0 - - + -
339C ASN* 3.4 22.7 - - + +
340C PRO 4.3 1.6 - - - -
341C GLU* 1.3 76.2 - - - +
343C THR* 1.3 71.3 + - - +
344C SER* 4.2 17.0 - - - -
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Residues in contact with THR 343 (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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254C ARG* 3.5 24.4 + - - +
258C ILE* 4.8 11.4 - - + -
325C ILE* 3.9 26.9 - - + -
326C GLY* 3.5 14.4 - - - +
327C LYS* 3.5 27.4 - - + +
342C PHE* 1.3 77.8 - - - +
344C SER* 1.3 63.1 + - - +
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Residues in contact with SER 344 (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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306C ALA* 5.8 0.2 - - - -
307C THR* 4.2 6.2 - - - +
324C GLU 3.5 2.3 - - - +
325C ILE* 3.3 2.5 - - - -
326C GLY 2.9 32.1 + - - +
328C VAL* 3.2 23.8 - - - +
342C PHE* 3.5 14.7 + - - -
343C THR* 1.3 78.2 - - - +
345C CYS* 1.3 61.0 + - - +
346C GLU* 4.0 17.9 + - - +
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Residues in contact with CYS 345 (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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261C LEU* 3.7 31.4 - - + -
265C LEU* 4.1 22.4 - - - -
323C TYR* 4.2 3.1 - - - -
324C GLU 3.1 6.3 - - - -
325C ILE* 3.7 27.4 - - + -
344C SER* 1.3 73.7 - - - +
346C GLU* 1.3 67.4 + - - +
347C PHE* 4.2 5.8 + - - -
360C TRP* 6.3 0.4 - - - -
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Residues in contact with GLU 346 (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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306C ALA* 3.4 10.8 - - - +
307C THR* 2.4 50.4 + - - +
308C GLU* 4.0 23.8 - - - +
311C LEU* 3.3 10.3 - - + +
323C TYR* 3.2 2.9 - - - -
324C GLU 2.9 30.9 + - - -
344C SER* 4.0 13.7 + - - +
345C CYS* 1.3 78.3 - - - +
347C PHE* 1.3 60.4 + - - +
348C TYR* 4.4 9.2 + - + -
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Residues in contact with PHE 347 (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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265C LEU* 4.3 9.0 - - + -
270C PHE* 3.3 34.3 - + + -
322C VAL 3.2 5.6 - - - +
323C TYR* 3.3 22.9 - - + -
345C CYS* 5.4 4.7 - - - -
346C GLU* 1.3 72.7 - - - +
348C TYR* 1.3 76.3 + - - +
349C TRP* 3.8 18.4 - + + -
357C LEU* 4.1 21.5 - - + -
360C TRP* 3.7 56.1 - + - -
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Residues in contact with TYR 348 (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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270C PHE* 3.8 1.0 - - - -
308C GLU* 3.2 48.0 + - + +
311C LEU* 3.7 24.5 - - + +
312C LYS* 4.4 24.5 + - + -
315C ILE* 3.5 29.3 - - + +
321C LYS* 3.5 1.7 - - - -
322C VAL* 2.9 36.2 + - + +
346C GLU* 4.4 11.8 + - + -
347C PHE* 1.3 83.2 - - - +
349C TRP* 1.3 60.0 + - - +
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Residues in contact with TRP 349 (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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268C ARG* 6.2 4.3 - - + -
270C PHE* 4.0 14.4 - + + -
315C ILE* 5.0 1.5 - - - +
320C ASP 3.8 1.1 - - - -
321C LYS* 3.4 31.2 - - + +
347C PHE* 3.8 28.0 - + + -
348C TYR* 1.3 74.3 - - - +
350C ALA* 1.3 81.4 + - - +
351C TYR 3.8 2.1 + - - -
352C ALA* 3.6 31.8 + - + +
356C ASP* 4.3 23.3 - - + -
357C LEU* 4.6 9.4 - - + -
360C TRP* 4.0 20.9 - + + -
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Residues in contact with ALA 350 (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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315C ILE* 4.3 16.1 - - + +
320C ASP* 2.9 39.2 + - + +
321C LYS* 5.7 0.2 - - + -
349C TRP* 1.3 87.2 + - - +
351C TYR* 1.3 94.5 + - + +
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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