Contacts of the helix formed by residues 1114 - 1123 (chain C) in PDB entry 4DAJ
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 PHE1114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102C MET* 4.1 11.4 - - + -
1106C MET* 3.6 31.0 - - + -
1110C GLY 3.3 19.5 - - - -
1111C VAL* 3.5 17.4 + - + +
1112C ALA 3.3 4.2 - - - -
1113C GLY* 1.3 80.5 - - - +
1115C THR* 1.3 61.3 + - - +
1116C ASN 3.6 0.4 - - - -
1117C SER* 4.4 24.0 - - - +
1118C LEU* 3.1 32.3 + - + +
1132C ASN 5.5 2.7 - - - -
1133C LEU* 5.0 10.3 - - + -
1136C SER* 3.2 37.5 - - - -
1137C ARG* 6.0 2.7 - - + -
1138C TRP* 4.3 5.2 - + + -
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Residues in contact with THR1115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C ALA 5.6 0.4 - - - -
1113C GLY 3.9 4.5 + - - -
1114C PHE* 1.3 73.2 + - - +
1116C ASN* 1.3 65.8 + - - +
1118C LEU* 4.2 1.8 - - - +
1119C ARG* 3.3 45.4 + - - +
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Residues in contact with ASN1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115C THR* 1.3 78.2 - - - +
1117C SER* 1.3 67.0 + - - +
1119C ARG* 3.2 10.3 + - - +
1120C MET* 2.9 34.4 + - + +
1132C ASN* 3.3 26.0 - - + +
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Residues in contact with SER1117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114C PHE* 4.4 17.9 + - - +
1115C THR 3.6 0.2 - - - -
1116C ASN* 1.3 78.2 - - - +
1118C LEU* 1.3 61.4 + - - +
1120C MET* 3.5 11.9 + - - -
1121C LEU* 2.9 34.7 + - - +
1129C ALA* 3.7 9.6 - - - +
1132C ASN* 3.3 23.9 + - - +
1133C LEU* 3.5 31.4 - - - +
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Residues in contact with LEU1118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083C LYS* 5.3 6.3 - - + +
1084C LEU* 4.2 17.5 - - + -
1087C VAL* 4.0 26.2 - - + +
1099C LEU* 5.0 12.8 - - + -
1102C MET* 6.2 2.2 - - + -
1111C VAL* 3.8 23.3 - - + +
1112C ALA* 4.8 4.7 - - - +
1114C PHE* 3.1 27.8 + - + +
1115C THR* 3.8 2.0 + - - +
1116C ASN 3.2 0.6 - - - -
1117C SER* 1.3 77.0 - - - +
1119C ARG* 1.3 62.3 + - - +
1121C LEU* 2.8 38.4 + - + +
1122C GLN* 2.9 20.2 + - - +
1133C LEU* 6.5 0.4 - - + -
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Residues in contact with ARG1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115C THR* 3.3 40.9 + - + +
1116C ASN* 3.2 9.1 + - - +
1118C LEU* 1.3 79.3 - - - +
1120C MET* 1.3 66.8 + - - +
1122C GLN* 3.5 20.2 + - - +
1123C GLN* 3.3 31.7 + - - +
2002C PO4 3.0 42.6 + - - -
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Residues in contact with MET1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C ASN* 2.9 28.5 + - + +
1117C SER* 3.6 6.3 - - - +
1119C ARG* 1.3 82.1 - - + +
1121C LEU* 1.3 62.1 + - - +
1123C GLN* 3.7 8.5 + - - -
1124C LYS 3.5 1.9 + - - -
1125C ARG* 3.1 59.8 + - + +
1128C GLU* 4.4 18.4 - - - +
1129C ALA* 3.7 16.2 - - + +
1132C ASN* 3.1 48.7 - - + +
2002C PO4 5.4 1.8 - - - +
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Residues in contact with LEU1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087C VAL* 4.4 13.5 - - + -
1091C LEU* 4.3 11.0 - - + +
1099C LEU* 5.9 1.1 - - + -
1117C SER* 2.9 18.4 + - - +
1118C LEU* 2.8 39.5 + - + +
1120C MET* 1.3 75.8 - - - +
1122C GLN* 1.3 56.8 + - - +
1123C GLN 3.1 2.0 - - - -
1124C LYS* 2.8 23.6 + - - +
1126C TRP* 3.5 42.2 - - + -
1129C ALA* 4.2 13.2 - - + -
1133C LEU* 6.0 4.9 - - + -
1153C PHE* 3.7 37.7 - - + -
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Residues in contact with GLN1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B LEU* 5.1 5.4 - - - +
1083C LYS 5.6 0.4 + - - -
1086C PRO* 3.3 30.1 - - - +
1087C VAL* 3.5 32.9 + - + +
1090C SER* 4.1 20.2 + - - +
1091C LEU* 5.5 0.2 - - - -
1118C LEU* 2.9 20.8 + - - +
1119C ARG* 3.5 17.0 + - - +
1121C LEU* 1.3 75.4 - - - +
1123C GLN* 1.3 61.5 + - + +
1124C LYS* 3.1 10.6 + - - +
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Residues in contact with GLN1123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B LEU* 4.7 27.3 - - + +
484B LYS* 4.8 4.0 - - - +
1009B ILE* 5.1 1.6 - - - +
1161B TYR 4.6 11.1 - - - +
1119C ARG* 3.3 38.1 + - - +
1120C MET 4.0 0.9 - - - +
1121C LEU 3.1 0.8 - - - -
1122C GLN* 1.3 77.5 - - + +
1124C LYS* 1.3 70.1 + - - +
1125C ARG* 2.8 48.5 + - - +
2002C PO4 4.4 6.5 + - - -
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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