Contacts of the strand formed by residues 1076 - 1082 (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 PHE1076 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986C GLU* 3.3 41.7 - - + -
989C ALA* 3.7 15.0 - - + -
990C ALA* 3.7 25.8 - - + +
1012C PHE* 4.1 19.7 - + - -
1029C PHE* 4.0 11.0 - - + -
1030C ILE 3.3 7.4 - - - -
1031C LYS* 3.7 45.1 - - + -
1032C LYS* 3.6 10.0 - - - +
1072C GLU* 3.5 2.6 - - - -
1073C ASN* 2.8 40.9 + - - +
1075C GLY* 1.3 99.6 - - - +
1077C PHE* 1.3 60.8 + - - +
1078C GLN* 3.8 11.8 - - - +
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Residues in contact with PHE1077 (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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1028C LYS 4.5 0.2 - - - -
1029C PHE* 3.5 5.5 - - - -
1030C ILE* 2.8 50.0 + - + +
1032C LYS* 3.7 24.2 - - + -
1048C LYS 3.2 26.5 - - - -
1049C VAL* 4.1 16.6 - - + -
1050C THR* 4.8 3.8 - - - -
1053C ILE* 3.6 33.7 - - + -
1070C ILE* 4.7 7.9 - - + -
1071C PHE 3.4 14.1 - - - +
1072C GLU* 3.3 33.2 - - + -
1076C PHE* 1.3 76.3 - - - +
1078C GLN* 1.3 65.5 + - - +
1079C LEU 3.9 0.4 - - - -
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Residues in contact with GLN1078 (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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990C ALA 2.8 29.0 - - - +
992C GLU 4.6 1.8 + - - -
994C GLU 5.8 0.4 - - - +
995C TYR* 3.5 42.5 - - + +
1027C VAL* 4.2 5.8 - - + -
1028C LYS 3.9 3.4 - - - -
1029C PHE* 4.0 9.4 - - + -
1069C ASP 3.7 0.5 - - - +
1070C ILE* 3.4 6.2 - - - -
1071C PHE* 2.9 69.8 + - + +
1072C GLU* 3.5 7.3 - - - +
1073C ASN* 2.8 21.7 + - - +
1076C PHE* 3.8 5.7 - - - +
1077C PHE* 1.3 74.3 - - - +
1079C LEU* 1.3 62.1 + - - +
1080C VAL* 3.6 3.6 + - + +
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Residues in contact with LEU1079 (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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1026C VAL 3.6 1.0 - - - +
1027C VAL* 3.4 2.8 - - - -
1028C LYS* 2.9 55.2 + - + +
1030C ILE* 4.0 13.9 - - + -
1052C GLU* 3.9 24.0 - - + +
1053C ILE* 4.5 12.8 - - + -
1056C LEU* 3.9 23.3 - - + -
1067C VAL* 4.1 26.0 - - + -
1069C ASP 4.0 1.8 - - - +
1070C ILE* 4.7 10.1 - - + +
1077C PHE* 3.9 0.6 - - - +
1078C GLN* 1.3 70.2 - - - +
1080C VAL* 1.3 64.5 + - - +
1081C MET* 3.9 27.1 - - + +
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Residues in contact with VAL1080 (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* 4.1 12.8 - - + -
999C TYR* 3.6 33.4 - - + +
1025C VAL* 3.6 32.5 - - + -
1026C VAL 3.4 4.3 - - - +
1027C VAL* 4.1 17.9 - - + -
1067C VAL* 3.5 5.9 - - - +
1068C LEU* 2.6 32.8 + - + -
1069C ASP* 2.8 32.4 + - + +
1071C PHE* 4.6 1.6 - - + -
1078C GLN 4.2 5.8 - - - +
1079C LEU* 1.3 77.7 - - - +
1081C MET* 1.3 57.0 - - - +
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Residues in contact with MET1081 (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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3C ADP 3.6 22.9 - - - +
1025C VAL* 3.3 6.1 - - - +
1026C VAL* 2.8 64.5 + - + +
1028C LYS* 4.0 22.2 - - + -
1056C LEU* 5.0 2.2 - - - -
1065C ILE* 3.9 22.7 - - + -
1066C LYS 3.2 14.1 - - - +
1067C VAL* 4.6 3.6 - - + -
1068C LEU* 3.8 6.7 - - - +
1079C LEU* 3.9 33.0 - - + +
1080C VAL* 1.3 76.8 - - - +
1082C GLU* 1.3 67.1 + - - +
1145C ILE* 5.2 2.0 - - - -
1146C ASP 6.1 1.3 - - - -
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Residues in contact with GLU1082 (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 21.5 + - - -
1023C LYS* 6.0 1.3 - - - +
1025C VAL* 4.9 1.1 - - - +
1026C VAL* 4.1 0.2 - - - +
1065C ILE* 3.6 17.5 - - + -
1066C LYS* 2.7 60.5 + - + +
1068C LEU* 3.6 17.2 - - + +
1081C MET* 1.3 75.5 - - - +
1083C LYS* 1.3 61.4 + - - +
1084C HIS* 4.2 12.8 + - - +
1143C LYS* 3.4 30.6 + - - -
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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