Contacts of the strand formed by residues 328 - 332 (chain C) in PDB entry 4CKG
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 CYS 328 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C TRP* 3.6 24.2 - - - -
319C LEU* 3.9 8.8 - - - +
320C CYS* 3.8 19.9 + - - +
323C SER* 3.7 22.8 + - - +
325C ARG* 3.3 37.0 + - - -
326C ARG 3.6 5.8 - - - -
327C PHE* 1.3 77.9 - - - +
329C PHE* 1.4 63.3 + - - +
339C LEU* 4.3 9.9 - - + -
340C LEU 3.2 6.5 - - - +
341C GLN* 3.7 8.3 - - - -
348C LEU* 3.8 1.1 - - - +
146D ARG* 4.8 2.6 + - - +
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Residues in contact with PHE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 4.1 22.0 - - + -
317C VAL* 3.9 15.5 - - + -
318C LYS 3.5 13.0 - - - +
319C LEU* 4.4 4.9 - - + -
320C CYS* 3.7 4.9 - - - -
328C CYS* 1.4 73.3 - - - +
330C GLU* 1.3 62.7 + - - +
331C VAL* 4.2 5.8 - - + -
339C LEU* 3.5 2.9 - - - +
340C LEU* 2.7 80.9 + - + +
341C GLN 4.4 0.7 - - - -
342C ALA* 4.6 2.5 - - + -
348C LEU* 3.8 22.9 - - + -
351C TRP* 4.0 23.3 - + + -
352C VAL* 3.4 36.8 - - + -
355C VAL* 5.1 8.3 - - + -
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Residues in contact with GLU 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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316C THR 4.2 0.5 - - - +
317C VAL* 3.4 5.9 - - - +
318C LYS* 2.5 73.0 + - + +
320C CYS* 3.7 17.2 - - - -
329C PHE* 1.3 77.5 - - - +
331C VAL* 1.3 59.8 + - - +
332C VAL* 3.9 14.4 - - + +
338C CYS 3.5 17.5 - - - +
339C LEU* 4.2 17.0 - - + +
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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
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295C LEU* 5.0 13.7 - - + -
308C VAL* 5.9 0.7 - - + -
309C VAL* 5.5 7.9 - - + +
312C LEU* 5.1 2.2 - - + -
315C CYS* 3.5 25.1 - - - -
316C THR 3.9 2.2 - - - -
317C VAL* 4.3 14.8 - - + +
329C PHE* 4.2 11.9 - - + -
330C GLU* 1.3 79.0 - - - +
332C VAL* 1.4 58.3 + - - +
333C SER* 5.7 0.2 - - - -
337C SER* 3.3 5.4 - - - -
338C CYS* 2.9 48.4 + - - +
340C LEU* 3.4 30.5 - - + -
355C VAL* 5.1 7.9 - - + -
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Residues in contact with VAL 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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314C LEU 4.6 0.5 - - - +
315C CYS* 3.3 6.9 - - - -
316C THR* 3.1 59.5 + - + +
318C LYS* 3.9 21.3 - - + +
330C GLU* 3.9 27.1 - - + +
331C VAL* 1.4 77.6 - - - +
333C SER* 1.3 61.2 + - - +
337C SER* 3.7 13.7 - - - +
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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