Contacts of the strand formed by residues 354 - 361 (chain A) in PDB entry 1FPQ
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 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A SER* 5.4 0.9 - - - -
352A PHE* 3.6 3.9 - - - +
353A SER* 1.3 85.1 + - - +
355A PHE* 1.3 67.3 + - - +
356A GLN* 3.8 30.1 - - - +
369A GLU 3.7 0.9 - - - +
370A PHE* 3.5 5.4 - - - -
371A TYR* 2.8 58.1 + - + -
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A GLU* 3.8 42.8 - - + -
343A TYR 4.1 0.2 - - - -
344A GLU* 3.4 61.6 + - + +
347A SER* 3.8 9.6 - - - +
348A LYS* 5.9 0.9 - - + -
354A LYS* 1.3 81.5 - - - +
356A GLN* 1.3 75.7 + - - +
357A VAL* 4.1 4.0 - - + -
368A MSE 3.9 28.0 - - + -
369A GLU 3.5 2.9 - - - -
370A PHE* 3.3 35.4 - + - +
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Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LYS* 3.8 21.9 - - - +
355A PHE* 1.3 90.0 - - - +
357A VAL* 1.3 69.5 + - - +
358A ALA* 3.4 7.2 + - - -
368A MSE 3.5 1.5 - - - -
369A GLU* 2.9 49.8 + - + +
371A TYR* 3.5 32.0 + - + -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ILE* 4.4 9.6 - - + -
340A GLU* 3.7 39.7 - - + +
355A PHE* 4.1 3.3 - - + -
356A GLN* 1.3 74.7 - - - +
358A ALA* 1.3 63.2 + - - +
359A CYS* 3.7 21.3 - - - +
360A ARG* 4.2 20.9 - - + +
367A VAL 3.9 5.4 - - - +
368A MSE 3.8 18.6 - - + -
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A TYR* 3.6 32.5 - - + -
356A GLN* 3.4 11.6 + - - +
357A VAL* 1.3 74.2 - - - +
359A CYS* 1.3 64.1 + - - +
367A VAL 2.9 15.1 + - - +
369A GLU* 4.1 17.3 - - - +
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Residues in contact with CYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 3.9 28.9 - - + +
204A TYR* 3.9 35.0 - - - -
357A VAL* 3.4 6.4 - - - +
358A ALA* 1.3 81.5 - - - +
360A ARG* 1.3 68.5 + - - +
366A GLY* 3.5 0.2 - - - -
367A VAL* 2.9 39.7 + - - -
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Residues in contact with ARG 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP* 4.7 4.7 - - - +
203A ILE* 3.4 14.2 - - - +
308A ILE* 3.7 43.0 + - - +
310A PRO* 6.2 1.8 - - - +
318A GLU* 5.9 3.0 - - - +
340A GLU* 3.5 23.4 + - - +
357A VAL* 4.2 12.8 - - + +
359A CYS* 1.3 82.0 - - - +
361A ALA* 1.3 59.3 + - - +
362A PHE 4.2 0.5 + - - -
363A ASN* 4.5 25.9 + - - +
364A SER* 4.4 12.4 - - - +
365A LEU 3.2 6.3 - - - +
366A GLY* 4.1 11.0 - - - +
367A VAL* 5.7 0.2 - - - -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP* 3.9 3.8 - - - -
199A ARG* 3.4 26.0 - - + -
200A MSE 4.7 7.2 - - + +
203A ILE* 4.0 10.3 - - + +
360A ARG* 1.3 72.1 - - - +
362A PHE* 1.3 77.8 + - + +
363A ASN 3.0 2.7 + - - -
365A LEU* 2.7 49.2 + - + +
367A VAL* 5.8 2.2 - - + +
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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