Contacts of the helix formed by residues 73 - 85 (chain A) in PDB entry 4XIH
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 PRO 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY* 1.3 85.1 - - - +
74A PRO* 1.3 78.8 - - + +
75A PRO* 3.8 10.5 - - + -
76A THR* 3.1 33.0 + - + +
77A HIS* 3.3 10.1 + - - -
92A SER* 3.2 5.4 - - - +
94A PHE* 3.9 36.5 - - + -
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Residues in contact with PRO 74 (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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14A ARG* 4.0 11.9 - - + -
15A ASP 3.6 20.4 - - - +
16A GLN* 3.7 14.4 - - - +
18A GLN* 3.6 33.4 - - + +
73A PRO* 1.3 88.9 - - + +
75A PRO* 1.3 59.3 - - + +
77A HIS* 3.2 3.8 + - - +
78A LYS* 2.7 36.9 + - - +
92A SER* 3.1 18.1 - - - +
94A PHE* 5.5 1.8 - - + -
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Residues in contact with PRO 75 (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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18A GLN* 4.5 8.3 - - - +
73A PRO* 3.4 14.4 - - + -
74A PRO* 1.3 99.4 - - + +
76A THR* 1.3 59.5 + - - +
78A LYS* 3.6 6.9 - - + +
79A ILE* 3.1 31.4 + - - +
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 3.8 17.3 - - + -
41A PHE* 3.6 28.9 - - + -
72A GLY* 4.9 4.3 - - - -
73A PRO* 3.1 33.2 + - + +
75A PRO* 1.3 80.6 - - - +
77A HIS* 1.3 66.6 + - + +
79A ILE* 3.5 1.7 + - - +
80A TRP* 3.1 22.7 + - - +
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Residues in contact with HIS 77 (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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16A GLN* 3.8 14.6 - - + -
37A PHE* 3.8 14.6 - + - -
40A ALA* 4.4 14.7 - - + +
70A SER* 2.7 28.6 + - - -
72A GLY* 3.0 28.7 + - - -
73A PRO 3.3 3.1 + - - -
74A PRO* 3.2 6.9 + - - +
76A THR* 1.3 79.1 - - + +
78A LYS* 1.3 60.8 + - - +
80A TRP* 3.9 4.2 - - - +
81A ALA* 2.8 33.3 + - - +
90A LEU* 3.7 30.5 + - + +
91A LEU 3.4 19.5 - - - -
92A SER* 3.3 13.3 + - - -
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Residues in contact with LYS 78 (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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16A GLN* 3.5 22.9 - - + +
17A ASN* 2.9 31.4 + - - +
74A PRO 2.7 21.7 + - - +
75A PRO* 3.6 9.4 - - + +
77A HIS* 1.3 74.7 - - - +
79A ILE* 1.3 67.4 + - + +
81A ALA* 3.6 1.7 - - + +
82A THR* 2.9 40.2 + - - +
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Residues in contact with ILE 79 (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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41A PHE* 4.2 13.2 - - + -
75A PRO* 3.1 17.1 + - + +
76A THR* 3.9 3.4 - - - +
78A LYS* 1.3 83.2 - - + +
80A TRP* 1.3 59.4 + - - +
82A THR* 3.3 8.4 + - - +
83A GLN* 3.0 48.1 + - + +
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Residues in contact with TRP 80 (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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37A PHE* 3.4 23.3 - + - -
40A ALA* 3.5 18.4 - - + -
41A PHE* 3.3 48.1 - + + +
45A CYS* 3.9 15.0 - - + -
46A GLN* 2.7 46.1 + - + -
49A LEU* 3.3 35.2 - - + -
76A THR 3.1 17.9 + - - +
77A HIS* 3.9 2.9 - + - +
79A ILE* 1.3 76.6 - - - +
81A ALA* 1.3 58.8 + - - +
83A GLN* 3.4 6.6 + - + +
84A SER* 2.9 39.8 + - - -
86A PHE* 3.9 11.9 - + - -
90A LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 81 (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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16A GLN* 4.2 18.8 - - + +
77A HIS 2.8 23.3 + - - +
78A LYS* 3.6 4.5 - - + +
80A TRP* 1.3 73.9 - - - +
82A THR* 1.3 54.8 + - - +
85A GLY* 2.7 30.1 + - - -
86A PHE* 2.8 46.2 + - + +
90A LEU* 4.6 3.1 - - + -
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Residues in contact with THR 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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78A LYS* 2.9 34.7 + - - +
79A ILE* 3.5 9.9 - - - +
81A ALA* 1.3 78.8 - - - +
83A GLN* 1.3 61.4 + - + +
85A GLY* 3.7 6.6 + - - -
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Residues in contact with GLN 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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41A PHE* 3.7 21.1 - - - -
79A ILE* 3.0 35.8 + - + +
80A TRP* 3.8 6.0 - - + +
82A THR* 1.3 78.4 - - + +
84A SER* 1.3 62.2 + - - +
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Residues in contact with SER 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 GLN* 2.7 30.6 + - - +
50A ASP* 4.5 0.4 - - - -
53A ARG* 2.6 33.2 + - - +
80A TRP* 2.9 23.8 + - - -
83A GLN* 1.3 77.9 - - - +
85A GLY* 1.3 63.6 + - - +
86A PHE* 3.2 28.7 - - - -
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Residues in contact with GLY 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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53A ARG* 3.6 17.8 - - - +
81A ALA 2.7 13.9 + - - -
82A THR* 3.7 6.4 + - - -
83A GLN 3.5 2.6 - - - -
84A SER* 1.3 74.8 - - - +
86A PHE* 1.3 60.1 + - - -
87A THR* 3.6 11.4 + - - +
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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