Contacts of the strand formed by residues 341 - 344 (chain K) in PDB entry 1FPY
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 ALA 341 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329K PRO* 3.6 10.7 - - - +
331K MET* 3.9 7.0 - - - -
333K ALA* 3.5 26.5 - - + +
334K TYR 4.2 8.3 - - - -
335K SER* 4.4 2.9 - - - -
338K ASN* 3.7 21.4 + - - +
339K ARG 4.3 4.2 - - - -
340K SER* 1.3 79.2 - - - +
342K SER* 1.3 63.8 + - - +
343K ILE 3.4 13.7 + - - +
344K ARG* 4.5 8.0 + - - +
359K ARG* 4.9 2.1 + - - -
392K MET* 5.0 0.7 - - + -
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Residues in contact with SER 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329K PRO* 3.4 29.2 - - - +
330K VAL 4.8 0.4 - - - -
331K MET 2.4 31.6 + - - -
332K LEU* 3.4 18.0 - - - +
333K ALA 3.6 0.2 + - - -
341K ALA* 1.3 71.7 - - - +
343K ILE* 1.3 61.8 + - - +
357K GLU 3.5 0.3 - - - +
358K VAL* 3.6 2.1 - - - +
359K ARG* 2.7 35.6 + - - +
360K PHE* 4.1 20.8 + - - -
410K VAL* 5.2 0.7 - - - -
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Residues in contact with ILE 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298K ILE* 4.2 17.3 - - + -
301K VAL* 5.1 8.5 - - + -
302K ILE* 4.0 23.6 - - + -
332K LEU* 4.5 6.3 - - + -
333K ALA 3.0 26.0 + - - +
334K TYR* 3.2 34.3 - - + -
335K SER 3.3 3.3 + - - -
341K ALA* 3.5 7.4 - - - +
342K SER* 1.3 92.4 - - - +
344K ARG* 1.3 68.6 + - - +
345K ILE* 4.2 8.7 - - + -
356K ILE* 4.3 11.2 - - + -
357K GLU 3.2 9.9 - - - +
358K VAL* 4.5 19.5 - - + -
360K PHE* 5.5 0.4 - - + -
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Residues in contact with ARG 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J ASP* 5.3 5.3 - - - +
64J ASP* 3.3 26.3 + - - -
271K HIS* 5.1 1.6 + - - -
335K SER 3.2 11.7 - - - +
336K ALA 4.9 9.3 + - - +
338K ASN 4.3 8.5 - - - +
339K ARG* 3.6 35.5 - - + +
341K ALA 4.6 8.3 - - - +
342K SER 4.0 0.6 - - - +
343K ILE* 1.3 75.7 - - - +
345K ILE* 1.3 67.8 + - - +
346K PRO* 3.4 34.0 - - - +
357K GLU* 2.9 59.3 + - - +
359K ARG* 4.4 16.4 - - + +
4481K ADP 4.0 18.4 + - - -
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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