Contacts of the strand formed by residues 1022 - 1031 (chain E) in PDB entry 5DFV
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 VAL1022 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012E PRO* 4.6 11.0 - - + -
1021E SER* 1.3 80.1 - - - +
1023E THR* 1.3 65.4 + - - +
1024E LEU* 3.5 24.8 + - + +
1067E VAL 4.2 0.2 - - - +
1068E THR* 3.4 3.5 - - - -
1069E VAL* 2.9 37.3 + - + +
1071E SER* 3.7 30.3 - - - +
1074E TRP* 3.8 18.2 - - + +
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Residues in contact with THR1023 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012E PRO* 4.3 8.1 - - - +
1021E SER 5.7 0.7 - - - +
1022E VAL* 1.3 79.4 - - - +
1024E LEU* 1.3 67.0 + - - +
1066E SER* 3.6 14.2 + - - -
1067E VAL 3.4 3.7 + - - -
1068E THR* 3.2 26.0 + - + +
2006F THR* 5.3 8.1 - - + -
2008F SER* 3.1 31.1 + - - +
2010F PHE* 3.3 20.8 - - - -
2027F PHE* 4.5 2.9 - - - +
2029F ASN* 5.3 1.1 + - - -
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Residues in contact with LEU1024 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010E LEU 3.8 1.1 - - - +
1012E PRO* 4.6 5.4 - - + -
1022E VAL* 3.5 19.1 - - + +
1023E THR* 1.3 75.9 + - - +
1025E GLY* 1.3 59.7 + - - +
1040E TRP* 5.2 0.7 - - + -
1066E SER* 3.7 2.0 - - - -
1067E VAL* 2.8 44.8 + - + +
1069E VAL* 5.4 2.2 - - + +
1074E TRP* 3.5 41.3 - - + +
1079E ILE* 3.8 26.0 - - + -
1096E ILE* 3.2 48.0 - - + -
2010F PHE* 3.8 9.9 - - - -
2027F PHE* 4.8 0.4 - - - -
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Residues in contact with GLY1025 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009E PRO* 3.8 1.6 - - - +
1010E LEU* 2.9 40.1 + - - +
1024E LEU* 1.3 78.1 - - - +
1026E CYS* 1.3 59.8 + - - +
1040E TRP* 3.7 9.0 - - - -
1065E SER 3.1 11.9 - - - -
1081E CYS* 5.8 0.2 - - - +
1096E ILE* 4.2 4.5 - - - +
2010F PHE* 4.0 1.6 - - - -
2027F PHE* 4.0 12.6 - - - -
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Residues in contact with CYS1026 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007E VAL* 3.7 19.1 - - - -
1008E TYR 3.7 8.7 - - - -
1009E PRO* 5.2 2.2 - - - -
1010E LEU* 3.8 4.9 - - - +
1025E GLY* 1.3 73.7 - - - -
1027E LEU* 1.3 65.2 + - - +
1028E VAL* 4.9 0.2 - - - -
1038E LEU* 3.9 13.0 - - + -
1040E TRP* 3.6 13.6 - - + -
1064E SER* 3.4 6.6 - - - -
1065E SER 2.8 28.3 + - - +
1081E CYS* 2.0 50.0 - - - -
1083E VAL* 4.4 0.4 - - - -
1094E LYS* 5.3 0.7 - - - -
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Residues in contact with LEU1027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006E SER 3.3 4.0 - - - +
1007E VAL* 3.5 0.7 - - - -
1008E TYR* 2.8 59.1 + - + +
1010E LEU* 3.8 19.5 - - + -
1026E CYS* 1.3 76.9 - - - +
1028E VAL* 1.3 65.5 + - - +
1029E LYS* 4.7 7.2 - - + -
1062E THR* 3.9 15.7 - - - +
1063E LEU 3.7 11.9 - - - +
1064E SER* 4.4 10.5 - - - -
2016F GLN* 4.1 4.0 - - - +
2023F SER* 4.0 28.3 - - - +
2025F VAL* 4.1 17.0 - - + -
2070F THR* 5.2 7.6 - - + +
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Residues in contact with VAL1028 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005E PRO* 3.3 33.2 - - + -
1006E SER 3.6 3.4 - - - +
1007E VAL* 4.5 3.4 - - + -
1026E CYS* 4.9 0.2 - - - -
1027E LEU* 1.3 74.0 - - - +
1029E LYS* 1.3 58.0 + - - +
1031E TYR* 3.8 12.7 - - + -
1036E VAL* 4.3 8.1 - - + -
1038E LEU* 4.0 17.7 - - + -
1062E THR* 3.3 5.1 + - - -
1063E LEU* 2.9 44.6 + - + +
1083E VAL* 3.5 38.6 - - + -
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Residues in contact with LYS1029 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005E PRO* 3.6 1.0 - - - +
1006E SER* 3.0 34.0 + - - -
1008E TYR* 4.1 29.6 - - + +
1027E LEU* 4.7 8.1 - - + -
1028E VAL* 1.3 74.4 - - - +
1030E GLY* 1.3 81.5 + - - +
1031E TYR* 3.7 2.9 - - - -
1057E GLN* 4.3 19.2 + - - +
1060E LEU* 5.5 0.6 - - - +
1062E THR* 3.7 19.1 - - + +
2016F GLN* 4.7 11.9 - - - +
2023F SER* 4.9 4.3 - - - +
2072F THR* 5.1 15.9 - - - +
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Residues in contact with GLY1030 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003E THR* 3.5 14.6 - - - +
1004E ALA 3.3 14.2 - - - +
1029E LYS* 1.3 95.9 - - - +
1031E TYR* 1.3 59.2 + - - +
1057E GLN* 4.7 0.4 - - - -
1060E LEU* 3.8 19.2 - - - +
1061E TYR 3.0 11.8 + - - -
1062E THR* 4.1 0.4 - - - -
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Residues in contact with TYR1031 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003E THR 3.4 13.0 - - - +
1005E PRO* 3.7 21.8 - - + -
1028E VAL* 3.8 32.5 - - + -
1030E GLY* 1.3 78.0 - - - +
1032E PHE* 1.3 63.2 + - - +
1033E PRO 3.4 22.0 - - - -
1034E GLU* 3.9 13.0 + - + +
1036E VAL* 3.1 34.7 - - + +
1054E ALA* 3.2 24.8 - - - +
1060E LEU* 3.6 4.0 - - - -
1061E TYR* 2.6 76.7 + - + +
1062E THR* 3.9 2.5 - - - -
1063E LEU* 3.7 9.2 - - + +
1085E HIS* 4.3 5.6 - + - +
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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