Contacts of the helix formed by residues 55 - 68 (chain A) in PDB entry 1XSC
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 ASP 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.2 5.7 - - - +
54A GLU* 1.3 78.9 - - - +
56A ASP* 1.3 69.2 + - - +
57A LEU* 3.0 13.5 + - - +
58A GLU* 2.9 62.4 + - + +
59A THR* 2.9 26.2 + - - -
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Residues in contact with ASP 56 (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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9A ARG* 4.2 22.1 + - - +
11A CYS* 2.9 39.3 - - - +
50A VAL* 4.2 10.0 - - - +
54A GLU 4.1 0.4 + - - -
55A ASP* 1.3 81.7 + - - +
57A LEU* 1.3 66.1 + - - +
59A THR 3.3 2.6 + - - -
82A LYS* 4.8 3.3 - - - -
97A ILE* 3.4 20.8 - - - +
99A TRP* 3.2 26.0 - - + -
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Residues in contact with LEU 57 (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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13A LEU* 4.5 0.4 - - + -
55A ASP* 3.0 7.8 + - - +
56A ASP* 1.3 75.8 - - - +
58A GLU* 1.3 54.8 + - - +
60A ALA* 2.7 11.4 + - + +
61A LEU* 2.6 60.2 + - + +
77A ILE* 3.4 34.8 - - + -
99A TRP* 3.3 53.3 - - + +
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Residues in contact with GLU 58 (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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54A GLU* 4.7 9.3 - - + +
55A ASP* 2.9 50.0 + - + +
57A LEU* 1.3 75.8 - - - +
59A THR* 1.3 53.1 + - - +
61A LEU* 2.7 20.7 + - + +
62A ARG* 2.6 39.7 + - + +
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Residues in contact with THR 59 (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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11A CYS* 3.7 5.6 - - + -
48A GLY* 3.4 21.9 - - - +
49A HIS 3.4 3.4 - - - +
50A VAL* 2.8 55.9 - - + +
54A GLU* 3.5 18.9 + - - +
55A ASP 2.9 7.8 + - - -
56A ASP 3.3 7.0 + - - -
57A LEU 3.2 0.4 - - - -
58A GLU* 1.3 77.9 - - - +
60A ALA* 1.3 57.0 + - - +
62A ARG* 4.3 2.6 - - - +
63A ALA* 3.1 30.1 + - - +
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Residues in contact with ALA 60 (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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11A CYS* 3.3 17.4 - - + +
12A GLY 3.1 29.4 - - - +
13A LEU* 3.5 8.4 - - + +
46A PRO 3.9 0.7 - - - +
56A ASP 3.5 1.8 + - - -
57A LEU* 2.7 18.0 + - + +
59A THR* 1.3 73.3 - - - +
61A LEU* 1.3 55.2 + - - +
63A ALA* 3.9 2.0 - - - +
64A THR* 2.4 33.7 + - - -
99A TRP* 3.7 17.9 - - + -
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Residues in contact with LEU 61 (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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13A LEU* 3.7 7.6 - - + -
57A LEU* 2.6 34.0 + - + +
58A GLU* 2.7 24.6 + - + +
60A ALA* 1.3 72.0 - - - +
62A ARG* 1.3 63.6 + - - +
64A THR* 3.0 21.1 + - - -
65A GLN* 3.2 11.2 + - - +
70A ILE 3.9 1.2 - - - +
71A GLU* 4.5 2.4 - - + -
72A ALA* 3.4 33.9 - - + +
77A ILE* 3.3 37.5 - - + -
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Residues in contact with ARG 62 (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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54A GLU* 4.8 13.7 + - - +
58A GLU* 2.6 21.0 + - + +
59A THR* 4.3 4.3 - - - +
61A LEU* 1.3 72.5 - - - +
63A ALA* 1.3 50.9 + - - +
65A GLN* 3.1 22.9 - - - +
66A GLU* 2.6 65.0 + - + +
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Residues in contact with ALA 63 (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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11A CYS 4.3 0.2 - - - +
46A PRO* 3.1 21.6 - - - +
48A GLY* 3.5 16.8 - - - +
59A THR 3.1 21.7 + - - +
60A ALA 3.9 1.1 - - - +
62A ARG* 1.3 77.0 - - - +
64A THR* 1.3 54.8 + - - +
66A GLU* 3.9 0.7 - - - -
67A GLU* 2.6 63.1 + - - +
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Residues in contact with THR 64 (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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13A LEU* 2.7 22.0 - - + +
15A ILE* 3.2 32.5 - - + -
46A PRO* 3.3 9.6 - - + +
60A ALA 2.4 23.8 + - - -
61A LEU* 3.0 9.1 + - - -
63A ALA* 1.3 76.5 - - - +
65A GLN* 1.3 52.8 - - - +
68A ALA* 2.6 41.5 + - + +
69A GLY 3.1 0.2 + - - -
70A ILE* 2.9 23.6 - - + +
75A LEU* 3.5 15.3 - - + -
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Residues in contact with GLN 65 (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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61A LEU 3.5 9.5 - - - +
62A ARG* 3.1 35.6 + - - +
64A THR* 1.3 75.8 - - - +
66A GLU* 1.3 63.3 + - - +
69A GLY* 2.8 26.4 + - - +
70A ILE 2.7 30.6 + - - +
71A GLU* 3.5 25.0 - - + +
111A ARG* 3.9 18.5 + - - +
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Residues in contact with GLU 66 (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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62A ARG* 2.6 56.5 + - + +
63A ALA* 3.9 0.7 - - - -
65A GLN* 1.3 81.3 - - + +
67A GLU* 1.3 70.3 + - - +
68A ALA 3.5 0.2 - - - -
111A ARG 3.7 6.2 - - - +
112A LEU 3.9 1.2 - - - +
113A SER* 2.6 33.8 + - - +
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Residues in contact with GLU 67 (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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34A LEU* 2.7 30.9 - - + +
46A PRO* 3.7 0.8 - - + +
47A LYS 2.7 34.0 + - - +
48A GLY* 5.4 0.5 - - - -
63A ALA* 2.6 40.7 + - - +
64A THR 3.5 0.2 - - - -
66A GLU* 1.3 95.9 - - - +
68A ALA* 1.3 56.8 + - - +
111A ARG 3.2 5.6 - - - -
112A LEU* 3.1 16.1 - - - +
113A SER* 4.0 16.9 + - - +
115A GLU* 4.4 12.5 - - - +
116A HIS* 3.4 29.9 - - + +
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Residues in contact with ALA 68 (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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32A LEU* 3.7 30.5 - - + -
34A LEU* 4.5 2.7 - - + -
46A PRO* 4.1 6.5 - - + -
64A THR* 2.6 21.6 + - + +
67A GLU* 1.3 77.6 - - - +
69A GLY* 1.3 52.9 + - - +
70A ILE* 3.1 12.3 + - + +
109A GLU 3.3 3.5 - - - +
110A ILE* 3.1 12.0 - - + -
111A ARG 2.6 31.4 + - - +
112A LEU* 4.2 3.6 - - - -
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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