Contacts of the helix formed by residues 75 - 90 (chain 2) in PDB entry 3SDI
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 SER 75 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412 ILE* 3.8 5.0 - - - +
662 TYR* 5.4 0.6 + - - -
732 THR 3.9 1.4 + - - -
742 PRO* 1.3 77.3 - - - +
762 THR* 1.3 63.0 + - - +
772 GLU* 3.7 10.8 + - - +
782 THR* 3.1 28.5 + - - -
792 ALA 3.1 17.7 + - - -
1052 ASP* 4.4 16.4 - - - -
1062 ASN* 4.9 11.2 - - - -
105T THR* 5.5 2.6 - - - +
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Residues in contact with THR 76 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 ILE* 4.2 13.2 - - + +
752 SER* 1.3 74.1 - - - +
772 GLU* 1.3 63.1 + - - +
792 ALA* 3.2 4.6 + - - +
802 ALA* 3.0 19.8 + - - +
1012 VAL* 4.5 7.8 - - + +
1022 ALA* 4.3 5.2 - - - -
1032 GLY* 3.3 45.9 + - - +
1042 TYR 4.1 0.5 + - - -
1052 ASP* 4.7 11.6 + - - +
1092 GLU* 4.0 20.6 + - + +
1112 TYR* 3.7 22.4 - - + -
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Residues in contact with GLU 77 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752 SER* 3.2 10.0 + - - +
762 THR* 1.3 77.7 - - - +
782 THR* 1.3 57.8 + - - +
802 ALA* 3.1 4.6 + - - +
812 SER* 2.9 26.9 + - - -
1092 GLU* 4.1 3.8 + - - +
1112 TYR* 3.3 35.8 + - + +
104T LYS* 3.6 40.3 + - + +
105T THR* 5.4 6.1 + - - -
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Residues in contact with THR 78 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632 LEU* 4.6 4.3 - - + -
662 TYR* 4.2 9.6 + - + -
742 PRO* 3.9 20.4 - - + -
752 SER* 3.1 23.1 + - - -
772 GLU* 1.3 76.7 - - - +
792 ALA* 1.3 65.8 + - - +
812 SER* 3.2 4.4 + - - -
822 VAL* 3.2 22.9 + - - +
102T LEU 4.7 0.2 - - - +
103T TYR* 2.7 50.3 + - + +
105T THR* 3.5 15.2 - - - +
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Residues in contact with ALA 79 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 VAL* 5.0 2.0 - - + -
412 ILE* 3.6 38.6 - - + -
592 VAL* 4.3 1.1 - - + +
632 LEU* 3.8 28.9 - - + +
752 SER 3.1 5.7 + - - -
762 THR 3.6 6.3 - - - +
782 THR* 1.3 78.1 - - - +
802 ALA* 1.3 61.8 + - - +
822 VAL* 3.5 3.6 + - - +
832 PHE* 3.2 29.8 + - + -
1012 VAL* 4.5 3.8 - - + -
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Residues in contact with ALA 80 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 THR 3.0 12.9 + - - +
772 GLU 3.1 9.4 + - - +
792 ALA* 1.3 73.8 - - - +
812 SER* 1.3 59.6 + - - +
832 PHE* 3.4 3.5 + - - +
842 LYS* 2.8 29.6 + - - +
1012 VAL* 4.4 15.2 - - + +
1112 TYR* 3.8 36.8 - - + -
1132 ILE* 4.3 3.6 - - + +
1192 VAL* 4.3 10.4 - - + +
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Residues in contact with SER 81 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772 GLU 2.9 12.5 + - - -
782 THR 3.2 8.7 + - - -
802 ALA* 1.3 77.0 - - - +
822 VAL* 1.3 57.0 + - - +
842 LYS* 3.5 12.1 - - - +
852 GLU* 2.9 32.1 + - - +
1192 VAL* 5.8 0.9 - - - -
101T LYS 4.0 6.4 + - - -
102T LEU 3.0 23.1 + - - +
103T TYR 4.1 2.0 - - - -
104T LYS* 3.7 27.8 + - - +
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Residues in contact with VAL 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 VAL* 4.0 26.2 - - + -
622 HIS* 4.0 26.7 - - + +
632 LEU* 4.4 10.3 - - + -
782 THR 3.2 13.3 + - - +
792 ALA* 3.9 7.2 - - - +
802 ALA 3.2 0.2 - - - -
812 SER* 1.3 73.8 - - - +
832 PHE* 1.3 64.8 + - - +
852 GLU* 3.3 2.9 + - - +
862 LEU* 3.1 28.2 + - + +
102T LEU* 3.9 27.3 - - + +
103T TYR* 4.0 22.2 - - + -
