Contacts of the helix formed by residues 107 - 117 (chain D) in PDB entry 1Z6T
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 THR 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D GLY* 3.6 5.9 + - - +
106D ILE* 1.3 78.4 - - - +
108D SER* 1.3 58.8 + - - +
109D TYR* 3.6 4.4 - - - +
110D VAL* 3.2 18.0 + - - +
111D ARG* 3.0 34.5 + - - +
171D HIS* 2.7 44.2 + - + +
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Residues in contact with SER 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TYR* 3.4 25.6 - - - -
73D ASN* 3.5 10.4 + - - -
76D LEU* 3.4 20.2 - - - +
107D THR* 1.3 70.8 - - - +
109D TYR* 1.3 61.5 + - - +
111D ARG* 3.3 8.4 + - - +
112D THR* 2.9 35.4 + - - -
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D THR* 3.6 8.5 - - - +
108D SER* 1.3 79.6 - - - +
110D VAL* 1.3 65.8 + - + +
112D THR* 3.5 3.9 + - - -
113D VAL* 3.0 50.6 + - + +
171D HIS* 3.6 28.7 - + + -
174D LEU* 4.1 15.5 + - + +
175D GLU* 3.7 43.0 + - + +
178D PHE 4.7 1.6 + - - -
179D PRO* 4.2 16.1 + - - +
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLY 3.6 5.8 - - - +
106D ILE* 4.4 6.5 - - + -
107D THR* 3.2 21.2 + - - +
109D TYR* 1.3 77.2 - - + +
111D ARG* 1.3 63.8 + - - +
113D VAL* 3.9 0.3 - - - +
114D LEU* 3.0 32.7 + - + +
169D ARG* 3.8 37.9 - - + -
170D ASP 3.6 2.7 - - - +
171D HIS* 3.3 40.2 - - - +
174D LEU* 4.0 13.7 - - + -
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ASN* 3.3 54.5 + - - +
76D LEU* 3.9 17.5 - - + +
77D HIS* 4.3 26.7 - - + +
106D ILE* 3.2 46.8 + - + +
107D THR* 3.0 22.3 + - - +
108D SER* 3.3 7.1 + - - +
110D VAL* 1.3 76.2 - - - +
112D THR* 1.3 56.2 + - - +
114D LEU* 4.1 3.2 - - - +
115D CYS* 3.2 29.8 + - - +
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU* 3.4 27.6 - - - +
81D LYS* 5.0 15.5 - - + -
108D SER 2.9 18.0 + - - -
109D TYR* 3.8 5.2 - - - -
111D ARG* 1.3 73.9 - - - +
113D VAL* 1.3 70.6 + - + +
114D LEU 3.3 0.2 + - - -
115D CYS* 3.4 4.2 + - - +
116D GLU* 2.9 47.1 + - + +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TYR* 3.0 45.8 + - + +
110D VAL 4.0 2.0 - - - +
112D THR* 1.3 81.7 - - + +
114D LEU* 1.3 65.4 + - + +
116D GLU* 3.6 14.1 + - - +
117D GLY* 3.1 18.7 + - - -
174D LEU* 3.7 30.5 - - + -
178D PHE 5.6 0.2 - - - +
181D GLY* 4.1 24.9 - - - -
182D VAL 4.3 7.2 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 3.0 24.8 + - + +
111D ARG* 4.1 3.4 - - - +
113D VAL* 1.3 71.1 - - - +
115D CYS* 1.3 64.9 + - - +
117D GLY 3.2 2.6 + - - -
118D GLY 3.1 4.2 + - - -
119D VAL* 3.0 46.3 + - + +
168D VAL* 3.6 33.0 - - + +
169D ARG* 3.6 56.3 - - + +
174D LEU* 4.1 9.6 - - + -
182D VAL* 3.8 15.0 - - + -
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Residues in contact with CYS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU 3.8 8.5 - - - +
77D HIS 4.2 6.7 - - - +
78D GLU 3.9 3.8 - - - -
79D GLY* 3.0 41.7 - - - -
111D ARG 3.2 17.1 + - - +
112D THR* 3.8 3.6 - - - +
114D LEU* 1.3 78.5 - - - +
116D GLU* 1.3 63.9 + - + +
118D GLY* 2.9 15.1 + - - -
119D VAL 5.0 4.0 - - - +
121D GLN* 4.7 2.2 - - - -
428D ARG 4.1 10.5 - - - -
429D ASN* 3.5 25.0 - - - +
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LYS* 2.9 47.4 + - + +
112D THR* 2.9 37.6 + - + +
113D VAL* 3.6 13.9 - - - +
115D CYS* 1.3 72.4 - - + +
117D GLY* 1.3 58.6 + - - +
118D GLY 3.6 0.7 + - - -
183D HIS* 4.3 10.7 + - - +
205D ARG* 5.5 2.9 + - - -
208D GLN* 5.5 4.5 + - - -
429D ASN* 5.0 2.7 - - - -
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL 3.1 11.1 + - - -
114D LEU 3.2 3.8 + - - -
115D CYS 3.1 0.4 - - - -
116D GLU* 1.3 75.6 - - - +
118D GLY* 1.3 59.6 + - - +
119D VAL* 3.3 3.4 - - - -
182D VAL* 3.1 27.1 + - - -
183D HIS* 3.6 7.6 - - - -
184D TRP 2.9 27.0 + - - -
205D ARG* 3.2 11.8 + - - -
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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