Contacts of the strand formed by residues 978 - 983 (chain A) in PDB entry 5IFE
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 LEU 978 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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970A TYR* 3.5 4.0 - - - -
971A ASP 3.2 30.0 + - - +
972A LEU 5.1 2.7 - - - +
973A GLY* 4.3 14.8 - - - +
975A LYS* 6.2 0.9 - - + -
976A LYS* 3.6 42.0 - - + +
977A LEU* 1.3 70.2 - - - +
979A ARG* 1.3 64.2 + - - +
980A LYS* 3.3 29.8 + - - +
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Residues in contact with ARG 979 (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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946A GLU* 5.7 0.6 + - - -
968A ARG* 3.6 32.5 - - - +
970A TYR* 3.6 25.8 + - + -
976A LYS* 6.1 0.2 - - - +
977A LEU 3.5 3.2 + - - +
978A LEU* 1.3 70.0 - - - +
980A LYS* 1.3 64.7 + - - +
981A CYS* 3.8 13.5 - - - +
982A GLU* 3.4 28.4 + - - -
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Residues in contact with LYS 980 (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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958A ARG* 3.9 23.6 - - - +
969A VAL* 2.7 20.1 + - + +
971A ASP* 3.7 39.5 - - + +
978A LEU* 3.8 30.5 - - - +
979A ARG* 1.3 79.0 - - - +
981A CYS* 1.3 58.9 + - - +
1019A ASN* 3.9 20.2 + - - +
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Residues in contact with CYS 981 (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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968A ARG* 3.2 10.0 - - - +
969A VAL* 2.9 41.2 + - + +
979A ARG* 3.7 6.9 - - - +
980A LYS* 1.3 79.1 - - - +
982A GLU* 1.3 81.1 + - - +
1019A ASN* 3.1 36.8 - - + +
1020A GLN* 4.1 0.4 - - - -
1021A LEU* 3.6 33.4 - - - -
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Residues in contact with GLU 982 (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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966A LEU* 3.2 26.1 - - + +
967A LEU 3.5 7.4 - - - -
968A ARG* 3.1 37.3 + - + +
979A ARG* 3.4 18.3 + - - -
981A CYS* 1.3 90.1 - - - +
983A ASN* 1.3 68.3 + - - +
984A LYS* 4.4 12.3 - - + +
1021A LEU* 4.8 2.1 + - - +
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Residues in contact with ASN 983 (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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965A LYS 3.9 1.4 - - - +
966A LEU* 3.2 5.2 - - - -
967A LEU* 2.9 42.5 + - + +
982A GLU* 1.3 78.2 - - - +
984A LYS* 1.3 76.2 + - - +
985A HIS* 3.0 25.2 + - - +
986A ILE* 4.4 6.1 + - - +
1012A VAL* 4.4 3.4 - - - +
1021A LEU* 2.7 48.1 + - + +
1022A ILE* 4.4 0.2 - - - +
1023A ILE* 4.1 21.7 - - - +
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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