Contacts of the strand formed by residues 321 - 326 (chain C) in PDB entry 1PL8
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 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C GLU* 3.8 17.0 - - + +
153C LEU* 3.8 28.5 - - + -
318C LYS* 3.0 15.7 + - - +
319C PRO* 4.1 3.8 - - - +
320C LEU* 1.3 74.3 - - - +
322C THR* 1.3 61.8 + - - +
323C HIS 3.9 20.4 - - - +
324C ARG* 3.7 28.2 + - - +
344C LYS* 3.4 7.6 - - + +
346C MET* 4.1 18.8 - - + -
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Residues in contact with THR 322 (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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211C LYS* 5.4 6.1 - - + +
319C PRO 4.6 6.1 - - - +
320C LEU 3.3 2.7 + - - +
321C VAL* 1.3 77.2 - - - +
323C HIS* 1.3 73.2 + - - +
342C GLY* 3.4 13.7 - - - -
343C LEU* 2.9 44.4 + - + +
344C LYS 3.0 9.2 + - - -
345C ILE* 4.8 2.4 - - - +
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Residues in contact with HIS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL* 3.6 7.8 - - - +
322C THR* 1.3 85.3 + - - +
324C ARG* 1.3 79.7 + - - +
325C PHE* 3.2 46.2 - + + -
336C THR* 4.6 12.1 - - + +
344C LYS 3.6 2.2 + - - +
345C ILE* 3.3 17.7 - - + -
346C MET 2.8 23.6 + - - -
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Residues in contact with ARG 324 (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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149C GLU* 2.8 42.0 + - - +
321C VAL* 3.7 17.2 - - - +
323C HIS* 1.3 90.0 + - - +
325C PHE* 1.3 65.9 + - - +
326C PRO* 5.0 0.2 - - - +
346C MET* 3.1 18.2 - - + +
348C LYS* 4.4 8.3 - - + -
354C GLN 4.4 15.3 - - - -
356C PRO* 3.8 23.3 - - - +
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Residues in contact with PHE 325 (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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323C HIS* 3.2 39.0 - + + -
324C ARG* 1.3 77.2 - - - +
326C PRO* 1.3 69.4 - - + +
329C LYS* 4.1 32.3 - - + -
332C GLU* 4.3 8.1 - - + -
333C ALA* 3.5 26.2 - - + -
336C THR* 3.5 26.9 - - - -
345C ILE* 3.7 23.8 - - + -
346C MET 2.8 6.0 + - - -
347C LEU* 3.2 12.9 - - + -
348C LYS* 2.7 35.7 + - - +
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Residues in contact with PRO 326 (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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324C ARG 5.0 0.2 - - - +
325C PHE* 1.3 92.2 - - + +
327C LEU* 1.3 66.8 + - - +
328C GLU* 3.7 15.0 - - + +
329C LYS* 2.9 45.7 + - + +
347C LEU* 3.8 2.8 - - - +
348C LYS 3.4 8.7 - - - +
354C GLN* 3.2 23.3 - - - +
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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