Contacts of the strand formed by residues 1023 - 1031 (chain C) in PDB entry 3DLS
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 LYS1023 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999C TYR* 5.6 0.8 + - - -
1017C VAL* 3.5 4.1 - - - -
1018C ASP* 2.9 47.9 + - + +
1021C LYS* 3.1 19.9 - - + +
1022C ASN* 1.3 78.7 - - - +
1024C GLU* 1.3 66.7 + - - +
1025C VAL* 3.5 17.5 + - + +
1068C LEU* 4.0 27.4 - - - +
1082C GLU* 6.0 1.3 - - - +
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Residues in contact with GLU1024 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002C MET* 5.9 0.3 - - - +
1015C THR* 3.6 21.8 - - + +
1016C ALA 3.4 6.5 - - - +
1017C VAL* 4.5 9.8 - - + +
1022C ASN 4.3 0.4 + - - -
1023C LYS* 1.3 79.9 - - - +
1025C VAL* 1.3 61.5 + - - +
1083C LYS* 2.8 49.1 + - + +
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Residues in contact with VAL1025 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999C TYR* 3.7 24.9 - - + -
1015C THR* 3.5 8.0 - - - +
1016C ALA* 2.9 44.2 + - + +
1018C ASP* 4.6 0.9 - - + +
1023C LYS* 3.9 22.0 - - + +
1024C GLU* 1.3 79.7 - - - +
1026C VAL* 1.3 66.8 + - - +
1068C LEU* 3.4 26.5 - - + -
1080C VAL* 3.6 20.9 - - + -
1081C MET 3.3 11.2 - - - +
1082C GLU* 5.1 0.9 - - - -
1083C LYS* 3.9 5.6 - - - +
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Residues in contact with VAL1026 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ADP 3.5 54.5 - - + +
1005C LEU* 3.6 19.7 - - + -
1013C VAL* 3.7 18.6 - - + -
1014C TRP 3.4 9.4 - - - +
1015C THR* 5.1 0.2 - - - -
1025C VAL* 1.3 77.1 - - - +
1027C VAL* 1.3 61.1 + - - +
1079C LEU 3.6 1.4 - - - +
1080C VAL* 3.4 5.1 - - - +
1081C MET* 2.8 50.2 + - + +
1083C LYS* 3.7 15.5 - - + -
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Residues in contact with VAL1027 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995C TYR* 3.4 42.8 - - + +
1001C THR* 4.2 0.9 - - + -
1012C PHE 3.8 1.0 - - - +
1013C VAL* 3.4 4.7 - - - +
1014C TRP* 2.9 48.1 + - + +
1016C ALA* 3.9 10.5 - - + +
1025C VAL 4.2 0.4 - - - -
1026C VAL* 1.3 75.3 - - - +
1028C LYS* 1.3 67.5 + - - +
1029C PHE* 3.7 31.9 - - + -
1078C GLN* 4.2 8.3 - - + -
1079C LEU 3.4 9.0 - - - +
1080C VAL* 4.1 9.0 - - + +
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Residues in contact with LYS1028 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ADP 3.0 48.0 + - - +
12C MG 4.1 0.8 - - - -
1012C PHE* 3.5 5.6 - - + +
1013C VAL* 4.1 16.2 - - + +
1027C VAL* 1.3 74.5 - - - +
1029C PHE* 1.3 71.7 + - - +
1030C ILE* 3.7 11.5 + - + +
1052C GLU* 2.7 37.2 + - - +
1077C PHE 3.8 0.2 - - - +
1078C GLN* 3.9 0.2 - - - -
1079C LEU* 2.9 44.3 + - + +
1081C MET* 4.0 17.5 - - + -
1146C ASP* 3.3 19.2 + - - +
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Residues in contact with PHE1029 (chain C).
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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990C ALA* 3.4 36.3 - - + -
991C CYS* 3.8 26.5 - - - -
995C TYR* 4.1 3.4 - + - -
1001C THR* 3.8 9.9 - - + -
1012C PHE* 2.9 56.6 + + + +
1014C TRP* 3.7 27.4 - + - -
1027C VAL* 3.7 32.8 - - + -
1028C LYS* 1.3 76.0 - - - +
1030C ILE* 1.3 63.1 + - - +
1031C LYS 4.1 0.8 + - - -
1076C PHE* 4.0 10.3 - + + -
1077C PHE 3.5 3.1 - - - -
1078C GLN* 4.0 14.8 - - + -
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Residues in contact with ILE1030 (chain C).
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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1028C LYS* 4.1 12.1 - - + +
1029C PHE* 1.3 78.7 - - - +
1031C LYS* 1.3 68.1 + - - +
1032C LYS 3.7 0.7 + - - -
1050C THR* 4.5 17.0 - - + -
1052C GLU* 4.3 15.0 - - - +
1053C ILE* 3.8 26.5 - - + -
1076C PHE* 3.3 4.7 - - - -
1077C PHE* 2.8 53.2 + - + +
1079C LEU* 4.0 30.3 - - + -
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Residues in contact with LYS1031 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984C GLU* 4.3 15.0 + - - -
986C GLU* 3.9 31.7 + - + +
1012C PHE* 5.2 13.1 - - + -
1029C PHE 4.1 0.6 + - - -
1030C ILE* 1.3 79.3 - - - +
1032C LYS* 1.3 58.1 + - - +
1033C GLU* 2.8 60.6 + - + +
1075C GLY* 3.6 8.6 + - - +
1076C PHE* 3.7 26.4 - - + -
1077C PHE* 5.9 0.2 - - - -
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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