Contacts of the strand formed by residues 343 - 350 (chain C) in PDB entry 3P9K
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 GLY 343 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341C PHE* 3.7 1.1 - - - +
342C THR* 1.3 82.2 + - - +
344C VAL* 1.3 64.4 + - - +
357C GLU 3.4 0.6 - - - +
358C PHE* 3.2 5.7 - - - +
359C THR* 2.6 51.7 + - - -
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Residues in contact with VAL 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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329C GLU* 5.8 1.6 - - + +
332C PHE* 5.7 0.4 - - + -
333C GLN* 4.0 43.0 + - + +
336C ALA* 3.8 27.8 - - + -
341C PHE 5.9 0.4 - - - +
342C THR 4.4 2.0 + - - +
343C GLY* 1.3 81.3 - - - +
345C LYS* 1.3 65.7 + - - +
346C SER* 4.7 3.8 - - - +
356C ILE* 4.0 13.0 - - + -
357C GLU 3.1 4.5 - - - +
358C PHE* 3.9 18.8 - - + -
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Residues in contact with LYS 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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192C TYR* 5.4 1.7 - - - -
344C VAL* 1.3 76.4 - - - +
346C SER* 1.3 65.6 + - - +
347C THR* 4.1 15.3 + - - +
355C ALA 3.5 3.3 - - - +
356C ILE* 3.6 0.2 - - - -
357C GLU* 2.9 73.7 + - + +
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Residues in contact with SER 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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296C ILE* 4.4 2.8 - - - +
329C GLU* 4.0 28.9 + - - +
344C VAL* 4.7 3.3 - - - +
345C LYS* 1.3 78.4 - - - +
347C THR* 1.3 62.3 + - - +
348C TYR 4.1 1.2 + - - -
354C TRP* 4.0 23.5 - - - -
355C ALA 3.5 4.7 - - - -
356C ILE* 3.8 21.7 - - - +
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Residues in contact with THR 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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191C LEU* 4.4 15.3 - - + +
192C TYR* 4.6 11.4 - - + -
345C LYS* 4.6 17.0 + - - +
346C SER* 1.3 77.2 + - - +
348C TYR* 1.3 77.7 + - - +
349C ILE* 3.5 10.8 + - + +
354C TRP* 3.5 2.2 - - - -
355C ALA* 2.8 45.6 + - - -
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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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191C LEU* 4.7 4.9 - - - +
347C THR* 1.3 84.3 - - - +
349C ILE* 1.3 78.7 + - - +
350C TYR* 3.8 11.0 - + - -
351C ALA* 3.7 0.2 - - - -
352C ASN* 2.9 39.9 + - - -
353C ALA 3.7 6.3 - - - -
354C TRP* 3.1 52.6 - + + -
14D GLU* 2.7 38.2 + - - -
18D MET* 4.3 5.7 - - - -
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Residues in contact with ILE 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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184C ILE* 4.4 9.9 - - + +
187C LYS* 4.0 13.5 - - + +
188C LEU* 3.8 42.6 - - + +
191C LEU* 3.2 30.8 - - + +
192C TYR* 4.3 8.5 - - + -
293C VAL* 6.0 2.0 - - + -
347C THR* 3.5 21.1 - - + +
348C TYR* 1.3 93.3 - - - +
350C TYR* 1.3 68.6 + - + +
353C ALA* 2.8 21.5 + - + +
354C TRP 4.1 1.8 - - - -
355C ALA* 3.8 23.8 - - + +
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Residues in contact with TYR 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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111C PHE* 4.8 5.0 - + - -
183C ILE* 5.7 4.5 - - + -
184C ILE* 4.0 9.8 - - + +
187C LYS* 3.8 51.9 + - + -
191C LEU* 5.5 1.8 - - + -
348C TYR* 3.6 3.2 - + - -
349C ILE* 1.3 85.2 - - + +
351C ALA* 1.3 84.2 + - + +
352C ASN 3.3 2.7 - - - -
353C ALA* 2.9 21.0 + - - +
10D ALA 3.4 21.1 + - - -
13D ASP* 3.5 9.0 + - - +
14D GLU* 3.2 56.9 + - + -
17D CYS* 4.3 17.3 - - + -
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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