Contacts of the helix formed by residues 1002 - 1011 (chain A) in PDB entry 3UON
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 ASN1002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A CYS 6.0 0.2 + - - -
128A PRO* 5.0 16.3 - - + +
217A ILE* 1.3 75.7 - - - +
383A LYS* 4.4 17.0 - - - +
1003A ILE* 1.3 66.7 + - + +
1004A PHE* 2.9 13.7 + - - +
1005A GLU* 2.9 35.9 + - - +
1006A MET* 2.8 21.7 + - - +
1158A TRP* 3.9 10.8 - - + -
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Residues in contact with ILE1003 (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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128A PRO* 4.8 15.7 - - + +
129A LEU* 3.9 19.5 - - + -
1002A ASN* 1.3 76.8 - - + +
1004A PHE* 1.3 61.7 - - + +
1006A MET* 3.5 8.1 - - - +
1007A LEU* 3.0 48.6 + - + +
1067A PHE* 4.0 15.7 - - + -
1071A VAL* 4.3 9.0 - - + -
1097A ALA* 3.9 21.8 - - + +
1100A ILE* 3.6 48.7 - - + -
1158A TRP* 3.8 9.1 - - - -
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Residues in contact with PHE1004 (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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383A LYS* 4.8 11.7 - - - +
1002A ASN* 3.0 11.8 + - - +
1003A ILE* 1.3 79.0 - - + +
1005A GLU* 1.3 92.3 + - - +
1007A LEU* 3.3 2.1 + - - +
1008A ARG* 2.9 40.9 + - - +
1013A LEU* 4.2 20.2 - - + -
1029A ILE* 3.6 21.0 - - + +
1060A LYS* 6.2 0.7 - - - -
1063A ALA 6.0 0.2 - - - -
1064A GLU* 4.1 38.6 - - + +
1067A PHE* 3.5 34.1 - + + -
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Residues in contact with GLU1005 (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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216A ARG 5.0 2.2 - - - +
217A ILE* 4.2 21.1 - - + -
379A PRO* 3.6 26.1 - - + +
383A LYS* 3.6 28.9 - - - +
1002A ASN* 2.9 40.0 + - - +
1004A PHE* 1.3 81.8 - - - +
1006A MET* 1.3 63.5 + - - +
1008A ARG* 3.1 24.4 + - + +
1009A ILE* 3.0 32.3 + - + +
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Residues in contact with MET1006 (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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217A ILE* 4.4 3.5 - - + +
1002A ASN 2.8 11.7 + - - +
1003A ILE* 3.5 11.0 - - - +
1005A GLU* 1.3 77.2 - - - +
1007A LEU* 1.3 61.1 + - + +
1009A ILE* 3.2 5.2 + - - +
1010A ASP* 3.0 33.6 + - - +
1097A ALA* 4.1 21.8 - - - +
1098A ALA* 4.5 7.4 - - - +
1101A ASN* 3.5 27.4 - - - +
1149A VAL* 5.5 0.9 - - + -
1152A THR* 4.0 17.0 - - + +
1158A TRP* 3.4 33.2 - - + -
1161A TYR* 3.5 41.7 - - + +
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Residues in contact with LEU1007 (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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1003A ILE* 3.0 32.2 + - + +
1004A PHE 4.1 0.2 - - - +
1006A MET* 1.3 73.7 - - + +
1008A ARG* 1.3 60.3 + - - +
1009A ILE 3.2 0.4 - - - -
1010A ASP* 3.8 2.5 - - + +
1011A GLU* 2.9 25.2 + - - +
1029A ILE* 3.3 17.8 - - + +
1067A PHE* 3.2 38.6 - - + -
1100A ILE* 4.9 1.3 - - + -
1101A ASN* 3.3 46.7 - - + +
1104A PHE* 3.8 31.2 - - + -
1145A ARG* 4.4 7.9 - - - +
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Residues in contact with ARG1008 (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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379A PRO* 6.0 4.5 - - - +
1004A PHE* 2.9 31.9 + - + +
1005A GLU* 3.1 36.3 + - - +
1007A LEU* 1.3 76.3 - - - +
1009A ILE* 1.3 63.0 + - + +
1012A GLY* 2.8 31.6 - - - -
1013A LEU* 4.0 33.9 + - + +
1029A ILE* 3.7 16.1 - - + +
1060A LYS* 4.4 23.4 - - - +
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Residues in contact with ILE1009 (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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217A ILE* 4.9 3.6 - - + -
377A PRO* 3.6 37.9 - - + +
1005A GLU* 3.0 23.5 + - + +
1006A MET 3.3 6.7 - - - +
1008A ARG* 1.3 84.5 - - + +
1010A ASP* 1.3 62.8 + - - +
1012A GLY* 4.0 2.8 + - - -
1148A ARG* 4.2 29.2 + - - +
1161A TYR* 3.7 23.3 - - + -
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Residues in contact with ASP1010 (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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1006A MET 3.0 16.9 + - - +
1007A LEU* 4.4 2.7 - - - +
1009A ILE* 1.3 79.7 - - - +
1011A GLU* 1.3 61.4 + - - +
1012A GLY 3.9 0.2 + - - -
1101A ASN* 2.6 27.7 + - - +
1145A ARG* 3.4 43.1 + - - +
1148A ARG* 2.7 43.6 + - - +
1161A TYR* 2.9 15.0 + - - -
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Residues in contact with GLU1011 (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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1007A LEU* 2.9 18.3 + - + +
1010A ASP* 1.3 73.2 - - + +
1012A GLY* 1.3 64.7 + - - +
1014A ARG* 6.0 0.7 - - - +
1018A TYR* 4.0 17.2 + - - -
1029A ILE* 3.4 8.4 - - + +
1030A GLY* 3.3 32.8 - - - +
1104A PHE* 3.4 37.7 - - - +
1105A GLN* 3.8 1.7 + - - -
1145A ARG* 3.0 42.6 + - - +
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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