Contacts of the helix formed by residues 130 - 140 (chain C) in PDB entry 2GJD
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 GLN 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.2 1.6 - - - -
80C GLY* 4.9 3.2 - - - +
81C PHE 3.0 22.7 + - - +
82C TYR* 3.5 29.1 - - - -
83C HIS 3.2 21.6 + - - +
84C PRO 3.2 3.6 + - - +
86C VAL 2.9 25.6 + - - +
87C TYR* 4.6 3.8 + - - -
88C PRO* 5.2 9.5 - - + +
128C PRO 3.4 0.8 - - - -
129C ALA* 1.3 77.3 - - - +
131C GLU* 1.3 65.5 + - - +
132C PRO* 4.0 14.0 - - + +
133C ALA* 3.4 10.2 + - + +
134C TRP* 3.1 24.8 + - - +
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 4.0 6.4 + - - -
87A TYR* 3.5 44.0 - - + +
89A SER* 2.6 31.5 + - - -
91A THR* 2.8 31.6 + - - +
130C GLN* 1.3 72.4 - - - +
132C PRO* 1.3 68.8 - - + +
134C TRP* 3.5 2.6 + - - +
135C ARG* 2.9 47.2 + - + +
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Residues in contact with PRO 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 4.6 7.9 - - + -
130C GLN* 3.7 15.7 - - + +
131C GLU* 1.3 96.8 - - + +
133C ALA* 1.3 58.3 + - - +
135C ARG* 3.2 29.8 + - - +
136C SER* 3.0 33.7 + - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.6 30.7 - - + -
83C HIS 3.8 7.4 - - - -
84C PRO* 3.7 29.4 - - + -
130C GLN* 3.4 15.4 + - + +
131C GLU 3.3 0.8 - - - -
132C PRO* 1.3 79.9 - - - +
134C TRP* 1.3 59.1 + - - +
136C SER 3.4 0.2 + - - -
137C PHE* 2.8 30.3 + - - +
144C TYR* 3.5 5.2 - - - -
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Residues in contact with TRP 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.3 6.1 - - - +
84C PRO* 3.1 39.2 + - + +
85C ASN* 4.1 0.7 - - - -
123C PRO* 4.3 13.0 - - + -
124C ASN 3.2 24.9 - - - -
125C PRO* 3.7 26.5 - - + -
127C SER 3.3 1.6 + - - -
128C PRO* 3.1 35.7 - - + +
130C GLN 3.1 17.7 + - - +
131C GLU 3.7 4.0 - - - +
133C ALA* 1.3 74.2 - - - +
135C ARG* 1.3 66.1 + - - +
137C PHE* 3.3 29.5 + + + +
138C SER* 3.0 47.7 + - - -
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Residues in contact with ARG 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 4.5 11.8 - - - +
131C GLU* 2.9 50.6 + - + +
132C PRO* 3.2 32.2 + - - +
134C TRP* 1.3 75.8 - - - +
136C SER* 1.3 54.9 + - - +
138C SER* 4.9 0.9 - - - -
139C ARG* 2.8 54.8 + - + +
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Residues in contact with SER 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.5 24.2 + - - -
132C PRO 3.0 11.8 + - - -
135C ARG* 1.3 74.7 + - - +
137C PHE* 1.3 66.5 + - - +
138C SER 3.1 1.6 - - - -
140C ASN* 2.8 36.8 + - - +
143C GLU* 2.7 29.2 + - - +
144C TYR* 3.8 15.0 - - - -
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Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 6.4 0.2 - - - -
34B GLY 6.0 2.0 - - - -
84C PRO* 4.3 4.3 - - + -
121C ASP 5.6 1.3 - - - -
123C PRO* 3.8 31.9 - - + -
133C ALA 2.8 22.3 + - - +
134C TRP* 3.6 37.9 - + - +
136C SER* 1.3 74.2 - - - +
138C SER* 1.3 62.3 + - - +
141C LYS* 3.6 40.7 - - + +
144C TYR* 3.6 38.2 - + + -
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASP* 4.0 7.9 - - - +
17B ARG* 3.2 23.6 + - - -
134C TRP* 3.0 36.4 + - - -
135C ARG* 3.9 2.2 - - - -
137C PHE* 1.3 81.4 - - - +
139C ARG* 1.3 83.4 + - - +
140C ASN 3.8 0.2 - - - -
141C LYS 5.4 0.2 - - - -
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS* 5.6 0.6 - - - +
98A ASN* 4.9 2.2 + - - -
99A GLU* 3.2 42.7 + - - +
100A ASP* 2.4 44.7 + - - -
17B ARG* 3.7 22.5 + - - +
135C ARG* 2.8 31.7 + - + +
138C SER* 1.3 101.3 + - - +
140C ASN* 1.3 64.8 + - + +
141C LYS 4.0 0.9 - - - -
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Residues in contact with ASN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C SER* 2.8 13.8 + - - +
139C ARG* 1.3 83.1 - - + +
141C LYS* 1.3 63.2 + - - +
142C ALA* 3.8 10.5 - - - +
143C GLU* 3.0 55.3 + - + +
144C TYR 3.0 10.2 + - - -
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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