Contacts of the strand formed by residues 425 - 434 (chain A) in PDB entry 3FZP
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 VAL 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ILE* 3.3 32.8 - - + -
422A ARG 3.1 14.6 + - - +
423A GLU 3.1 2.2 - - - +
424A ASP* 1.3 83.8 - - - +
426A VAL* 1.3 70.9 + - - +
427A LEU* 4.9 0.2 - - + -
443A VAL 3.7 4.9 - - - +
444A TYR* 3.7 15.0 - - + -
454A VAL* 4.7 5.6 - - + -
456A VAL* 3.9 22.7 - - + -
499A TRP* 3.7 37.6 - - + -
501A ILE* 3.9 10.8 - - + -
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Residues in contact with VAL 426 (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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423A GLU 4.7 9.0 - - - +
424A ASP 5.5 0.7 - - - -
425A VAL* 1.3 79.1 - - - +
427A LEU* 1.3 64.1 + - - +
428A ASN* 3.4 20.7 - - - +
442A GLY* 2.9 24.9 - - - -
443A VAL* 2.9 21.1 + - + +
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Residues in contact with LEU 427 (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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426A VAL* 1.3 74.5 - - - +
428A ASN* 1.3 67.8 + - - +
429A ARG 5.2 0.2 - - - +
440A TYR* 3.7 50.5 - - + -
441A GLU 3.7 3.8 - - - +
456A VAL* 3.8 28.5 - - + -
499A TRP* 3.6 39.2 - - + +
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Residues in contact with ASN 428 (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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426A VAL* 3.4 18.3 + - - +
427A LEU* 1.3 82.1 - - - +
429A ARG* 1.3 64.8 + - + +
441A GLU* 2.7 19.4 + - + +
442A GLY 4.3 1.6 - - - -
443A VAL* 3.6 33.7 - - - +
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Residues in contact with ARG 429 (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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427A LEU 3.9 0.4 - - - -
428A ASN* 1.3 81.1 - - + +
430A ILE* 1.3 71.4 + - - +
440A TYR* 3.4 11.2 - - - +
441A GLU* 2.8 63.4 + - + +
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Residues in contact with ILE 430 (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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429A ARG* 1.3 91.9 + - - +
431A LEU* 1.3 65.3 + - - +
432A GLY* 3.7 8.1 - - - +
438A GLU* 3.2 28.0 - - + +
439A VAL 4.1 1.8 - - - -
440A TYR* 3.7 25.6 - - + -
441A GLU 4.4 0.4 - - - -
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Residues in contact with LEU 431 (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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429A ARG 3.7 1.2 + - - -
430A ILE* 1.3 77.8 - - - +
432A GLY* 1.3 58.0 + - - +
439A VAL* 2.7 30.3 + - + +
440A TYR 3.8 4.9 - - - +
441A GLU* 3.9 31.4 - - + +
455A ALA* 3.4 33.4 - - + -
504A LEU* 3.8 20.4 - - + -
999A AGS 3.8 32.4 + - + +
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Residues in contact with GLY 432 (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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430A ILE* 3.7 3.5 - - - +
431A LEU* 1.3 81.0 - - - +
433A GLU* 1.3 59.3 + - - -
438A GLU* 3.3 12.2 + - - -
439A VAL* 2.6 40.3 + - - +
999A AGS 4.2 12.6 - - - -
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Residues in contact with GLU 433 (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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432A GLY* 1.3 69.1 - - - -
434A GLY* 1.3 87.9 + - - +
435A PHE 4.6 1.4 - - - +
437A GLY* 3.6 12.6 + - - +
438A GLU* 2.9 34.5 + - - +
460A LYS* 4.7 10.9 - - - +
999A AGS 3.9 11.5 - - - +
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Residues in contact with GLY 434 (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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432A GLY 3.5 4.2 + - - -
433A GLU* 1.3 92.1 - - - +
435A PHE* 1.3 67.5 + - - +
437A GLY 2.7 19.2 + - - -
439A VAL* 4.2 2.3 - - - +
999A AGS 3.1 34.5 - - - -
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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