Contacts of the helix formed by residues 1090 - 1104 (chain E) in PDB entry 5IJO
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 SER1090 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088E ASN* 3.1 4.6 - - - +
1089E ARG* 1.3 81.7 - - - +
1091E PHE* 1.3 63.9 + - - +
1092E SER* 4.4 6.3 - - - -
1093E ASN* 4.5 14.1 - - - -
1094E ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1091 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089E ARG 3.4 4.2 + - - -
1090E SER* 1.3 70.0 - - - +
1092E SER* 1.3 66.8 + - - +
1094E ALA* 3.1 5.3 + - - +
1095E ALA* 2.9 24.9 + - - +
1124E SER* 3.6 33.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1092 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090E SER* 3.4 3.4 - - - -
1091E PHE* 1.3 81.1 - - - +
1093E ASN* 1.3 63.6 + - - +
1095E ALA* 3.2 5.9 + - - +
1096E ARG* 3.1 22.2 + - - +
1124E SER 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1093 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088E ASN* 3.9 18.4 - - + -
1090E SER* 3.8 12.2 + - - +
1091E PHE 3.3 0.4 - - - -
1092E SER* 1.3 78.4 - - - +
1094E ALA* 1.3 65.4 + - - +
1096E ARG* 3.3 14.2 + - - +
1097E VAL* 3.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1094 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085E TYR* 3.4 38.4 - - + +
1088E ASN* 3.8 9.6 - - - +
1090E SER 3.2 17.1 + - - +
1091E PHE* 3.1 7.7 + - - +
1093E ASN* 1.3 79.1 - - - +
1095E ALA* 1.3 63.1 + - - +
1097E VAL* 3.1 14.0 + - - +
1098E LEU* 3.2 10.6 + - - +
1124E SER* 5.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1095 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091E PHE 2.9 16.2 + - - +
1092E SER* 3.6 6.3 - - - +
1094E ALA* 1.3 77.8 - - - +
1096E ARG* 1.3 64.5 + - - +
1098E LEU* 3.1 3.8 + - - +
1099E SER* 3.0 22.9 + - - -
1121E ALA* 3.7 36.4 - - + +
1124E SER* 3.9 8.1 - - - -
1140E PHE* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1096 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092E SER 3.1 12.6 + - - +
1093E ASN* 3.8 9.6 - - - +
1094E ALA 3.2 0.4 - - - -
1095E ALA* 1.3 77.1 - - - +
1097E VAL* 1.3 62.1 + - - +
1099E SER* 3.4 7.4 + - - -
1100E ARG* 3.3 19.2 + - - +
1140E PHE* 6.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1097 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081E LEU* 5.5 8.3 - - + +
1084E TYR* 5.1 8.1 - - + -
1085E TYR* 4.4 18.4 - - + +
1093E ASN 3.3 8.5 + - - +
1094E ALA 3.1 9.3 + - - +
1096E ARG* 1.3 78.3 - - - +
1098E LEU* 1.4 60.0 + - - +
1100E ARG* 3.0 9.6 + - - +
1101E LEU* 2.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1098 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085E TYR* 4.8 8.5 - - + +
1094E ALA 3.2 7.7 + - - +
1095E ALA* 3.1 7.7 + - - +
1097E VAL* 1.4 79.0 - - - +
1099E SER* 1.3 64.4 + - - +
1101E LEU* 2.9 10.8 + - - +
1102E ALA* 2.8 19.8 + - - +
1117E TYR* 3.6 38.0 - - + +
1120E ARG* 5.3 3.4 - - + -
1121E ALA* 4.0 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1099 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095E ALA 3.0 11.7 + - - -
1096E ARG* 3.5 12.6 - - - -
1098E LEU* 1.3 77.3 - - - +
1100E ARG* 1.3 64.4 + - - +
1102E ALA* 2.9 9.9 + - - +
1103E ASP* 2.9 22.3 + - - +
1118E ILE* 6.4 1.1 - - - +
1121E ALA* 4.6 7.1 - - - +
1144E LEU* 5.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096E ARG 3.3 9.1 + - - +
1097E VAL* 3.0 11.5 + - - +
1099E SER* 1.3 78.0 - - - +
1101E LEU* 1.3 57.4 + - - +
1103E ASP* 3.8 7.2 - - - +
1104E MET* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081E LEU* 5.6 10.8 - - + -
1097E VAL 2.7 12.9 + - - +
1098E LEU* 3.0 18.6 - - + +
1100E ARG* 1.3 78.7 - - - +
1102E ALA* 1.3 61.4 + - - +
1104E MET* 3.3 17.3 - - - +
1109E ILE* 5.5 6.9 - - - +
1117E TYR* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098E LEU 2.8 11.8 + - - +
1099E SER* 2.9 10.1 + - - +
1101E LEU* 1.3 79.8 - - - +
1103E ASP* 1.3 60.6 + - - +
1104E MET 3.4 4.7 + - - +
1114E ARG* 3.8 42.0 - - + +
1117E TYR* 4.4 2.6 - - + +
1118E ILE* 5.3 5.2 - - + +
1147E LYS* 6.3 2.7 - - + -
1181E GLU* 5.8 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099E SER 2.9 15.7 + - - +
1100E ARG* 3.8 7.4 - - - +
1102E ALA* 1.3 74.2 - - - +
1104E MET* 1.3 70.1 + - - +
1105E HIS* 3.6 1.2 + - - -
1181E GLU* 5.6 4.3 - - - +
1182E LEU* 6.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100E ARG 2.8 13.4 + - - +
1101E LEU* 3.3 18.8 - - - +
1102E ALA 3.2 5.3 - - - +
1103E ASP* 1.3 83.2 - - - +
1105E HIS* 1.3 66.6 + - - +
1107E THR* 4.4 15.6 + - - +
1180E SER 5.0 4.2 - - - +
1181E GLU* 5.3 3.8 - - - +
----------------------------------------------------------
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