Contacts of the helix formed by residues 124 - 132 (chain D) in PDB entry 1C7G
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 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B VAL* 6.2 0.4 - - - -
122D TYR* 4.3 10.3 - - + -
123D PHE* 1.3 94.4 - - + +
125D THR* 1.3 72.9 + - - +
127D ARG* 3.9 2.8 - - - +
128D PHE* 3.0 25.4 + - - +
186D LEU* 5.9 2.7 - - + +
381D ARG* 5.9 4.5 - - - +
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Residues in contact with THR 125 (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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283B VAL* 4.6 5.8 - - + +
284B VAL* 5.0 10.8 - - + -
100D ARG* 3.4 51.9 - - + +
103D GLU* 2.8 16.8 + - - -
123D PHE* 3.1 25.8 - - + -
124D THR* 1.3 85.5 + - - +
126D THR* 1.3 69.8 + - - +
128D PHE* 3.3 6.2 + - - +
129D HIS* 3.1 30.1 + - - -
1000D PLP 4.2 1.7 + - - -
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Residues in contact with THR 126 (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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103D GLU* 2.9 36.4 - - - +
107D SER* 4.7 0.5 + - - -
122D TYR* 5.5 1.7 - - - +
123D PHE* 3.2 44.1 + - + +
125D THR* 1.3 76.9 + - - +
127D ARG* 1.3 63.1 + - - +
128D PHE 3.4 0.2 + - - -
129D HIS* 3.4 4.0 + - - +
130D GLN* 3.2 36.6 + - - +
179D CYS* 4.9 6.6 - - - -
214D ASP* 4.0 7.3 + - - +
1000D PLP 3.9 5.4 - - - +
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Residues in contact with ARG 127 (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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122D TYR* 3.3 59.3 + - + -
123D PHE 2.8 19.7 + - - +
124D THR* 3.9 2.7 - - - +
126D THR* 1.3 74.0 + - - +
128D PHE* 1.3 68.0 + - - +
130D GLN* 3.1 23.0 + - - +
131D GLU* 2.6 50.9 + - - +
137D PHE* 3.5 31.2 + - + +
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Residues in contact with PHE 128 (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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281B LEU* 6.0 2.9 - - + -
284B VAL* 3.8 40.8 - - + -
285B TYR* 4.5 7.6 - + - -
124D THR 3.0 18.1 + - - +
125D THR* 3.5 5.4 - - - +
127D ARG* 1.3 75.8 - - - +
129D HIS* 1.3 99.2 + + - +
130D GLN 3.0 0.7 + - - -
131D GLU* 3.1 8.0 + - - +
132D LYS* 2.6 65.9 + - + +
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Residues in contact with HIS 129 (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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284B VAL 2.9 28.2 + - - -
285B TYR* 4.0 11.2 - + - -
100D ARG* 4.0 5.9 + - - +
103D GLU* 4.1 10.8 - - + +
104D ASN* 3.6 39.4 - - + +
107D SER* 3.3 21.1 + - - +
125D THR* 3.1 25.4 + - - -
126D THR 3.9 5.2 - - - +
127D ARG 3.4 0.2 - - - -
128D PHE* 1.3 97.6 - + - +
130D GLN* 1.3 61.4 + - - +
132D LYS* 3.0 25.9 + - - +
133D ASN* 2.6 28.5 + - - +
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Residues in contact with GLN 130 (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 SER* 3.8 2.0 - - - +
111D ILE* 3.7 12.6 - - + +
117D VAL* 3.7 26.4 - - + +
122D TYR* 5.6 0.8 - - - +
126D THR* 3.2 27.9 + - - +
127D ARG* 3.1 23.0 + - - +
128D PHE 3.0 0.6 - - - -
129D HIS* 1.3 77.8 - - - +
131D GLU* 1.3 64.7 + - + +
133D ASN* 3.2 11.6 + - - -
135D ALA* 3.3 22.6 + - + +
137D PHE* 3.7 31.5 - - + +
177D TYR* 3.9 20.6 + - - +
179D CYS* 4.1 15.1 - - - +
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Residues in contact with GLU 131 (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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127D ARG* 2.6 53.4 + - + +
128D PHE* 3.8 7.0 - - - +
130D GLN* 1.3 76.5 - - + +
132D LYS* 1.3 67.1 + - - +
133D ASN 3.0 2.2 - - - -
134D GLY* 3.0 14.9 + - - -
135D ALA 3.5 21.4 + - - +
136D THR* 5.2 0.2 - - - -
137D PHE* 4.2 10.0 + - - +
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Residues in contact with LYS 132 (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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285B TYR* 3.6 22.0 - - - +
104D ASN* 2.9 26.0 + - - -
108D GLN* 3.9 10.8 - - + +
128D PHE* 2.6 45.0 + - + +
129D HIS* 3.0 23.8 + - - +
131D GLU* 1.3 72.6 - - - +
133D ASN* 1.3 85.9 + - - +
134D GLY 3.4 3.1 + - - -
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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