Contacts of the helix formed by residues 1099 - 1111 (chain A) in PDB entry 5JQE
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 SER1099 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1028A ASP* 3.1 23.7 + - - -
1097A GLN 3.0 8.8 + - - -
1098A ILE* 1.3 72.5 - - - +
1100A ALA* 1.3 59.4 + - - +
1101A TYR* 3.7 10.6 + - - +
1102A ARG* 2.8 32.4 + - - +
1103A VAL* 3.1 11.8 + - - +
1154A GLU* 4.2 13.8 + - - -
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Residues in contact with ALA1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098A ILE 3.5 1.8 + - - -
1099A SER* 1.3 72.4 - - - +
1101A TYR* 1.3 52.8 + - - +
1103A VAL* 3.6 12.0 - - + +
1104A MET* 2.7 36.9 + - - +
1178A TYR* 3.8 20.7 - - + -
1181A PHE* 6.3 3.8 - - + -
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Residues in contact with TYR1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028A ASP* 5.8 1.3 - - - -
1099A SER* 3.1 10.9 + - - +
1100A ALA* 1.3 79.2 - - - +
1102A ARG* 1.3 72.9 + - + +
1104A MET* 3.7 18.2 - - + +
1105A LEU* 3.3 48.4 + - + +
1147A GLU* 2.7 33.1 + - - +
1152A LEU* 3.3 27.2 + - + +
1153A GLY* 3.4 24.7 - - - -
1154A GLU* 3.6 35.4 - - + +
1157A LEU* 5.1 0.2 - - + -
1178A TYR* 3.6 25.0 - + + +
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Residues in contact with ARG1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A PHE* 3.7 50.2 - - - -
1025A LEU* 4.6 8.7 - - + +
1027A LEU* 3.9 28.5 + - - +
1028A ASP* 3.1 44.8 + - + +
1098A ILE* 3.7 17.3 - - + -
1099A SER* 2.8 16.5 + - - +
1101A TYR* 1.3 81.4 - - + +
1103A VAL* 1.3 64.9 + - - +
1105A LEU* 3.3 2.8 + - - +
1106A TYR* 3.1 22.9 + - - +
1147A GLU* 3.2 39.8 + - - -
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Residues in contact with VAL1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A LEU* 4.8 3.1 - - + -
1068A ARG* 3.7 45.1 - - + +
1098A ILE* 3.7 26.0 - - + +
1099A SER 3.1 17.4 + - - +
1100A ALA* 3.2 9.2 + - + +
1102A ARG* 1.3 74.5 - - - +
1104A MET* 1.3 62.9 + - - +
1106A TYR* 4.0 8.5 - - + +
1107A GLN* 3.2 50.9 + - + +
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Residues in contact with MET1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100A ALA 2.7 21.4 + - - +
1101A TYR* 3.7 24.7 - - + +
1103A VAL* 1.3 75.0 - - - +
1105A LEU* 1.3 75.8 + - + +
1107A GLN* 3.5 9.0 + - - +
1108A ILE* 3.3 47.6 + - - +
1157A LEU* 4.3 15.7 - - + -
1160A LEU* 4.2 6.5 - - + -
1174A ILE* 4.1 16.4 - - + +
1175A ILE* 4.3 9.0 - - + -
1178A TYR* 3.9 44.2 - - + -
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Residues in contact with LEU1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A PHE* 3.8 25.8 - - + -
1101A TYR* 3.3 45.7 + - + +
1102A ARG* 3.3 3.6 + - - +
1104A MET* 1.3 83.1 - - + +
1106A TYR* 1.3 65.4 + - - +
1108A ILE* 3.2 6.4 + - + +
1109A SER* 3.1 20.4 + - - -
1140A LEU* 4.8 0.4 - - - -
1143A PHE* 3.6 45.2 - - + -
1147A GLU* 4.7 2.9 - - - +
1152A LEU* 4.3 13.0 - - + -
1160A LEU* 4.0 22.9 - - + -
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Residues in contact with TYR1106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021A SER* 3.3 36.6 + - - -
1024A PHE* 4.3 5.5 - + + -
1025A LEU* 3.9 24.7 - - + -
1068A ARG* 3.5 24.5 - - + -
1069A ILE* 3.5 29.5 + - + +
1102A ARG 3.1 15.7 + - - +
1103A VAL* 4.0 6.5 - - + +
1104A MET 3.3 0.2 - - - -
1105A LEU* 1.3 78.5 - - - +
1107A GLN* 1.3 71.3 + - + +
1109A SER* 3.1 26.7 + - - -
1110A GLU* 3.2 44.0 + - + +
1140A LEU* 4.5 12.3 - - + -
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Residues in contact with GLN1107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A ARG* 5.2 4.4 - - - +
1103A VAL* 3.2 36.8 + - + +
1104A MET* 3.9 5.8 - - - +
1106A TYR* 1.3 83.3 - - + +
1108A ILE* 1.3 61.7 + - - +
1110A GLU* 3.6 17.9 + - + +
1111A GLU* 3.7 15.6 + - - +
1174A ILE* 3.9 26.9 - - + +
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Residues in contact with ILE1108 (chain A).
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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1104A MET* 3.3 37.4 + - + +
1105A LEU* 3.2 10.7 + - + +
1106A TYR 3.1 0.6 - - - -
1107A GLN* 1.3 73.9 - - - +
1109A SER* 1.3 61.9 + - - +
1110A GLU 3.0 6.9 + - - -
1111A GLU* 3.2 12.4 + - - +
1112A VAL* 3.4 19.1 - - + +
1120A PHE* 6.0 0.7 - - + -
1139A LEU* 4.3 7.0 - - + -
1143A PHE* 4.1 16.8 - - + -
1160A LEU* 4.4 10.1 - - + -
1164A CYS* 4.5 14.4 - - - -
1171A LEU* 4.5 12.7 - - + +
1174A ILE* 4.0 21.1 - - + -
1175A ILE* 3.9 23.6 - - + -
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Residues in contact with SER1109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105A LEU 3.1 7.3 + - - -
1106A TYR* 3.1 16.1 + - - -
1108A ILE* 1.3 76.4 - - - +
1110A GLU* 1.3 67.2 + - - +
1111A GLU 3.5 0.2 - - - -
1112A VAL* 3.7 15.8 - - - +
1139A LEU* 3.6 26.5 - - - +
1140A LEU* 3.7 40.6 - - - +
1143A PHE* 4.9 0.4 - - - -
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Residues in contact with GLU1110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017A GLU* 5.3 6.8 - - - +
1021A SER* 5.0 2.6 + - - -
1106A TYR* 3.2 49.7 + - + +
1107A GLN* 3.6 13.9 - - - +
1108A ILE 3.0 0.6 - - - -
1109A SER* 1.3 86.9 + - - +
1111A GLU* 1.3 61.4 + - + +
1112A VAL 3.3 6.2 + - - +
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Residues in contact with GLU1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107A GLN 3.7 13.4 + - - +
1108A ILE 3.2 4.1 + - - +
1110A GLU* 1.3 79.2 - - + +
1112A VAL* 1.3 62.7 + - - +
1116A GLU* 2.8 18.0 - - - +
1168A ASN* 4.5 7.7 + - - +
1171A LEU* 3.6 27.2 - - + +
1174A ILE* 4.6 9.6 - - + -
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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