Contacts of the strand formed by residues 341 - 344 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329I PRO* 3.6 10.7 - - - +
331I MET* 3.9 7.4 - - - -
333I ALA* 3.5 26.2 - - + +
334I TYR 4.2 7.9 - - - -
335I SER* 4.4 2.7 - - - -
338I ASN* 3.7 22.1 - - - +
339I ARG* 3.2 4.5 - - - -
340I SER* 1.3 78.8 - - - +
342I SER* 1.3 63.6 + - - +
343I ILE 3.4 14.8 + - - +
344I ARG* 4.5 7.1 + - - +
359I ARG* 4.9 2.4 + - - -
392I MET* 5.0 0.7 - - + -
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Residues in contact with SER 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329I PRO* 3.4 29.0 - - - +
330I VAL 4.8 0.7 - - - -
331I MET 2.4 31.9 + - - -
332I LEU* 3.4 17.7 - - - +
333I ALA 3.6 0.2 + - - -
341I ALA* 1.3 72.9 - - - +
343I ILE* 1.3 61.6 + - - +
344I ARG 4.0 0.2 - - - -
357I GLU 3.5 0.2 - - - +
358I VAL* 3.6 1.9 - - - +
359I ARG* 2.7 36.2 + - - +
360I PHE* 4.1 20.4 + - - -
410I VAL* 5.2 0.7 - - - -
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Residues in contact with ILE 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I ILE* 4.2 17.3 - - + -
301I VAL* 5.1 8.3 - - + -
302I ILE* 4.0 23.8 - - + -
332I LEU* 4.5 6.3 - - + -
333I ALA 3.0 26.1 + - - +
334I TYR* 3.2 32.6 - - + -
335I SER 3.3 3.5 + - - -
341I ALA* 3.5 7.6 - - - +
342I SER* 1.3 92.0 - - - +
344I ARG* 1.3 68.5 + - - +
345I ILE* 4.2 9.6 - - + -
356I ILE* 4.3 10.3 - - + -
357I GLU 3.2 10.1 - - - +
358I VAL* 4.5 20.2 - - + -
360I PHE* 5.5 0.7 - - + -
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Residues in contact with ARG 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ASP* 5.4 4.9 - - - +
64H ASP* 3.5 23.7 + - - -
271I HIS* 5.1 1.8 + - - -
335I SER 3.2 11.0 - - - +
336I ALA 4.9 9.3 + - - +
338I ASN 4.3 9.2 - - - +
339I ARG* 3.6 36.7 - - + +
341I ALA 4.6 7.6 - - - +
342I SER 4.0 1.1 - - - +
343I ILE* 1.3 75.8 - - - +
345I ILE* 1.3 67.2 + - - +
346I PRO* 3.4 33.9 - - - +
357I GLU* 2.9 61.3 + - - +
359I ARG* 4.4 16.8 - - + +
4479I ADP 4.0 18.0 + - - -
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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