Contacts of the strand formed by residues 794 - 797 (chain B) in PDB entry 5FLM
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 794 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792B ASP 3.8 9.2 - - - +
793B SER* 1.3 82.1 - - - +
795B ILE* 1.3 67.2 + - - +
796B MET* 4.7 5.6 - - + +
935B PHE* 5.1 15.0 - - + +
942B LYS 5.7 0.4 - - - -
943B GLY* 4.5 9.0 - - - +
944B THR 2.6 16.4 + - - +
945B CYS* 2.9 29.3 - - + -
946B GLY 2.9 6.3 + - - -
965B ILE* 3.4 29.6 - - + -
966B ILE 3.4 12.6 - - - +
967B ILE* 3.8 19.3 - - + -
1048B TYR* 6.0 2.5 - - + -
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Residues in contact with ILE 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785B TYR* 4.3 18.2 - - + -
786B THR* 3.8 21.8 - - - +
788B TYR* 4.2 11.0 - - + +
789B ASN* 3.8 39.5 - - + +
794B VAL* 1.3 73.3 - - - +
796B MET* 1.3 67.0 + - - +
947B ILE* 3.6 10.1 - - + +
949B TYR* 3.6 26.5 - - + -
954B MET* 4.5 12.8 - - + +
964B ASP 4.5 0.2 - - - -
965B ILE* 3.4 3.1 - - - -
966B ILE* 2.9 48.7 + - + +
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Residues in contact with MET 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B VAL* 4.8 2.9 - - + -
795B ILE* 1.3 78.1 - - - +
797B ASN* 1.3 67.1 + - - +
801B VAL* 4.0 12.8 - - - -
805B PHE* 4.9 4.7 - - + -
806B PHE* 4.7 8.7 - - - -
929B PRO* 4.0 11.2 - - + -
930B GLN 3.3 19.7 - - - +
935B PHE* 3.2 34.1 - - + -
945B CYS* 3.5 17.1 - - + -
947B ILE 3.3 6.7 + - - +
948B GLN* 3.3 34.1 - - + +
949B TYR 3.1 24.1 + - - -
954B MET* 4.4 1.1 - - - +
964B ASP 3.5 4.7 - - - +
965B ILE* 4.3 15.5 - - + -
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Residues in contact with ASN 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B MET* 1.3 70.8 - - - +
798B ARG* 1.3 63.0 + - - +
799B SER* 2.9 27.8 + - - -
800B ALA* 3.9 16.6 - - + +
801B VAL* 3.3 23.6 + - - +
805B PHE* 5.5 0.5 - - - -
949B TYR 3.3 8.8 - - - +
951B GLN* 3.5 11.1 + - - +
954B MET* 3.9 14.8 - - + +
962B THR* 3.5 23.2 + - - -
963B PRO 3.6 14.6 + - - +
964B ASP* 2.7 33.5 + - - +
9J THR 4.5 6.7 + - - -
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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