Contacts of the helix formed by residues 1114 - 1123 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102B MET* 3.7 28.3 - - + -
1106B MET* 4.0 15.9 - - - -
1110B GLY 3.3 20.9 - - - -
1111B VAL* 3.6 15.9 - - + -
1112B ALA 3.5 2.1 - - - -
1113B GLY* 1.3 78.4 - - - +
1115B THR* 1.3 60.6 + - - +
1116B ASN 3.6 0.7 - - - +
1117B SER* 4.3 22.9 - - - +
1118B LEU* 2.8 36.6 + - + +
1132B ASN 5.6 2.9 - - - -
1133B LEU* 5.2 6.3 - - + -
1136B SER* 3.3 34.1 - - - -
1137B ARG 5.1 1.1 - - - -
1138B TRP* 4.5 5.8 - + + -
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Residues in contact with THR1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B GLY 3.7 6.4 + - - -
1114B PHE* 1.3 71.8 - - - +
1116B ASN* 1.3 66.6 + - - +
1118B LEU* 3.3 7.5 + - - +
1119B ARG* 2.9 45.9 + - + +
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Residues in contact with ASN1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114B PHE* 3.6 0.6 - - - +
1115B THR* 1.3 77.7 - - - +
1117B SER* 1.3 64.0 + - - +
1119B ARG* 3.0 27.0 + - - +
1120B MET* 2.9 33.2 + - + +
1132B ASN* 3.2 25.8 - - + +
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Residues in contact with SER1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114B PHE* 4.3 16.9 + - - +
1115B THR 3.5 0.2 - - - -
1116B ASN* 1.3 76.3 - - - +
1118B LEU* 1.3 61.2 + - - +
1120B MET* 3.9 9.0 - - - -
1121B LEU* 2.9 35.6 + - - +
1129B ALA* 3.7 6.5 - - - +
1132B ASN* 3.1 23.8 + - - +
1133B LEU* 3.3 37.9 + - - +
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Residues in contact with LEU1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083B LYS* 5.1 11.9 - - + +
1084B LEU* 4.1 20.4 - - + -
1087B VAL* 4.2 23.1 - - + +
1099B LEU* 5.0 14.8 - - + -
1102B MET* 6.3 1.3 - - + -
1111B VAL* 4.0 21.8 - - + +
1112B ALA* 5.0 5.6 - - - +
1114B PHE* 2.8 27.6 - - + +
1115B THR* 3.5 8.3 - - - +
1116B ASN 3.1 0.6 - - - -
1117B SER* 1.3 78.8 - - - +
1119B ARG* 1.3 66.5 + - + +
1121B LEU* 3.2 14.1 + - + +
1122B GLN* 2.9 25.9 + - - +
1133B LEU* 6.3 0.7 - - + -
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Residues in contact with ARG1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115B THR* 2.9 38.2 + - + +
1116B ASN* 3.0 23.3 + - - +
1118B LEU* 1.3 78.0 - - + +
1120B MET* 1.3 70.6 + - - +
1122B GLN* 3.4 12.8 + - - +
1123B GLN* 3.2 38.2 + - - +
1125B ARG* 6.1 1.0 - - - +
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Residues in contact with MET1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116B ASN* 2.9 29.6 + - + +
1119B ARG* 1.3 83.3 - - + +
1121B LEU* 1.3 64.6 + - - +
1123B GLN* 3.0 17.5 + - - +
1125B ARG* 3.0 51.2 + - + +
1128B GLU* 3.4 33.2 - - - +
1129B ALA* 3.6 16.8 - - + -
1132B ASN* 3.0 37.5 - - + +
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Residues in contact with LEU1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087B VAL* 4.8 5.2 - - + -
1091B LEU* 3.6 15.1 - - + +
1095B ARG* 4.9 0.4 - - - -
1099B LEU* 5.8 1.6 - - + -
1102B MET* 6.4 0.2 - - - -
1117B SER* 2.9 26.1 + - - +
1118B LEU* 3.7 15.3 - - + +
1120B MET* 1.3 75.4 - - - +
1122B GLN* 1.3 58.6 + - - +
1123B GLN 3.1 0.2 - - - -
1124B LYS* 3.1 14.6 + - - -
1125B ARG 3.9 1.7 + - - -
1126B TRP* 3.2 50.5 - - + +
1129B ALA* 3.9 13.7 - - + -
1133B LEU* 5.0 9.9 - - + -
1153B PHE* 3.2 51.4 - - + +
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Residues in contact with GLN1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086B PRO* 3.5 30.7 + - - +
1087B VAL* 3.6 26.6 - - + +
1090B SER* 3.6 29.7 + - - +
1118B LEU 2.9 17.9 + - - +
1119B ARG* 3.6 11.1 - - - +
1121B LEU* 1.3 77.1 - - - +
1123B GLN* 1.3 59.3 + - + +
1124B LYS* 3.3 1.2 + - - +
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Residues in contact with GLN1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119B ARG* 3.2 25.4 + - - +
1120B MET* 3.0 12.7 + - - +
1122B GLN* 1.3 79.5 - - + +
1124B LYS* 1.3 64.7 + - - +
1125B ARG* 2.7 52.9 + - - +
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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