Contacts of the helix formed by residues 1004 - 1015 (chain A) in PDB entry 6UPX
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 ASN1004 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002A GLY* 3.3 2.4 - - - -
1003A LYS* 1.3 87.3 + - - +
1005A GLU* 1.3 65.4 + - - +
1006A ILE* 3.4 8.1 - - + +
1007A ILE* 3.3 31.6 - - + +
1008A GLN* 3.2 24.5 + - - +
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Residues in contact with GLU1005 (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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1003A LYS 4.1 0.2 + - - -
1004A ASN* 1.3 72.3 - - - +
1006A ILE* 1.3 62.8 + - + +
1008A GLN* 3.5 3.2 + - - -
1009A ASN* 2.4 55.5 + - - +
1012A ARG* 5.9 1.3 - - - +
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Residues in contact with ILE1006 (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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1004A ASN* 3.4 5.1 - - + -
1005A GLU* 1.3 80.9 - - + +
1007A ILE* 1.3 63.7 + - + +
1009A ASN* 3.3 6.6 + - + +
1010A ALA* 2.9 28.5 + - + +
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Residues in contact with ILE1007 (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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1000A LEU* 3.8 40.5 - - + +
1002A GLY* 4.0 26.9 - - - +
1004A ASN* 3.3 31.5 + - + +
1005A GLU 3.4 0.2 - - - -
1006A ILE* 1.3 80.0 - - + +
1008A GLN* 1.3 58.1 + - - +
1010A ALA* 3.3 5.9 + - - +
1011A GLN* 2.9 26.7 + - - +
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Residues in contact with GLN1008 (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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998A LEU* 5.7 2.8 - - - +
1000A LEU 4.5 6.6 + - - -
1001A ARG* 4.5 7.5 + - - +
1002A GLY 2.5 24.5 + - - +
1003A LYS* 4.2 12.8 - - - +
1004A ASN 3.2 19.8 + - - +
1005A GLU* 4.0 4.7 - - - +
1007A ILE* 1.3 75.0 - - - +
1009A ASN* 1.3 59.2 + - - +
1011A GLN* 3.2 15.1 + - - +
1012A ARG* 2.9 48.4 + - - +
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Residues in contact with ASN1009 (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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1005A GLU* 2.4 57.8 + - - +
1006A ILE* 3.6 7.0 - - + +
1008A GLN* 1.3 75.6 - - - +
1010A ALA* 1.3 60.9 + - - +
1012A ARG* 3.3 30.2 + - - +
1013A ASP* 2.9 38.3 + - - +
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Residues in contact with ALA1010 (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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867A ILE* 4.1 18.8 - - + +
1000A LEU* 4.8 11.0 - - + -
1006A ILE* 2.9 17.4 + - + +
1007A ILE* 3.6 9.2 - - + +
1009A ASN* 1.3 75.0 - - - +
1011A GLN* 1.3 58.3 + - - +
1013A ASP* 3.7 9.9 - - - +
1014A ALA* 2.9 30.5 + - - +
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Residues in contact with GLN1011 (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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994A GLN 5.2 4.4 + - - -
995A GLU 5.4 3.8 + - - -
997A LEU 2.9 27.4 + - - +
998A LEU* 4.4 6.0 - - + +
999A VAL* 3.0 16.2 + - + +
1000A LEU* 3.5 38.6 - - + +
1007A ILE 2.9 14.7 + - - +
1008A GLN* 3.4 19.5 + - - +
1009A ASN 3.2 0.4 - - - -
1010A ALA* 1.3 74.8 - - - +
1012A ARG* 1.3 69.2 + - - +
1014A ALA* 3.3 11.9 + - - +
1015A VAL* 3.2 29.9 + - - +
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Residues in contact with ARG1012 (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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995A GLU* 5.8 2.5 + - - -
1005A GLU* 5.9 1.4 - - - +
1008A GLN* 2.9 33.5 + - - +
1009A ASN* 3.4 43.9 + - - +
1011A GLN* 1.3 82.6 - - - +
1013A ASP* 1.3 53.6 + - - +
1015A VAL* 3.8 8.4 - - - +
1016A THR* 2.3 33.3 + - - -
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Residues in contact with ASP1013 (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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867A ILE* 5.8 2.9 - - + -
870A GLU 5.3 0.9 - - - +
1009A ASN* 2.9 26.6 + - - +
1010A ALA* 3.7 8.9 - - - +
1011A GLN 3.2 0.2 - - - -
1012A ARG* 1.3 80.6 - - - +
1014A ALA* 1.3 61.2 + - - +
1016A THR* 3.1 20.7 + - - -
1017A LEU 5.1 0.2 + - - -
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Residues in contact with ALA1014 (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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867A ILE* 4.3 16.4 - - + +
870A GLU 4.5 9.0 - - - -
871A ASP* 3.7 37.7 - - - +
999A VAL* 4.5 14.9 - - + +
1000A LEU* 6.5 0.2 - - + -
1010A ALA 2.9 18.7 + - - +
1011A GLN* 3.3 7.3 + - - +
1013A ASP* 1.3 76.3 - - - +
1015A VAL* 1.3 61.5 + - + +
1016A THR 3.5 0.4 - - - -
1017A LEU 5.5 0.2 + - - -
1018A PHE* 5.9 0.2 - - - +
1053A PHE* 5.8 0.5 - - - -
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Residues in contact with VAL1015 (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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994A GLN 5.2 3.8 - - - +
997A LEU* 3.9 12.1 - - + +
999A VAL* 4.1 5.8 - - + -
1011A GLN* 3.2 43.5 - - - +
1012A ARG* 3.8 11.7 - - - +
1013A ASP 3.3 0.2 - - - -
1014A ALA* 1.3 78.6 - - - +
1016A THR* 1.3 54.8 + - - +
1017A LEU 3.4 2.0 - - - -
1018A PHE* 3.3 9.5 + - + +
1019A CYS* 2.7 52.7 + - - +
1053A PHE* 3.9 23.1 - - + -
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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