Contacts of the helix formed by residues 104 - 111 (chain A) in PDB entry 1XTE
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 HIS 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.8 18.3 - - + +
58A GLN* 2.7 35.4 + - - -
59A PHE* 4.3 10.1 - - - -
100A GLU 3.6 15.4 + - - +
101A LEU* 2.9 18.6 + - + +
103A ASN* 1.3 77.6 - - - +
105A PRO* 1.3 78.6 - - + +
106A ASP* 3.0 52.4 + - + +
107A VAL* 3.0 8.5 + - + +
108A ARG* 2.9 23.0 + - - +
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Residues in contact with PRO 105 (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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103A ASN 3.6 7.2 - - - +
104A HIS* 1.3 94.2 - - + +
106A ASP* 1.3 63.6 + - - +
108A ARG* 3.5 8.1 + - + +
109A ALA* 3.0 28.6 + - - +
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Residues in contact with ASP 106 (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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51A LEU* 3.7 20.7 - - + +
54A SER* 4.3 19.2 + - - -
55A LEU* 5.4 0.7 - - + -
58A GLN* 4.8 3.6 + - - -
104A HIS* 3.0 25.3 + - + +
105A PRO* 1.3 84.0 - - - +
107A VAL* 1.3 58.5 + - - +
109A ALA* 3.6 5.0 + - - +
110A PHE* 3.0 27.5 + - - +
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Residues in contact with VAL 107 (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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51A LEU* 4.2 7.9 - - + -
55A LEU* 3.8 28.9 - - + -
95A LEU* 4.4 15.9 - - + +
96A VAL* 5.1 4.5 - - + -
101A LEU* 3.2 32.8 - - + +
102A TYR* 4.1 12.1 - - + -
104A HIS* 3.0 11.3 + - + +
106A ASP* 1.3 73.7 - - - +
108A ARG* 1.3 68.6 + - - +
110A PHE* 3.1 5.5 + - - +
111A LEU* 2.9 44.2 + - + +
113A MET* 5.2 0.9 - - - -
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Residues in contact with ARG 108 (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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5A GLU* 5.4 6.9 + - - -
102A TYR* 3.0 41.9 + - - +
103A ASN* 3.9 29.1 - - - +
104A HIS 2.9 16.5 + - - +
105A PRO* 3.9 6.7 - - + +
107A VAL* 1.3 77.6 - - - +
109A ALA* 1.3 57.0 + - - +
111A LEU 3.5 0.2 + - - -
112A GLN* 2.9 8.0 + - - -
113A MET* 2.9 66.5 + - + +
114A ASP* 2.8 47.7 + - - +
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Residues in contact with ALA 109 (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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43A ARG* 3.2 5.6 + - - -
105A PRO 3.0 18.7 + - - +
106A ASP* 3.9 5.8 - - - +
108A ARG* 1.3 76.1 - - - +
110A PHE* 1.3 66.3 + - - +
112A GLN* 3.0 31.9 + - - +
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Residues in contact with PHE 110 (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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30A VAL* 5.2 3.1 - - + -
41A VAL* 3.5 8.1 - - - +
43A ARG* 3.0 65.9 + - + +
47A GLU* 3.7 33.2 - - + -
48A PHE* 3.5 41.5 - + - -
51A LEU* 3.8 27.6 - - + -
92A ILE* 4.2 8.7 - - + -
106A ASP 3.0 19.0 + - - +
107A VAL 3.1 4.7 + - - +
109A ALA* 1.3 76.2 - - - +
111A LEU* 1.3 79.8 + - + +
112A GLN 3.4 0.2 - - - -
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Residues in contact with LEU 111 (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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8A PRO* 5.4 1.1 - - + -
10A VAL* 4.2 11.9 - - + -
30A VAL* 4.3 12.1 - - + -
32A VAL* 3.9 22.2 - - + +
39A TRP* 2.9 27.0 + - - -
41A VAL* 3.6 7.7 - - + +
92A ILE* 4.8 8.3 - - + -
96A VAL* 3.7 29.8 - - + -
107A VAL* 2.9 31.4 + - + +
110A PHE* 1.3 102.4 - - + +
112A GLN* 1.3 61.7 + - - +
113A MET* 3.3 22.5 + - + -
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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