Contacts of the strand formed by residues 1015 - 1022 (chain A) in PDB entry 4YOC
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 LYS1015 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999A ILE* 3.5 0.5 - - - +
1000A PHE* 2.7 74.7 + - + +
1002A PRO* 4.6 6.9 - - + +
1013A ASP* 3.5 31.4 + - - +
1014A ILE* 1.3 78.5 - - - +
1016A ILE* 1.3 71.0 + - - +
1050A VAL* 5.6 5.8 - - + +
1051A VAL 3.7 10.1 - - - +
1052A ASP* 3.3 23.4 + - - +
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Residues in contact with ILE1016 (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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926A ALA* 5.2 0.2 - - + -
933A TYR* 6.3 0.2 - - + -
939A VAL* 5.5 2.2 - - + -
996A ILE* 3.9 23.3 - - + -
998A GLU 3.4 8.1 - - - +
999A ILE* 3.9 27.6 - - + -
1000A PHE* 4.4 2.2 - - - -
1014A ILE* 4.7 0.7 - - + -
1015A LYS* 1.3 82.6 - - - +
1017A ARG* 1.3 62.8 + - - +
1018A VAL* 3.6 22.0 - - + -
1049A ALA 3.7 0.9 - - - +
1050A VAL* 3.3 3.0 - - - -
1051A VAL* 2.9 49.4 + - + +
1052A ASP 4.8 0.2 - - - -
1053A PHE* 3.7 45.3 - - + -
1056A VAL* 4.6 7.6 - - + -
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Residues in contact with ARG1017 (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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920A ARG* 4.4 13.3 - - - +
996A ILE* 3.9 0.7 - - - -
997A LYS* 2.9 35.7 + - + +
998A GLU* 2.8 54.6 + - + +
1000A PHE* 4.2 5.8 - - + -
1016A ILE* 1.3 72.8 - - - +
1018A VAL* 1.3 65.0 + - - +
1048A GLU* 3.4 36.8 + - + +
1049A ALA* 3.5 10.2 - - - +
1050A VAL* 3.8 28.5 - - + +
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Residues in contact with VAL1018 (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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939A VAL* 4.8 9.6 - - + -
941A LEU* 4.4 18.2 - - + -
946A PHE* 4.5 12.3 - - + -
994A GLY* 4.2 6.7 - - - -
995A ARG 3.1 25.1 - - - +
996A ILE* 4.1 4.3 - - + +
997A LYS* 4.7 1.3 - - - -
1016A ILE* 3.6 22.2 - - + -
1017A ARG* 1.3 81.2 - - - +
1019A ASN* 1.3 63.4 + - - +
1020A LYS 3.8 0.2 + - - -
1048A GLU* 3.2 8.7 - - - +
1049A ALA* 2.9 47.6 + - + +
1051A VAL* 4.8 7.9 - - + -
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Residues in contact with ASN1019 (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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994A GLY* 3.1 7.9 - - - -
995A ARG* 2.9 40.7 + - + +
997A LYS* 3.9 24.4 - - - +
1018A VAL* 1.3 73.0 - - - +
1020A LYS* 1.3 63.8 + - - +
1021A PHE* 3.7 2.1 + - + -
1044A TRP* 3.5 43.9 - - + -
1045A SER 3.9 11.5 + - - +
1046A ASP* 4.4 4.9 + - - +
1047A GLU 3.5 2.7 + - - -
1048A GLU* 3.9 24.4 + - - +
1102A HIS* 5.8 1.2 - - - -
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Residues in contact with LYS1020 (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 PHE* 3.6 40.2 - - + -
947A THR 2.8 24.4 + - - +
948A PHE* 4.5 7.9 - - + -
949A ASN* 3.4 12.5 + - - -
1018A VAL* 4.9 0.4 - - + +
1019A ASN* 1.3 73.8 - - - +
1021A PHE* 1.3 63.3 + - - +
1022A TYR* 5.1 0.4 - - + -
1044A TRP* 5.5 0.2 - - - -
1045A SER* 2.4 39.1 + - - +
1047A GLU* 3.0 42.9 + - + +
1048A GLU 3.3 27.6 + - - +
1049A ALA* 4.1 10.3 - - + -
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Residues in contact with PHE1021 (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 PHE* 4.7 0.7 - - - -
948A PHE* 3.2 20.1 - - - -
993A ILE* 3.0 45.0 + - + +
994A GLY 3.9 1.8 - - - -
995A ARG* 3.5 35.4 - - + -
1019A ASN 3.8 6.7 - - - -
1020A LYS* 1.3 73.7 - - - +
1022A TYR* 1.3 63.8 + - - +
1023A ARG* 4.0 1.6 + - - +
1026A ASN* 4.7 0.2 - - - +
1042A LEU* 4.0 24.9 - - + -
1043A TYR 3.5 17.7 - - - +
1044A TRP* 3.8 30.1 - + - -
1062A VAL* 3.6 36.6 - - + -
1085A PHE* 3.7 18.6 - + - -
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Residues in contact with TYR1022 (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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948A PHE* 3.4 35.4 - + + +
949A ASN 3.5 4.5 + - - -
950A ILE* 3.9 4.1 + - + -
1020A LYS* 5.1 0.7 - - + -
1021A PHE* 1.3 74.6 - - - +
1023A ARG* 1.3 64.4 + - - +
1026A ASN* 3.9 28.5 - - + -
1027A THR* 4.1 5.8 - - + -
1042A LEU* 3.4 7.8 - - - -
1043A TYR* 2.9 47.4 + - + +
1045A SER* 3.7 28.3 - - - -
1047A GLU* 2.3 39.7 + - - -
1089A TYR* 3.7 36.3 - + + -
1091A ALA* 3.6 7.6 - - - +
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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