Contacts of the strand formed by residues 550 - 553 (chain F) in PDB entry 3GUT
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 ILE 550 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549F LYS* 1.3 82.8 + - - +
551F VAL* 1.3 68.2 + - - +
552F ARG 4.2 0.9 - - - +
553F MET* 3.7 22.0 - - + -
568F LEU* 3.1 40.2 - - + -
569F LEU 3.9 2.2 - - - +
629F VAL* 5.2 2.2 - - + +
630F GLN* 4.6 6.3 - - - -
631F LEU* 3.8 16.8 - - + +
640F SER* 2.9 35.9 - - - +
641F GLU* 4.0 17.1 - - - +
643F LYS* 3.8 30.7 + - + -
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Residues in contact with VAL 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E HIS* 4.0 25.6 - - + +
246E ARG* 4.9 3.4 - - - +
549F LYS* 3.5 11.9 + - + +
550F ILE* 1.3 78.7 - - - +
552F ARG* 1.3 73.9 + - + +
569F LEU* 3.0 26.7 + - + +
570F CYS* 4.6 1.3 - - - -
571F ASP* 3.9 21.1 - - - +
643F LYS* 5.0 5.4 + - - +
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Residues in contact with ARG 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E GLU* 4.8 10.3 + - - -
213E PHE* 3.7 26.5 - - + -
242E ALA 5.1 1.0 + - - -
243E ASP* 2.9 37.4 + - - +
251E VAL* 3.8 34.0 - - - +
551F VAL* 1.3 90.4 - - + +
553F MET* 1.3 84.1 + - - +
569F LEU* 3.0 34.7 + - + +
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Residues in contact with MET 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E GLU* 5.3 1.0 - - - +
213E PHE* 3.7 5.5 - - - -
550F ILE* 3.7 24.2 - - + -
552F ARG* 1.3 88.8 - - - +
554F ASP* 1.3 59.2 + - - +
555F ARG 3.0 29.4 + - - +
556F THR* 4.5 22.7 - - + +
566F ILE* 4.2 12.6 - - + -
567F TYR 3.6 8.3 - - - +
568F LEU* 3.9 15.3 - - + -
611F PHE* 4.8 6.7 - - + -
629F VAL* 4.3 26.0 - - + -
643F LYS* 4.4 14.8 - - + -
644F PRO 5.7 0.4 - - - +
645F PHE* 4.6 8.1 - - + -
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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
------------------------------------------------------------
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