Contacts of the strand formed by residues 328 - 332 (chain C) in PDB entry 1K8F
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 LYS 328 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324C LEU* 3.6 2.5 - - - -
325C GLU* 2.7 48.2 + - - +
326C GLY 3.3 0.4 - - - -
327C LYS* 1.3 78.4 - - - +
329C TRP* 1.3 60.1 + - - +
330C ARG* 3.3 34.9 + - + +
332C GLU* 5.6 1.1 - - - +
350C VAL* 3.6 22.2 - - + -
352C TYR* 3.9 35.0 - - + -
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Residues in contact with TRP 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LEU* 4.2 14.1 - - + -
323C GLU* 3.9 9.4 - - - -
324C LEU* 3.6 45.5 - - + +
327C LYS 3.7 0.2 + - - -
328C LYS* 1.3 69.7 - - - +
330C ARG* 1.3 62.5 + - - +
331C VAL* 3.5 6.4 + - - +
342C ILE* 3.6 41.5 - - + +
344C ASP* 2.8 39.0 + - - -
345C THR* 4.6 2.8 + - - -
349C GLN* 2.5 38.7 + - + -
350C VAL 2.8 22.9 + - - +
351C ALA* 3.6 11.5 - - + -
352C TYR 3.0 22.9 + - - -
363C ILE* 6.1 1.3 - - + -
367C ILE* 5.4 3.8 - - + -
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Residues in contact with ARG 330 (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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321C VAL* 3.5 22.4 - - + +
322C LEU* 2.9 7.5 + - - +
323C GLU* 2.9 66.7 + - - +
325C GLU* 3.4 39.3 + - + +
328C LYS* 3.6 33.4 - - + +
329C TRP* 1.3 69.3 - - - +
331C VAL* 1.3 59.3 + - - +
332C GLU* 3.2 36.0 + - + +
352C TYR 4.0 5.2 - - - -
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL 3.2 6.5 - - - +
322C LEU* 4.1 13.5 - - + -
329C TRP 3.6 12.6 - - - +
330C ARG* 1.3 75.9 - - - +
332C GLU* 1.3 59.3 + - - +
334C GLN* 4.0 12.3 - - + +
340C LEU* 4.7 5.4 - - + -
342C ILE* 4.6 16.6 - - + -
351C ALA* 5.3 1.8 - - + -
352C TYR 3.3 4.7 + - - +
353C ILE* 3.1 30.5 - - + -
354C TYR 2.9 21.8 + - - -
356C CYS* 3.7 17.2 - - - -
359C THR* 5.9 0.7 - - + -
361C LEU* 4.7 14.1 - - + -
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Residues in contact with GLU 332 (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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320C ALA* 3.6 0.3 - - - -
321C VAL* 2.9 47.2 + - + +
328C LYS* 5.6 1.0 - - - +
330C ARG* 3.2 44.5 + - - +
331C VAL* 1.3 79.8 - - - +
333C ASN* 1.3 73.5 + - - +
334C GLN* 3.0 12.5 + - - +
352C TYR* 4.4 8.5 - - - +
354C TYR* 3.0 36.8 - - + +
356C CYS* 3.9 0.9 - - - -
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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