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Residues in contact with PHE 83 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 VAL* 4.0 20.0 - - + -
432 CYS* 3.6 29.2 - - + -
552 ILE* 3.6 20.2 - - + -
562 ALA* 4.3 8.5 - - + -
592 VAL* 3.8 31.0 - - + -
792 ALA 3.2 22.4 + - - -
802 ALA 3.4 6.5 + - - +
822 VAL* 1.3 76.6 - - - +
842 LYS* 1.3 63.5 + - - +
862 LEU* 3.2 5.5 + - - +
872 CYS* 2.9 29.7 + - - -
992 ILE* 3.6 31.2 - - + -
1012 VAL* 3.7 22.7 - - + -
1132 ILE* 3.8 13.9 - - + -
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Residues in contact with LYS 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491 SER 5.7 2.0 - - - -
521 GLN* 3.6 33.5 + - - +
531 HIS* 5.8 0.4 - - - +
561 ARG* 6.3 1.2 - - - +
802 ALA 2.8 17.8 + - - +
812 SER* 3.5 11.7 - - - +
832 PHE* 1.3 76.7 - - - +
852 GLU* 1.3 72.4 + - - +
872 CYS* 3.1 5.0 + - - +
882 TYR* 2.8 37.7 + - + +
1132 ILE* 4.6 6.7 - - + +
1172 GLY 3.5 18.8 - - - +
1192 VAL* 3.4 33.1 - - + +
104T LYS* 5.3 11.3 - - - +
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Residues in contact with GLU 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561 ARG* 4.9 8.7 + - - -
812 SER* 2.9 19.6 + - - +
822 VAL 3.3 4.7 + - - +
842 LYS* 1.3 88.3 - - - +
862 LEU* 1.3 65.7 + - + +
882 TYR* 4.2 6.1 - - - +
892 GLU* 3.0 53.5 + - + +
101T LYS* 3.5 43.0 + - + +
102T LEU* 4.2 22.7 - - + -
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Residues in contact with LEU 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 ILE* 3.8 25.1 - - + +
582 ILE* 3.8 35.9 - - + -
592 VAL* 3.7 30.3 - - + -
622 HIS* 5.5 3.8 - - - +
822 VAL* 3.1 15.2 + - + +
832 PHE 3.5 6.5 - - - +
852 GLU* 1.3 80.0 - - + +
872 CYS* 1.3 59.9 + - - +
902 ASN* 3.0 41.0 + - - +
952 LEU* 3.7 4.7 - - + +
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Residues in contact with CYS 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 ILE* 4.4 12.3 - - - -
832 PHE* 2.9 21.1 + - - +
842 LYS 3.8 2.5 - - - +
862 LEU* 1.3 75.1 - - - +
882 TYR* 1.3 65.3 + - - +
902 ASN 3.7 1.0 - - - -
912 LYS* 3.3 24.6 + - - +
952 LEU* 4.2 9.1 - - + +
972 ALA* 4.4 26.0 - - - +
992 ILE* 4.4 12.6 - - - -
1132 ILE* 4.1 17.0 - - + -
1152 LEU 4.8 4.9 - - - +
1162 GLY 4.3 1.7 - - - +
1172 GLY* 4.1 17.3 - - - +
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Residues in contact with TYR 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 SER* 3.3 34.1 - - - -
501 ASP* 2.6 31.8 + - - -
531 HIS* 3.3 44.0 - + + +
941 ARG* 5.1 5.1 + - - -
1011 LEU* 3.8 6.2 - - - +
842 LYS* 2.8 29.5 + - + +
852 GLU* 4.2 6.1 - - - +
872 CYS* 1.3 72.1 - - - +
892 GLU* 1.3 85.9 + - - +
902 ASN 3.3 0.7 + - - -
912 LYS* 3.4 28.2 - - - +
1162 GLY 3.7 12.1 - - - -
1172 GLY* 3.9 10.5 - - - +
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Residues in contact with GLU 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531 HIS* 5.6 5.6 + - - -
852 GLU* 3.0 40.6 + - + +
882 TYR* 1.3 98.1 - - - +
902 ASN* 1.3 66.3 + - - +
912 LYS* 3.5 1.8 + - - +
101T LYS* 4.1 11.2 + - - -
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Residues in contact with ASN 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862 LEU* 3.0 37.8 + - - +
872 CYS 3.7 3.4 - - - -
882 TYR 3.2 0.4 - - - -
892 GLU* 1.3 85.6 - - - +
912 LYS* 1.3 62.1 + - - +
922 ASP* 3.3 3.4 - - - -
942 ASN* 3.2 26.8 + - + +
952 LEU* 3.4 28.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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