Contacts of the helix formed by residues 85 - 101 (chain 2) in PDB entry 5IY6
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 GLU 85 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462 ARG* 2.9 57.7 + - - +
832 GLN 3.8 3.3 + - - +
842 GLU* 1.3 82.9 + - - +
862 SER* 1.3 67.1 + - - +
872 THR 3.0 9.1 - - - +
892 LEU* 3.0 14.6 + - - +
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Residues in contact with SER 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 ARG* 4.9 1.5 - - - +
842 GLU 3.5 2.5 + - - -
852 GLU* 1.3 68.9 + - - +
872 THR* 1.3 68.9 + - - +
892 LEU* 2.9 14.7 + - - +
902 LEU* 2.7 26.6 + - - +
1362 LEU* 4.3 14.2 - - - +
1402 LYS* 2.9 32.8 - - - +
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Residues in contact with THR 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 ARG* 3.1 49.8 + - - +
472 GLU 5.0 4.9 + - - +
852 GLU 3.0 8.9 - - - +
862 SER* 1.3 76.7 - - - +
882 GLY* 1.3 54.4 + - - +
892 LEU 2.6 12.3 + - - -
902 LEU* 4.6 2.9 - - - +
1402 LYS* 3.5 24.5 - - - +
1622 PHE* 6.2 1.8 - - + -
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Residues in contact with GLY 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422 LEU* 5.6 3.9 - - - +
462 ARG* 5.4 2.7 - - - -
522 ALA* 4.0 15.8 - - - +
562 VAL* 3.9 5.4 - - - +
592 MET* 6.0 1.4 - - - +
862 SER 3.4 0.2 + - - -
872 THR* 1.3 72.2 - - - +
892 LEU* 1.3 53.7 + - - +
902 LEU* 3.1 2.8 - - - +
912 SER* 3.3 25.4 + - - +
922 GLY* 2.7 29.3 + - - -
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Residues in contact with LEU 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812 LYS* 2.9 64.4 - - + +
822 ALA* 3.5 16.2 - - - +
842 GLU* 3.4 18.8 - - + +
852 GLU 3.0 11.6 + - - +
862 SER* 3.0 14.4 - - - +
872 THR 2.6 9.1 + - - -
882 GLY* 1.3 71.7 - - - -
902 LEU* 1.3 56.5 + - + +
922 GLY* 3.2 2.9 + - - -
932 LEU* 2.7 38.4 + - + -
1362 LEU* 4.1 14.1 - - + -
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Residues in contact with LEU 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862 SER* 2.7 39.6 + - - +
872 THR* 5.0 1.8 - - - -
882 GLY 3.1 2.7 - - - +
892 LEU* 1.3 74.8 - - - +
912 SER* 1.3 53.3 + - - +
932 LEU* 2.9 13.0 + - + +
942 ARG* 2.6 36.3 + - - +
1362 LEU* 3.6 30.3 - - + -
1372 GLY* 5.4 7.2 - - - -
1402 LYS* 3.1 34.8 - - + +
1622 PHE* 4.1 10.1 - - + -
1652 GLY* 4.7 9.2 - - - +
1662 SER* 4.5 18.4 - - - +
1692 ALA* 4.5 11.9 - - + +
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Residues in contact with SER 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522 ALA* 3.8 11.4 - - - +
532 LYS* 4.8 7.3 + - - +
562 VAL* 3.3 28.0 - - - -
882 GLY* 3.1 19.2 + - - +
902 LEU* 1.3 78.5 - - - +
922 GLY* 1.3 62.7 + - - +
942 ARG* 3.1 22.0 + - - +
952 ILE* 3.1 21.2 + - - +
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Residues in contact with GLY 92 (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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562 VAL* 3.9 8.7 - - - +
592 MET* 5.8 5.8 - - - -
602 LEU* 3.2 19.5 - - - +
882 GLY 2.7 19.1 + - - -
892 LEU* 3.6 2.2 - - - -
912 SER* 1.3 72.7 - - - +
932 LEU* 1.3 61.8 + - - +
962 TRP* 2.9 28.2 + - - +
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Residues in contact with LEU 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 GLU* 4.7 1.3 - - + -
812 LYS* 2.9 36.8 - - + +
892 LEU* 2.7 37.0 + - + +
902 LEU* 2.9 17.7 + - + +
922 GLY* 1.3 77.2 - - - +
942 ARG* 1.3 62.9 + - - +
962 TRP* 2.7 43.8 + - + +
972 HIS* 3.7 10.2 - - - -
1332 THR* 3.3 26.7 - - - +
1362 LEU* 3.8 15.3 - - + -
1692 ALA* 4.9 9.1 - - + +
1722 SER* 5.1 0.2 - - - -
