Contacts of the strand formed by residues 966 - 974 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925A LYS* 4.6 5.0 - - - -
926A GLN* 4.8 8.1 + - - -
929A ASN* 3.6 47.8 + - - +
932A ARG* 4.4 9.6 - - + -
933A LEU* 3.4 39.3 - - + +
936A TYR* 4.4 12.1 - - + -
964A ARG 4.2 0.8 + - - -
965A LYS* 1.3 78.8 - - - +
967A ILE* 1.3 64.8 + - - +
968A HIS* 4.3 6.1 - - - +
969A GLU* 3.8 35.4 - - - +
987A LEU* 4.8 4.7 - - + -
988A LEU 3.9 4.3 - - - +
989A LEU* 3.8 20.9 - - + -
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Residues in contact with ILE 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925A LYS* 4.0 23.1 + - - +
929A ASN* 5.0 2.1 + - - -
965A LYS 5.1 0.2 - - - +
966A MET* 1.3 80.0 - - - +
968A HIS* 1.3 61.1 + - + +
988A LEU* 2.8 42.7 + - + +
989A LEU 3.4 21.1 - - - +
990A GLU* 4.3 11.4 - - + +
1073A LEU* 4.2 24.5 - - + +
1077A ALA* 3.7 19.3 - - + +
68B ARG* 5.5 1.4 + - - -
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Residues in contact with HIS 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A MET* 3.8 6.5 - - - +
967A ILE* 1.3 83.8 - - + +
969A GLU* 1.3 86.7 + - + +
987A LEU* 3.9 0.2 - - - -
988A LEU* 2.8 36.7 + - + +
1066A ASP* 4.9 3.8 - - - -
1069A THR* 4.5 9.1 + - - -
1070A TRP* 3.7 42.3 - + + -
1073A LEU* 3.3 34.1 - - + +
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Residues in contact with GLU 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A ARG* 3.1 30.6 + - - +
936A TYR* 2.9 33.2 + - - -
966A MET* 3.8 22.3 - - - +
968A HIS* 1.3 99.5 + - + +
970A GLY* 1.3 58.7 + - - +
985A HIS* 3.3 12.8 - - + -
986A VAL 3.5 12.3 - - - +
987A LEU* 4.0 6.5 - - + +
1070A TRP* 4.1 7.0 - - - -
105B HIS* 5.8 2.1 + - - -
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Residues in contact with GLY 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A GLU* 1.3 79.3 - - - +
971A PRO* 1.3 75.2 - - - +
985A HIS* 3.8 16.7 + - - -
986A VAL* 3.1 28.6 + - - +
1070A TRP* 3.9 11.2 - - - -
105B HIS* 5.9 3.8 - - - -
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Residues in contact with PRO 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970A GLY* 1.3 85.1 - - - +
972A LEU* 1.3 77.5 + - - +
984A LEU 3.5 12.1 - - - +
985A HIS* 4.1 7.5 - - + -
1062A LEU* 3.5 40.5 - - + +
1066A ASP* 4.5 4.1 - - - +
1070A TRP* 4.3 5.0 + - - +
105B HIS* 5.7 9.2 - - + -
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Residues in contact with LEU 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A PRO* 1.3 87.8 - - - +
973A THR* 1.3 62.1 + - - +
983A ASP* 5.7 0.2 - - - -
984A LEU* 2.8 37.0 + - + +
986A VAL* 3.7 40.4 - - + -
1043A PHE* 4.2 15.0 - - + -
1059A LEU* 4.1 32.5 - - + -
1060A VAL 3.6 17.7 - - - +
1061A ALA* 3.7 16.8 - - + -
1062A LEU* 5.4 1.5 - - - +
1070A TRP* 4.1 24.7 - - + +
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Residues in contact with THR 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A LEU* 1.3 73.4 - - - +
974A TRP* 1.3 64.0 + - - +
975A ARG* 3.5 3.1 + - - +
981A THR* 3.9 27.1 - - + +
982A LEU 3.4 5.4 - - - +
983A ASP* 3.0 24.7 + - - +
1059A LEU* 3.5 4.6 - - - -
1060A VAL* 2.8 55.9 + - + +
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Residues in contact with TRP 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A LEU 3.9 1.0 + - - -
973A THR* 1.3 69.6 - - - +
975A ARG* 1.3 68.5 + - - +
976A ILE* 3.1 34.0 + - + +
981A THR* 3.2 3.3 - - - -
982A LEU* 2.5 55.7 + - + +
984A LEU* 3.9 28.0 - - + -
995A LEU* 4.3 12.3 - - + -
1006A LYS 5.8 3.6 - - - -
1007A CYS 6.0 2.7 - - - -
1022A PHE* 3.5 37.4 - + + -
1023A SER 4.7 1.8 - - - -
1024A PRO* 5.8 3.6 - - + -
1056A ILE 4.9 1.8 + - - -
1057A TYR* 3.0 52.6 - + - +
1058A GLU 3.4 12.9 - - - +
1059A LEU* 3.6 18.2 - - + -
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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