Contacts of the strand formed by residues 966 - 975 (chain E) in PDB entry 3T06
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 MET 966 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925E LYS* 4.7 2.6 - - - +
926E GLN* 4.0 12.3 + - - +
929E ASN* 3.1 61.3 + - + +
932E ARG* 4.2 11.0 - - + -
933E LEU* 3.6 35.0 - - + +
936E TYR* 4.5 2.2 - - + -
965E LYS* 1.3 72.1 - - - +
967E ILE* 1.3 65.6 + - - +
968E HIS 4.0 14.6 - - - +
969E GLU* 3.6 40.4 - - - +
987E LEU* 4.5 10.5 - - + -
988E LEU 3.9 4.0 - - - +
989E LEU* 4.1 9.2 - - + -
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Residues in contact with ILE 967 (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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925E LYS* 3.2 31.2 + - - +
926E GLN* 5.6 3.6 - - - +
929E ASN* 4.4 2.4 + - - -
965E LYS* 3.9 25.8 - - + +
966E MET* 1.3 81.3 - - - +
968E HIS* 1.3 68.7 + - + +
988E LEU* 2.6 34.3 + - + +
989E LEU 4.1 10.8 - - - +
990E GLU* 4.4 10.1 - - + +
1073E LEU* 4.2 21.6 - - + +
1077E ALA* 5.3 7.6 - - + -
68F ARG* 5.8 0.5 + - - -
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Residues in contact with HIS 968 (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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929E ASN* 5.4 1.3 - - - +
966E MET* 3.7 7.0 - - - +
967E ILE* 1.3 86.2 + - + +
969E GLU* 1.3 83.4 + - - +
987E LEU* 3.6 0.3 - - - -
988E LEU* 2.5 42.2 + - + +
1066E ASP* 5.3 2.4 + - - -
1069E THR* 4.3 12.1 - - + +
1070E TRP* 3.7 42.5 + + - -
1073E LEU* 3.5 34.3 - - + +
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Residues in contact with GLU 969 (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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929E ASN* 4.6 2.4 + - - +
932E ARG* 3.4 26.2 + - - -
936E TYR* 2.5 36.7 + - - -
966E MET* 3.6 28.7 - - - +
968E HIS* 1.3 98.8 + - - +
970E GLY* 1.3 60.4 + - - +
985E HIS* 3.5 14.4 + - + +
986E VAL 3.2 13.9 - - - +
987E LEU* 4.1 4.0 - - + -
1070E TRP* 4.1 7.6 - - - -
68F ARG* 5.4 1.7 + - - -
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Residues in contact with GLY 970 (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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969E GLU* 1.3 79.6 - - - +
971E PRO* 1.3 77.6 - - - +
985E HIS* 3.7 15.7 + - - -
986E VAL* 3.1 27.9 + - - +
1070E TRP* 4.0 11.4 - - - -
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Residues in contact with PRO 971 (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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970E GLY* 1.3 82.6 - - - +
972E LEU* 1.3 75.8 + - - +
984E LEU 3.7 10.1 - - - +
985E HIS* 4.0 7.1 - - + +
998E LYS* 4.8 11.4 - - + +
1062E LEU* 3.9 39.4 - - + +
1066E ASP* 4.5 4.5 - - - +
1070E TRP* 4.7 1.2 + - - -
105F HIS* 5.8 11.0 - - + +
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Residues in contact with LEU 972 (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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970E GLY 4.3 0.4 - - - +
971E PRO* 1.3 84.3 - - - +
973E THR* 1.3 62.9 + - - +
983E ASP* 5.0 0.2 - - - -
984E LEU* 2.8 38.8 + - - +
986E VAL* 3.7 37.2 - - + -
1043E PHE* 4.0 16.6 - - + -
1059E LEU* 3.9 28.0 - - + -
1060E VAL 3.6 21.5 - - - +
1061E ALA* 3.8 13.7 - - + +
1062E LEU* 5.0 1.5 - - - +
1070E TRP* 3.6 28.9 - - + +
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Residues in contact with THR 973 (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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972E LEU* 1.3 73.9 - - - +
974E TRP* 1.3 60.7 + - - +
975E ARG* 3.6 3.1 + - - -
981E THR* 4.9 11.7 - - + +
982E LEU 3.3 3.8 - - - +
983E ASP* 2.9 40.2 - - - +
1059E LEU* 3.1 7.2 - - - -
1060E VAL* 2.7 58.0 + - - +
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Residues in contact with TRP 974 (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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972E LEU 4.0 0.6 + - - -
973E THR* 1.3 70.7 - - - +
975E ARG* 1.3 65.1 + - - +
976E ILE* 3.0 31.4 + - + +
981E THR* 3.9 1.7 - - - -
982E LEU* 2.8 47.2 + - + +
984E LEU* 3.7 33.0 - - + -
995E LEU* 3.9 14.4 - - + -
1008E HIS* 3.6 31.0 - + + -
1022E PHE* 3.4 42.2 - + + -
1023E SER 4.5 2.7 - - - -
1024E PRO* 5.5 1.3 - - + -
1056E ILE 5.0 1.2 + - - -
1057E TYR* 3.3 40.3 - + - +
1058E GLU 3.2 18.6 + - - +
1059E LEU* 3.8 7.4 - - + -
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Residues in contact with ARG 975 (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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973E THR* 3.6 5.3 + - - -
974E TRP* 1.3 75.8 + - - +
976E ILE* 1.3 64.9 + - - +
977E SER 3.8 11.6 - - - +
978E LYS* 5.8 6.3 - - + -
979E ASP 6.1 0.4 - - - +
980E LYS 4.4 3.4 - - - +
981E THR* 4.2 16.4 - - - +
1039E ASP* 2.8 30.3 + - - +
1041E ARG* 6.3 0.2 - - - +
1042E ALA* 4.1 4.6 - - - +
1056E ILE 5.4 0.7 - - - +
1058E GLU* 3.2 59.9 + - + +
1060E VAL* 3.7 26.3 - - + +
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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