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Residues in contact with ARG 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532 LYS* 3.2 33.5 - - - +
902 LEU 2.6 15.5 + - - +
912 SER* 3.1 15.7 + - - +
932 LEU* 1.3 75.4 - - - +
952 ILE* 1.3 78.8 + - + +
962 TRP 3.4 0.2 + - - -
972 HIS 3.8 0.9 + - - -
982 THR* 3.6 5.0 + - - +
1642 VAL* 4.3 10.5 + - - +
1652 GLY* 3.9 20.2 + - - +
1682 SER* 2.7 47.7 + - - +
1692 ALA* 4.2 15.0 - - + +
1722 SER* 2.8 29.3 + - - -
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Residues in contact with ILE 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532 LYS* 3.1 34.3 - - + -
562 VAL* 3.6 18.6 - - + -
572 MET* 4.0 15.7 - - + -
602 LEU* 2.9 33.0 - - + -
912 SER 3.1 14.7 + - - +
942 ARG* 1.3 91.8 - - + +
962 TRP* 1.4 65.3 + - - +
982 THR* 3.0 16.0 + - + +
992 GLN* 2.9 26.6 + - - +
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Residues in contact with TRP 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 LEU* 3.5 16.3 - - + +
772 LYS* 3.5 35.1 - - + +
782 GLU* 3.1 36.6 - - + -
922 GLY 2.9 14.0 + - - +
932 LEU* 2.7 59.0 + - + +
952 ILE* 1.4 76.0 - - - +
972 HIS* 1.3 116.1 + + - +
992 GLN* 3.1 17.2 + - - +
1002 LEU* 3.3 12.3 + - + +
1222 LEU 5.5 3.1 - - - -
1232 LEU* 6.4 0.4 - - - -
1262 GLY* 3.8 15.3 - - - -
1332 THR* 6.1 1.3 - - + -
1782 LEU* 5.0 1.3 - - + -
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Residues in contact with HIS 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 GLU* 5.1 0.2 - - - -
932 LEU 3.7 11.9 - - - -
942 ARG 3.8 0.8 + - - -
952 ILE 3.3 0.6 - - - -
962 TRP* 1.3 132.9 + + - +
982 THR* 1.3 63.6 + - - +
1002 LEU* 3.3 19.3 + - - +
1012 LEU* 4.2 1.6 + - - +
1262 GLY 5.1 0.7 - - - -
1302 SER* 6.3 0.2 - - - -
1332 THR* 5.5 1.4 - - - +
1692 ALA 5.4 0.7 - - - -
1722 SER* 3.2 25.8 - - - +
1732 GLN* 3.7 38.4 + - + +
1752 LEU* 5.4 2.4 - - + +
1762 ALA* 3.3 21.9 - - + +
1782 LEU* 3.6 19.8 - - + +
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Residues in contact with THR 98 (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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942 ARG* 3.6 7.3 + - - +
952 ILE* 3.0 21.7 + - + +
972 HIS* 1.3 80.3 - - - +
992 GLN* 1.3 61.5 + - - +
1012 LEU* 3.2 23.2 + - + +
1722 SER* 3.5 15.1 + - - -
1752 LEU* 5.2 14.9 - - + +
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Residues in contact with GLN 99 (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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572 MET* 4.9 4.7 - - - +
602 LEU* 3.6 25.2 - - + +
612 PHE* 2.9 50.0 - - + +
952 ILE* 2.9 14.5 + - - +
962 TRP* 3.1 14.8 + - - +
982 THR* 1.3 73.1 - - - +
1002 LEU* 1.3 65.3 + - - +
1012 LEU* 3.1 8.6 + - - -
2243 LEU* 5.4 13.6 - - + +
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Residues in contact with LEU 100 (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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962 TRP* 3.3 7.3 + - + +
972 HIS* 3.3 15.5 + - - +
982 THR 3.2 1.0 - - - -
992 GLN* 1.3 79.6 - - - +
1012 LEU* 1.3 61.7 + - - +
1192 ARG* 3.0 58.2 + - + +
1222 LEU* 3.5 34.1 - - + -
1232 LEU* 4.0 35.4 - - + -
1762 ALA* 6.4 1.6 - - + -
433 VAL* 4.8 10.7 - - + +
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Residues in contact with LEU 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972 HIS 4.2 1.5 + - - +
982 THR* 3.2 14.9 + - + +
992 GLN 3.1 7.2 - - - -
1002 LEU* 1.3 83.7 - - - +
1192 ARG* 3.4 33.1 + - - +
1752 LEU* 6.2 4.5 - - + -
433 VAL* 6.0 2.3 - - - +
2283 LEU* 5.9 2.9 - - - +
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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
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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