Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1DXO
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 SER 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LYS 4.1 7.3 + - - -
54A ASP* 2.8 32.2 + - - -
56A THR* 3.8 7.6 - - - +
80A LEU* 1.3 72.6 - - - +
82A PRO* 1.3 70.6 - - - +
83A ASP* 2.6 22.7 + - - -
84A ILE* 2.9 28.4 + - - +
85A VAL 3.0 9.5 + - - -
118A ARG* 4.5 3.5 + - - -
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Residues in contact with PRO 82 (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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56A THR* 3.9 14.4 - - + +
80A LEU 3.2 6.3 - - - +
81A SER* 1.3 87.4 - - - +
83A ASP* 1.3 61.0 + - - +
85A VAL* 3.7 8.7 - - + +
86A ALA* 3.0 24.1 + - - +
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Residues in contact with ASP 83 (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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44A MET* 5.9 0.5 - - - +
46A PHE* 4.7 8.1 - - + -
47A ASN* 4.4 6.8 + - - +
81A SER* 2.6 31.9 + - - -
82A PRO* 1.3 76.9 - - - +
84A ILE* 1.3 66.7 + - - +
86A ALA* 3.6 7.8 + - - +
87A GLU* 3.4 23.9 + - - +
118A ARG* 2.3 31.5 + - - -
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Residues in contact with ILE 84 (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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46A PHE* 5.8 1.6 - - + -
54A ASP* 3.7 26.9 - - + +
67A TYR* 4.5 2.2 - - - +
80A LEU* 4.0 17.0 - - + -
81A SER* 2.9 14.2 + - - +
83A ASP* 1.3 77.2 + - - +
85A VAL* 1.3 67.4 + - - +
87A GLU* 3.0 18.9 + - - +
88A GLN* 3.1 36.8 + - + +
118A ARG* 3.4 67.1 - - + +
119A VAL* 4.5 5.2 - - + +
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Residues in contact with VAL 85 (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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78A GLY 6.3 0.7 - - - -
80A LEU* 3.4 35.4 - - + +
81A SER 3.0 13.0 + - - +
82A PRO* 3.4 9.8 + - + +
84A ILE* 1.3 77.0 - - - +
86A ALA* 1.3 55.8 + - - +
88A GLN* 3.3 13.6 + - + +
89A LYS* 2.9 55.5 + - + +
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Residues in contact with ALA 86 (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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82A PRO 3.0 18.3 + - - +
83A ASP* 3.6 9.6 - - - +
85A VAL* 1.3 76.4 - - - +
87A GLU* 1.3 67.1 + - - +
89A LYS* 3.5 12.0 + - - +
90A LYS* 3.2 31.0 + - - +
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Residues in contact with GLU 87 (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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6A LEU* 5.1 0.2 - - - +
39A SER* 2.8 22.3 + - - -
44A MET* 3.2 20.5 - - + +
46A PHE* 4.2 8.7 - - + -
83A ASP 3.4 15.6 - - - +
84A ILE 3.0 6.6 + - - +
86A ALA* 1.3 76.4 - - - +
88A GLN* 1.3 66.1 + - - +
90A LYS* 2.9 36.1 + - - +
91A LEU* 3.1 23.2 + - - +
115A TRP* 2.7 33.9 + - + +
119A VAL* 3.5 23.8 - - + -
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Residues in contact with GLN 88 (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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75A TYR* 3.6 14.4 - - - -
80A LEU* 3.4 34.3 - - - +
84A ILE* 3.1 23.8 + - + +
85A VAL* 3.3 15.4 + - + +
87A GLU* 1.3 76.5 - - - +
89A LYS* 1.3 61.5 + - + +
91A LEU* 3.1 5.5 + - - +
92A GLU* 3.0 29.5 + - - +
119A VAL* 3.0 25.9 + - + +
121A ILE* 4.0 5.7 - - - +
124A PHE* 3.3 39.6 - - + -
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Residues in contact with LYS 89 (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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85A VAL* 2.9 43.3 + - + +
86A ALA* 3.6 11.2 - - - +
87A GLU 3.2 0.2 - - - -
88A GLN* 1.3 75.7 - - + +
90A LYS* 1.3 62.9 + - + +
92A GLU* 3.4 16.8 + - - +
93A ALA* 3.2 22.5 + - - +
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Residues in contact with LYS 90 (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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6A LEU* 4.0 25.1 - - + +
37A VAL* 4.2 15.5 - - + +
38A GLU 3.2 14.9 + - - +
39A SER* 3.1 23.4 + - - +
44A MET* 3.9 12.1 - - - +
86A ALA* 3.2 19.5 - - - +
87A GLU* 2.9 35.2 + - - +
89A LYS* 1.3 76.9 - - + +
91A LEU* 1.3 57.1 + - - +
93A ALA* 3.4 6.9 + - - +
94A ALA* 3.1 28.2 + - - +
115A TRP* 6.4 0.2 - - + -
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Residues in contact with LEU 91 (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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6A LEU* 4.4 8.5 - - + +
87A GLU 3.1 8.1 + - - +
88A GLN 3.1 8.5 + - - +
90A LYS* 1.3 75.0 - - - +
92A GLU* 1.3 62.5 + - - +
93A ALA 3.0 2.4 + - - -
94A ALA* 3.2 8.7 + - - +
97A VAL* 4.2 13.7 - - + -
99A PHE* 6.1 0.2 - - + -
115A TRP* 4.4 11.4 - - + -
119A VAL* 3.7 20.9 - - + -
120A PHE* 3.4 32.1 - - + -
124A PHE* 3.7 20.4 - - + -
137A PHE* 3.9 10.3 - - + -
140A LYS* 2.8 30.4 + - + +
181A PHE* 4.2 26.2 - - + -
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Residues in contact with GLU 92 (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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4A ARG* 5.3 0.2 + - - -
75A TYR* 4.2 9.4 + - - -
88A GLN* 3.0 20.4 + - - +
89A LYS* 3.4 19.5 + - - +
91A LEU* 1.3 76.7 - - - +
93A ALA* 1.3 57.3 + - - +
124A PHE* 3.6 28.6 - - + -
137A PHE* 5.6 2.0 - - + -
140A LYS* 3.1 18.6 + - - +
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Residues in contact with ALA 93 (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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4A ARG* 2.6 52.6 + - - +
37A VAL* 6.3 3.4 - - + -
89A LYS 3.2 13.4 + - - +
90A LYS* 3.6 11.0 - - - +
91A LEU 3.0 0.6 - - - -
92A GLU* 1.3 79.7 - - - +
94A ALA* 1.3 63.3 + - - +
95A ASP* 3.6 1.7 + - - +
140A LYS* 4.6 0.2 + - - -
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Residues in contact with ALA 94 (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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4A ARG* 3.8 7.2 - - - -
5A ALA 4.5 0.9 - - - -
6A LEU* 3.7 15.7 - - + +
90A LYS 3.1 16.3 + - - +
91A LEU* 3.2 5.5 + - - +
93A ALA* 1.3 76.9 - - - +
95A ASP* 1.3 59.5 + - - +
96A LEU 3.7 7.9 - - - +
97A VAL* 3.7 26.7 - - + -
140A LYS* 2.5 36.4 + - - +
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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