Contacts of the strand formed by residues 362 - 366 (chain C) in PDB entry 4LEY
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 THR 362 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C TYR* 4.3 13.4 - - + -
234C PHE* 4.0 14.8 - - + -
235C TYR 3.6 5.8 - - - +
236C LEU* 4.1 6.3 - - - +
259C ALA* 4.1 6.8 - - - +
349C PRO 4.1 0.5 - - - -
350C LYS* 3.1 51.3 + - + +
351C ASN 4.5 1.4 + - - -
358C PHE* 2.6 30.0 + - - +
359C GLN* 4.0 8.0 + - - +
360C GLY 3.6 1.2 - - - -
361C GLU* 1.3 77.7 - - - +
363C TRP* 1.3 73.1 + - - +
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Residues in contact with TRP 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C PHE* 3.3 5.7 - - - -
235C TYR 2.9 36.1 + - - +
237C VAL* 3.5 24.5 - - + +
257C LEU* 3.4 39.8 + - + -
258C SER 4.0 1.1 - - - -
259C ALA* 3.6 29.9 - - + +
262C MET* 4.0 18.8 - - + -
310C LEU* 4.9 5.8 - - + -
312C LEU* 3.6 32.5 - - + -
347C LEU* 3.5 36.8 - - + -
348C VAL 3.5 16.6 - - - -
349C PRO* 3.6 20.6 - - + -
350C LYS 4.5 0.4 - - - -
361C GLU 3.3 15.1 + - - -
362C THR* 1.3 79.9 - - - +
364C ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 364 (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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233C ALA* 3.5 12.1 - - + +
234C PHE* 3.8 29.4 - - + -
290C GLY 4.6 13.1 + - - -
292C PRO* 3.9 17.9 - - - +
347C LEU* 3.4 6.7 - - - -
348C VAL* 2.8 62.5 + - - +
349C PRO 5.3 2.7 + - - -
350C LYS* 4.6 12.8 + - - +
363C TRP* 1.3 76.2 - - - +
365C LEU* 1.3 75.7 + - - +
366C SER* 5.3 4.4 + - - -
473C PHE* 6.2 2.2 - - - -
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Residues in contact with LEU 365 (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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225C LEU* 5.0 0.2 - - + -
232C GLY 3.8 11.0 - - - +
233C ALA* 3.2 8.1 + - - +
235C TYR* 3.6 30.3 - - + +
319C PRO* 3.9 26.0 - - + -
321C SER* 4.2 4.7 - - - +
322C THR* 4.3 3.6 - - + -
345C PHE* 4.1 16.6 - - + -
346C TYR 3.4 4.0 - - - +
347C LEU* 3.8 18.8 - - + +
364C ARG* 1.3 90.9 + - - +
366C SER* 1.3 59.0 + - - +
367C PHE* 3.9 25.4 - - + -
467C HIS* 5.7 2.6 + - - -
470C ILE* 3.8 23.2 - - + +
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Residues in contact with SER 366 (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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215C MET* 4.8 7.8 - - - -
309C ILE* 6.1 0.2 - - - +
346C TYR* 2.9 33.5 + - - +
348C VAL* 4.1 29.2 - - - +
364C ARG* 5.3 3.8 + - - -
365C LEU* 1.3 75.6 - - - +
367C PHE* 1.3 70.9 + - - +
368C SER* 3.2 23.7 + - - -
369C HIS* 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