Contacts of the helix formed by residues 106 - 116 (chain A) in PDB entry 2XFR
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A TRP* 3.6 50.9 - - + +
55A GLY* 3.9 9.4 - - - +
58A GLU 3.6 16.6 - - - +
59A GLY* 4.5 4.7 - - - -
105A ILE* 1.4 91.1 - - + +
107A GLN* 1.3 65.6 + - - +
108A TRP* 3.5 25.8 - - + +
109A VAL* 3.0 20.8 + - + +
110A ARG* 3.1 11.6 + - - +
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Residues in contact with GLN 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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59A GLY* 4.9 6.6 + - - +
105A ILE 3.3 3.9 + - - -
106A PRO* 1.3 72.1 - - - +
108A TRP* 1.3 59.4 + - - +
110A ARG* 3.1 12.7 + - + +
111A ASP* 2.8 42.7 + - - +
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Residues in contact with TRP 108 (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 TRP* 5.2 0.2 - - - -
58A GLU* 2.9 45.8 + - + -
59A GLY 3.6 12.6 - - - -
60A LYS 4.0 2.9 - - - +
61A GLY* 3.5 30.6 - - - -
62A PRO* 3.8 20.0 - - + -
106A PRO* 3.5 7.6 - - + +
107A GLN* 1.3 77.8 - - - +
109A VAL* 1.3 87.0 + - + +
111A ASP* 3.6 21.5 + - - +
112A VAL* 3.9 10.8 - - + +
143A PHE* 4.4 11.2 - - + -
144A HIS* 4.0 28.6 + + - +
146A ARG* 3.5 21.5 - - - -
151A MET* 3.6 13.7 - - - -
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Residues in contact with VAL 109 (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 TRP* 3.9 19.5 - - + -
105A ILE* 4.1 12.1 - - + -
106A PRO* 3.0 16.9 + - + +
108A TRP* 1.3 113.9 - - + +
110A ARG* 1.3 65.6 + - - +
112A VAL* 3.1 21.5 + - - +
119A ILE* 3.8 5.4 - - - +
133A LEU* 3.9 35.0 - - + -
143A PHE* 4.0 13.7 - - + -
151A MET* 4.2 3.8 - - - -
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Residues in contact with ARG 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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92A GLN* 4.5 3.6 + - - -
104A PRO* 3.4 27.6 - - - +
105A ILE* 3.8 35.7 - - + -
106A PRO 3.1 6.7 + - - +
107A GLN* 3.1 13.1 + - + +
109A VAL* 1.3 77.5 - - - +
111A ASP* 1.3 57.0 + - - +
113A GLY* 2.8 23.2 + - - -
114A THR* 3.9 2.9 + - - -
120A PHE* 4.4 19.1 - - + -
130A ILE* 3.8 39.1 - - - +
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Residues in contact with ASP 111 (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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107A GLN* 2.8 36.1 + - - +
108A TRP* 3.7 17.1 - - - +
109A VAL 3.2 0.6 - - - -
110A ARG* 1.3 77.4 - - - +
112A VAL* 1.3 62.6 + - + +
114A THR* 3.1 26.1 + - - -
115A ARG 4.4 0.9 + - - -
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Residues in contact with VAL 112 (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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108A TRP* 3.9 10.3 - - + +
109A VAL* 3.1 16.0 + - - +
111A ASP* 1.3 76.9 - - + +
113A GLY* 1.3 56.0 + - - +
114A THR 3.3 0.7 + - - -
115A ARG* 3.4 4.5 + - - +
116A ASP* 3.0 27.8 + - + +
119A ILE* 4.2 12.6 - - + -
142A LEU* 3.6 27.8 - - + +
143A PHE* 3.8 31.9 - - + -
144A HIS* 4.9 13.5 - - + +
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Residues in contact with GLY 113 (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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110A ARG 2.8 13.1 + - - -
112A VAL* 1.3 76.7 - - - +
114A THR* 1.3 63.3 + - - +
115A ARG 3.4 0.2 - - - -
116A ASP 3.3 14.6 - - - -
117A PRO* 3.2 24.6 - - - +
119A ILE* 3.6 14.7 - - - +
120A PHE* 4.2 10.2 - - - -
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Residues in contact with THR 114 (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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110A ARG 3.9 1.6 + - - -
111A ASP* 3.1 21.9 + - - -
113A GLY* 1.3 78.1 - - - +
115A ARG* 1.3 88.0 + - + +
117A PRO* 4.5 3.6 - - - +
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Residues in contact with ARG 115 (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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111A ASP 4.4 0.8 + - - -
112A VAL 3.4 5.0 + - - +
114A THR* 1.3 104.9 + - + +
116A ASP* 1.4 60.4 + - + +
117A PRO* 3.6 7.6 - - - +
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Residues in contact with ASP 116 (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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112A VAL* 3.0 16.5 + - + +
113A GLY* 3.3 14.8 - - - -
115A ARG* 1.4 79.2 - - + +
117A PRO* 1.3 63.4 - - - +
118A ASP* 3.1 24.8 + - - +
119A ILE* 3.3 19.1 + - + +
142A LEU* 3.6 17.7 - - - +
209A LYS* 3.8 12.3 + - - +
210A TYR* 2.6 27.1 + - - -
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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