Contacts of the helix formed by residues 103 - 119 (chain 3) in PDB entry 5IY8
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 LEU 103 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723 PRO* 6.1 5.6 - - + -
1003 LYS* 3.0 44.8 + - + +
1013 TYR 3.0 0.2 - - - -
1023 GLU* 1.3 82.9 - - + +
1043 LEU* 1.3 51.8 + - - -
1053 THR* 3.2 3.6 - - - -
1063 SER* 2.7 38.2 + - - -
1073 ALA* 2.9 12.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN* 2.5 75.4 + - + +
1202 ILE* 4.8 7.9 - - + -
423 MET* 3.6 11.0 - - + +
453 GLY* 5.0 2.2 - - - -
463 ASN* 2.9 46.4 - - + +
493 LEU* 6.0 4.3 - - + -
1003 LYS 3.6 1.9 + - - -
1013 TYR* 2.9 21.7 + - - +
1023 GLU 3.2 0.8 - - - +
1033 LEU* 1.3 76.3 - - - +
1053 THR* 1.3 55.7 + - - +
1073 ALA* 2.9 13.1 + - + +
1083 ASN 2.8 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN* 3.8 8.3 - - - +
1023 GLU 4.4 12.0 + - - +
1033 LEU* 4.3 1.8 - - - +
1043 LEU* 1.3 80.1 - - - +
1063 SER* 1.3 77.8 + - - +
1083 ASN* 3.3 3.8 + - - +
1093 GLU* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033 LEU* 2.7 29.5 + - - +
1053 THR* 1.3 78.8 - - - +
1073 ALA* 1.3 60.1 + - - -
1093 GLU* 3.0 16.7 + - - +
1103 VAL* 2.9 34.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423 MET* 4.4 4.5 - - - -
573 LEU* 6.6 0.4 - - + -
713 TYR* 5.2 17.7 - - + -
1033 LEU* 2.9 11.1 + - + +
1043 LEU* 2.9 22.5 + - + +
1063 SER* 1.3 74.3 - - - +
1083 ASN* 1.3 66.5 + - - +
1103 VAL* 3.4 5.4 + - - +
1113 ILE* 3.0 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN* 1.6 67.7 + - - +
1182 LEU* 3.1 24.1 - - - +
423 MET* 3.2 15.8 - - - +
1043 LEU 2.8 0.2 + - - -
1053 THR 3.7 4.0 - - - +
1063 SER 3.2 0.2 - - - -
1073 ALA* 1.3 75.4 - - - +
1093 GLU* 1.3 59.2 + - - +
1113 ILE* 2.7 23.7 - - - +
1123 VAL* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053 THR 3.3 6.7 + - - +
1063 SER* 3.0 25.1 + - - +
1083 ASN* 1.3 78.2 - - - +
1103 VAL* 1.3 82.1 + - + +
1113 ILE 3.3 0.2 + - - -
1123 VAL* 3.3 6.4 + - - +
1133 GLU* 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703 LEU 2.8 32.1 - - - +
713 TYR* 4.3 9.4 - - + -
723 PRO* 5.6 0.7 - - + -
1063 SER* 2.9 35.3 + - - +
1073 ALA* 3.9 5.8 - - - +
1093 GLU* 1.3 93.7 + - - +
1113 ILE* 1.3 58.9 + - - +
1133 GLU* 4.1 3.2 - - - +
1143 GLU* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 ILE* 3.4 23.8 - - + -
413 VAL* 4.8 4.0 - - + -
423 MET* 2.9 46.2 - - + -
593 VAL* 4.2 26.7 - - + -
703 LEU* 4.7 3.8 - - + -
713 TYR* 4.7 6.7 - - + -
1073 ALA* 3.0 16.1 + - + +
1083 ASN* 2.7 26.2 - - - +
1103 VAL* 1.3 75.7 - - - +
1123 VAL* 1.3 71.2 + - + +
1143 GLU* 4.6 2.2 - - - -
1153 ILE* 2.7 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 ILE* 5.0 8.7 - - + -
1083 ASN* 3.1 30.4 + - - +
1093 GLU* 3.9 5.2 - - - +
1113 ILE* 1.3 88.8 - - + +
1133 GLU* 1.3 66.0 + - - +
1153 ILE* 3.5 3.3 + - - +
1163 LYS* 3.3 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093 GLU* 3.0 29.0 + - - +
1103 VAL* 4.1 4.0 - - - +
1123 VAL* 1.3 82.2 - - - +
1143 GLU* 1.3 70.0 + - + +
1163 LYS* 3.2 14.6 + - - +
1173 ASP* 3.3 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683 ARG* 3.1 42.4 + - - -
693 PHE 4.2 5.5 - - - +
703 LEU* 3.3 44.1 - - + +
1103 VAL* 2.8 34.1 + - + +
1113 ILE 3.9 2.0 - - - +
1133 GLU* 1.3 81.6 - - + +
1153 ILE* 1.3 61.5 + - + +
1173 ASP* 3.2 11.8 + - - +
1183 LEU* 2.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 VAL* 5.6 4.0 - - + -
343 LEU* 4.0 24.7 - - + -
383 ILE* 4.1 24.2 - - + -
613 ALA* 5.9 1.1 - - + -
703 LEU* 3.1 39.3 - - + -
1113 ILE* 2.7 32.3 + - + +
1123 VAL* 4.1 3.8 - - - +
1143 GLU* 1.3 71.7 - - - +
1163 LYS* 1.3 70.1 + - - +
1183 LEU* 2.8 25.9 + - + +
1193 MET* 3.3 18.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123 VAL* 3.3 11.7 + - + +
1133 GLU* 3.2 12.8 + - - +
1153 ILE* 1.3 79.3 - - - +
1173 ASP* 1.3 62.6 + - - +
1193 MET* 3.1 33.1 + - + +
1203 THR 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683 ARG* 3.2 27.8 + - - +
1133 GLU* 3.3 8.2 + - + +
1143 GLU* 3.2 13.4 + - - +
1153 ILE 3.1 0.6 - - - -
1163 LYS* 1.3 79.0 - - - +
1183 LEU* 1.3 62.4 + - - +
1193 MET 3.2 1.2 + - - -
1203 THR* 3.4 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173 ALA* 5.2 3.6 - - + -
613 ALA* 4.7 15.5 - - + -
633 HIS* 3.4 55.5 + - + +
663 GLU* 4.9 6.7 - - - +
683 ARG* 4.2 35.2 - - + +
703 LEU* 4.6 6.7 - - + -
1143 GLU 2.7 30.3 - - - +
1153 ILE* 2.8 17.5 + - + +
1173 ASP* 1.3 77.7 - - - +
1193 MET* 1.3 59.0 + - - +
1203 THR* 2.8 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173 ALA 5.9 2.7 - - - +
213 TRP* 6.5 0.7 - - + -
343 LEU* 5.1 14.8 - - + -
633 HIS* 5.3 1.8 - - - -
1153 ILE* 3.7 23.8 - - + +
1163 LYS* 3.1 34.2 + - + +
1183 LEU* 1.3 78.1 - - - +
1203 THR* 1.4 66.5 + - - +
1213 LYS* 4.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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