Contacts of the strand formed by residues 1019 - 1025 (chain A) in PDB entry 4YKN
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 ARG1019 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017A PRO* 3.7 15.6 - - - +
1018A PRO* 1.3 84.4 - - + +
1020A ILE* 1.3 60.9 + - - +
1035A GLU* 3.1 33.2 - - + +
1036A CYS 3.4 8.3 - - - +
1037A LEU* 4.1 19.3 - - + -
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Residues in contact with ILE1020 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A LEU* 3.8 29.2 - - + -
1016A MET* 4.1 26.7 - - + -
1017A PRO* 4.6 18.8 - - + +
1019A ARG* 1.3 74.2 - - - +
1021A LEU* 1.3 75.4 + - - +
1022A VAL* 3.9 2.4 + - + +
1034A LEU 3.8 0.5 - - - +
1035A GLU* 3.6 3.1 - - - -
1036A CYS* 2.9 35.6 + - + +
1038A ARG* 4.8 5.6 - - - -
1089A LEU* 3.8 27.8 - - + -
1097A PRO* 4.0 12.8 - - + -
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Residues in contact with LEU1021 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A ILE* 1.3 78.5 - - - +
1022A VAL* 1.3 59.4 + - - +
1023A GLU* 4.3 2.7 - - + +
1033A THR* 4.0 27.6 - - + -
1034A LEU 3.7 0.7 - - - -
1035A GLU* 3.8 34.5 - - + +
1097A PRO* 3.7 20.8 - - - +
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Residues in contact with VAL1022 (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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1020A ILE* 4.9 2.0 - - + +
1021A LEU* 1.3 74.7 - - - +
1023A GLU* 1.3 65.3 + - - +
1024A CYS* 3.6 8.6 + - - -
1033A THR* 4.0 1.0 - - - -
1034A LEU* 3.1 40.3 + - + +
1036A CYS* 3.3 27.4 - - + -
1089A LEU* 5.1 15.5 - - + -
1094A LEU* 5.4 0.7 - - + -
1097A PRO* 3.3 26.0 - - + +
1098A PHE* 3.6 14.4 - - - +
1099A LEU* 4.0 20.9 - - + +
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Residues in contact with GLU1023 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A PHE* 5.3 2.7 - - + -
530A LYS* 5.9 2.8 - - - +
534A ARG* 2.5 47.6 + - - +
1021A LEU* 5.5 2.7 - - + +
1022A VAL* 1.3 71.0 - - - +
1024A CYS* 1.3 61.2 + - - +
1025A LEU* 3.6 4.5 - - + +
1031A ILE* 3.5 26.6 - - + +
1032A VAL 3.6 4.0 - - - +
1033A THR* 2.4 35.5 + - - -
1097A PRO 3.1 12.8 + - - +
1098A PHE* 3.1 12.3 - - + +
1099A LEU 3.0 22.5 + - - +
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Residues in contact with CYS1024 (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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1022A VAL* 4.1 20.9 - - - -
1023A GLU* 1.3 73.9 - - - +
1025A LEU* 1.3 62.7 + - - +
1026A LEU* 3.7 2.2 + - + -
1031A ILE* 3.6 3.6 - - - -
1032A VAL* 2.9 47.4 + - + +
1034A LEU* 4.2 17.3 - - - -
1045A ILE* 5.2 1.3 - - - -
1049A LEU* 3.6 38.4 - - + -
1070A PHE* 5.0 0.7 - - + -
1099A LEU* 3.2 18.8 - - + +
1101A VAL* 5.2 0.4 - - + -
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Residues in contact with LEU1025 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A ILE* 3.7 28.5 - - + -
494A PHE* 4.0 39.5 - - + -
497A GLN* 3.5 40.2 - - + +
1023A GLU 3.6 15.5 - - - +
1024A CYS* 1.3 75.7 - - - +
1026A LEU* 1.4 61.8 + - - +
1030A MET 4.0 1.3 - - - -
1031A ILE* 4.3 12.6 - - + +
1098A PHE* 4.7 4.9 - - + -
1099A LEU 2.6 15.6 + - - +
1100A LYS* 4.0 8.8 - - + +
1101A VAL* 2.8 32.8 + - - +
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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