Contacts of the strand formed by residues 1060 - 1069 (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 LEU1060 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003E THR* 4.0 16.8 - - + +
1029E LYS* 5.5 0.4 - - - +
1030E GLY* 3.8 23.6 - - - +
1031E TYR 3.6 22.4 - - - +
1032E PHE* 3.9 6.7 - - + -
1055E LEU 3.4 0.3 - - - +
1056E LEU* 3.5 6.1 - - - +
1057E GLN* 2.8 51.1 + - - +
1058E SER* 3.2 26.2 - - - +
1059E GLY* 1.3 85.6 - - - +
1061E TYR* 1.3 60.7 + - - +
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Residues in contact with TYR1061 (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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1030E GLY* 3.0 23.7 + - - -
1031E TYR* 2.6 49.2 + - + +
1032E PHE* 4.0 23.2 - + - -
1033E PRO* 4.4 1.1 - - + -
1034E GLU* 3.3 50.7 + - + -
1054E ALA* 4.0 10.1 - - + -
1055E LEU 3.2 15.9 - - - -
1056E LEU* 3.7 35.5 - - + +
1057E GLN* 3.8 0.2 - - - -
1060E LEU* 1.3 74.3 - - - +
1062E THR* 1.3 62.4 + - - +
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Residues in contact with THR1062 (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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1027E LEU* 3.9 12.8 - - - +
1028E VAL 3.3 14.6 + - - -
1029E LYS* 3.7 21.0 - - + +
1031E TYR* 3.9 1.1 - - - -
1053E PRO 4.5 0.7 - - - +
1054E ALA* 3.4 1.7 - - - -
1055E LEU* 3.0 39.0 + - + +
1057E GLN* 3.1 28.9 - - + +
1061E TYR* 1.3 78.1 - - - +
1063E LEU* 1.3 61.5 + - - +
2052F LEU* 5.2 5.2 - - + -
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Residues in contact with LEU1063 (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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1027E LEU* 3.7 5.7 - - - +
1028E VAL* 2.9 42.2 + - + +
1031E TYR* 3.7 18.0 - - - +
1034E GLU* 5.8 0.2 - - - +
1036E VAL* 4.4 16.8 - - + +
1038E LEU* 4.3 17.5 - - + -
1051E THR* 4.0 20.2 - - + -
1052E PHE 3.5 17.9 - - - +
1053E PRO* 4.7 2.2 - - + -
1054E ALA* 3.7 14.4 - - + +
1062E THR* 1.3 75.1 - - - +
1064E SER* 1.3 78.7 + - - +
1065E SER 4.3 0.9 - - - +
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Residues in contact with SER1064 (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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1026E CYS 3.4 13.5 - - - -
1027E LEU* 4.4 11.7 - - - +
1052E PHE* 3.0 32.7 + - - +
1063E LEU* 1.3 82.5 - - - +
1065E SER* 1.3 60.6 + - - +
2025F VAL* 4.6 7.4 - - - -
2027F PHE* 4.1 12.6 - - - -
2068F SER* 3.0 31.7 + - - -
2070F THR* 4.9 3.1 + - - -
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Residues in contact with SER1065 (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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1025E GLY* 3.1 5.2 - - - -
1026E CYS* 2.8 37.1 + - - +
1038E LEU* 3.6 30.0 - - - +
1040E TRP* 3.0 25.3 + - - -
1049E VAL* 3.9 0.7 - - - +
1050E HIS 3.3 6.7 + - - -
1051E THR* 3.3 18.8 + - - -
1052E PHE* 4.3 0.4 - - - -
1063E LEU* 4.3 0.2 - - - +
1064E SER* 1.3 75.7 - - - +
1066E SER* 1.3 61.9 + - - +
2027F PHE* 3.6 5.4 - - - -
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Residues in contact with SER1066 (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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1023E THR* 3.6 14.7 + - - -
1024E LEU 3.7 4.0 - - - -
1040E TRP* 4.4 0.4 - - - -
1048E GLY 4.2 1.3 + - - -
1049E VAL* 3.2 2.6 - - - -
1050E HIS* 2.6 42.1 + - - +
1052E PHE* 3.9 2.2 - - - -
1065E SER* 1.3 77.6 + - - +
1067E VAL* 1.3 62.7 + - - +
1068E THR* 4.1 3.3 + - - -
2027F PHE* 3.7 27.3 - - - -
2029F ASN* 3.1 28.8 + - - -
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Residues in contact with VAL1067 (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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1022E VAL 4.2 0.2 - - - +
1023E THR* 3.4 1.6 + - - -
1024E LEU* 2.8 55.3 + - + +
1040E TRP* 3.7 37.0 - - + +
1045E LEU* 4.1 22.9 - - + -
1047E SER 4.9 2.7 - - - +
1048E GLY 3.6 3.8 - - - -
1049E VAL* 3.7 24.2 - - + +
1065E SER 4.2 0.2 + - - -
1066E SER* 1.3 73.9 - - - +
1068E THR* 1.3 71.0 + - - +
1069E VAL* 4.2 3.4 + - + +
1079E ILE* 4.7 5.4 - - + -
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Residues in contact with THR1068 (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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1021E SER* 3.7 25.6 - - - +
1022E VAL 3.4 17.3 - - - +
1023E THR* 3.2 21.4 + - + +
1047E SER 4.4 4.5 - - - +
1048E GLY* 3.3 27.9 + - - -
1050E HIS* 5.8 0.3 - - - -
1066E SER* 4.1 5.5 + - - -
1067E VAL* 1.3 74.0 - - - +
1069E VAL* 1.3 57.7 + - - +
2006F THR* 6.5 1.1 - - + -
2029F ASN* 4.8 5.4 + - - -
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Residues in contact with VAL1069 (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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1021E SER* 3.6 4.1 - - - -
1022E VAL* 2.9 32.6 + - + +
1024E LEU* 5.4 2.7 - - + -
1045E LEU* 4.9 19.1 - - + -
1067E VAL* 4.0 3.6 + - + -
1068E THR* 1.3 73.9 - - - +
1070E THR* 1.3 71.1 + - + +
1071E SER* 5.3 0.7 - - - -
1073E THR* 3.1 31.6 - - + +
1074E TRP* 4.2 11.7 - - + -
1079E ILE* 3.6 30.5 - - + -
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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