Contacts of the helix formed by residues 1090 - 1104 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1088Q ASN* 3.1 4.4 - - - +
1089Q ARG* 1.3 80.6 - - - +
1091Q PHE* 1.3 65.3 + - - +
1092Q SER* 3.4 6.7 - - - -
1093Q ASN* 4.5 13.9 - - - -
1094Q ALA* 3.2 22.7 + - - +
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Residues in contact with PHE1091 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089Q ARG 3.4 4.6 + - - -
1090Q SER* 1.3 70.0 - - - +
1092Q SER* 1.3 68.6 + - - +
1094Q ALA* 3.1 5.9 + - - +
1095Q ALA* 2.9 24.8 + - - +
1124Q SER* 3.6 33.3 - - - +
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Residues in contact with SER1092 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090Q SER* 3.4 3.2 - - - -
1091Q PHE* 1.3 80.2 - - - +
1093Q ASN* 1.3 62.9 + - - +
1095Q ALA* 3.2 5.6 + - - +
1096Q ARG* 3.1 22.6 + - - +
1124Q SER 5.6 0.9 - - - -
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Residues in contact with ASN1093 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088Q ASN* 3.9 17.5 - - + -
1090Q SER* 3.8 12.4 + - - +
1091Q PHE 3.3 0.2 - - - -
1092Q SER* 1.3 78.6 - - - +
1094Q ALA* 1.3 65.9 + - - +
1096Q ARG* 3.3 14.7 + - - +
1097Q VAL* 3.3 12.0 + - - +
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Residues in contact with ALA1094 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085Q TYR* 3.4 36.3 - - + +
1088Q ASN* 3.8 8.9 - - - +
1090Q SER 3.2 16.7 + - - +
1091Q PHE* 3.1 7.0 + - - +
1093Q ASN* 1.3 78.9 - - - +
1095Q ALA* 1.3 61.6 + - - +
1097Q VAL* 3.1 14.4 + - - +
1098Q LEU* 3.2 10.0 + - - +
1124Q SER* 5.4 3.6 - - - -
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Residues in contact with ALA1095 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091Q PHE 2.9 16.1 + - - +
1092Q SER* 3.6 6.1 - - - +
1094Q ALA* 1.3 76.8 - - - +
1096Q ARG* 1.3 62.6 + - - +
1098Q LEU* 3.1 3.8 + - - +
1099Q SER* 3.0 23.1 + - - -
1121Q ALA* 3.7 35.7 - - + +
1124Q SER* 3.9 8.0 - - - -
1140Q PHE* 6.5 0.7 - - + -
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Residues in contact with ARG1096 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092Q SER 3.1 12.6 + - - +
1093Q ASN* 3.8 10.1 - - - +
1094Q ALA 3.2 0.4 - - - -
1095Q ALA* 1.3 78.3 - - - +
1097Q VAL* 1.3 62.7 + - - +
1099Q SER* 3.4 7.9 + - - -
1100Q ARG* 3.3 19.4 + - - +
1140Q PHE* 6.3 3.8 - - + -
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Residues in contact with VAL1097 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081Q LEU* 5.5 7.6 - - + +
1084Q TYR* 5.1 8.5 - - + -
1085Q TYR* 4.4 17.7 - - + +
1093Q ASN 3.3 7.3 + - - +
1094Q ALA 3.1 9.4 + - - +
1096Q ARG* 1.3 77.0 - - - +
1098Q LEU* 1.4 60.6 + - - +
1100Q ARG* 3.0 9.9 + - - +
1101Q LEU* 2.7 26.5 + - - +
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Residues in contact with LEU1098 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085Q TYR* 4.8 8.4 - - + +
1094Q ALA 3.2 7.9 + - - +
1095Q ALA* 3.1 7.5 + - - +
1097Q VAL* 1.4 77.7 - - - +
1099Q SER* 1.3 63.8 + - - +
1101Q LEU* 2.9 12.0 + - + +
1102Q ALA* 2.8 19.6 + - - +
1117Q TYR* 3.6 37.1 - - + +
1120Q ARG* 5.3 3.4 - - + -
1121Q ALA* 4.0 9.6 - - + +
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Residues in contact with SER1099 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095Q ALA 3.0 12.7 + - - -
1096Q ARG* 3.5 12.3 - - - -
1098Q LEU* 1.3 76.4 - - - +
1100Q ARG* 1.3 63.7 + - - +
1102Q ALA* 2.9 9.9 + - - +
1103Q ASP* 2.9 23.2 + - - +
1118Q ILE* 6.4 1.1 - - - +
1121Q ALA* 4.6 6.7 - - - +
1144Q LEU* 5.7 10.3 - - - -
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Residues in contact with ARG1100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096Q ARG 3.3 8.7 + - - +
1097Q VAL* 3.0 11.5 + - - +
1099Q SER* 1.3 77.7 - - - +
1101Q LEU* 1.3 57.1 + - - +
1103Q ASP* 3.7 7.5 - - - +
1104Q MET* 2.8 32.6 + - - +
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Residues in contact with LEU1101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081Q LEU* 5.6 10.5 - - + -
1097Q VAL 2.7 12.5 + - - +
1098Q LEU* 2.9 19.9 + - + +
1100Q ARG* 1.3 80.1 - - - +
1102Q ALA* 1.3 60.6 + - - +
1104Q MET* 3.3 16.7 - - - +
1109Q ILE* 5.5 6.8 - - - +
1117Q TYR* 4.6 7.9 - - + -
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Residues in contact with ALA1102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098Q LEU 2.8 11.9 + - - +
1099Q SER* 2.9 10.1 + - - +
1101Q LEU* 1.3 79.1 - - - +
1103Q ASP* 1.3 61.9 + - - +
1104Q MET 3.4 4.3 + - - +
1114Q ARG* 3.8 40.7 - - + +
1117Q TYR* 4.4 3.3 - - + +
1118Q ILE* 5.3 5.2 - - + +
1147Q LYS* 6.3 2.5 - - + -
1181Q GLU* 5.8 3.8 - - - -
1182Q LEU 5.8 1.0 + - - -
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Residues in contact with ASP1103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099Q SER 2.9 14.6 + - - +
1100Q ARG* 3.8 7.9 - - - +
1102Q ALA* 1.3 73.0 - - - +
1104Q MET* 1.3 69.5 + - - +
1105Q HIS* 3.6 1.2 + - - -
1181Q GLU* 5.6 4.2 - - - +
1182Q LEU* 6.4 2.0 - - - -
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Residues in contact with MET1104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100Q ARG 2.8 12.7 + - - +
1101Q LEU* 3.3 19.1 - - - +
1102Q ALA 3.2 4.9 - - - +
1103Q ASP* 1.3 83.3 - - - +
1105Q HIS* 1.3 67.5 + - - +
1107Q THR* 4.4 16.3 - - - +
1180Q SER 5.0 4.5 - - - +
1181Q GLU* 5.3 4.0 - - - +
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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