Contacts of the helix formed by residues 115 - 121 (chain C) in PDB entry 2X7N
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 LYS 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B ALA 5.2 1.6 - - - +
55B GLY* 3.9 22.9 + - - +
56B THR* 3.1 39.4 - - + -
58B ILE* 5.3 1.4 - - - +
5C LYS* 5.8 0.4 - - - -
6C PHE* 2.7 44.6 - - + -
82C ARG* 4.1 15.3 - - - +
114C GLY* 1.3 70.6 - - - -
116C GLU* 1.3 72.1 + - - +
118C ALA* 3.2 2.6 + - - +
119C ASP* 3.0 24.4 + - - +
131C VAL* 3.1 11.6 - - - +
132C VAL* 2.6 20.7 + - - +
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Residues in contact with GLU 116 (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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4C THR* 2.7 56.3 - - + +
5C LYS* 5.0 1.5 + - - +
6C PHE* 1.9 50.6 - - + +
50C GLY* 5.9 0.7 - - - -
80C TRP* 3.2 26.0 - - + -
82C ARG* 3.9 10.7 + - - -
114C GLY* 3.9 2.4 - - - -
115C LYS* 1.3 91.0 + - - +
117C CYS* 1.3 61.3 + - - +
119C ASP* 3.4 6.6 + - - +
120C LEU* 3.3 23.8 + - - +
132C VAL 4.5 0.7 - - - +
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Residues in contact with CYS 117 (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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49C LEU* 6.4 0.4 - - + -
50C GLY* 4.7 20.2 - - - +
72C ILE* 4.9 9.2 - - + -
73C VAL 4.7 8.5 - - - +
74C VAL* 5.2 11.2 - - - +
80C TRP* 5.1 2.8 - - + -
113C VAL* 3.7 16.6 - - - -
114C GLY* 2.9 37.3 + - - +
116C GLU* 1.3 79.0 - - - +
118C ALA* 1.3 75.0 + - - +
120C LEU* 2.9 9.1 + - - +
121C TRP* 2.9 24.8 + - - +
124C VAL* 5.0 9.6 - - + -
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Residues in contact with ALA 118 (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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58B ILE* 3.8 22.2 - - + +
113C VAL* 4.7 3.4 - - + -
114C GLY 3.0 6.5 + - - +
115C LYS 3.2 7.6 + - - +
117C CYS* 1.3 86.0 - - - +
119C ASP* 1.3 63.6 + - - +
121C TRP 3.1 22.0 - - - +
122C PRO* 3.3 8.3 - - - +
124C VAL* 4.6 0.9 - - - -
125C ALA* 3.1 30.9 - - + +
131C VAL* 4.2 7.6 - - + -
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Residues in contact with ASP 119 (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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7B PHE* 4.6 0.9 - - - -
8B GLU* 4.4 1.4 - - - +
16B PHE* 3.6 26.4 - - - -
57B ARG* 2.8 20.0 + - - +
58B ILE* 4.4 10.7 - - + +
2C GLN* 2.3 40.0 + - - +
5C LYS* 2.7 21.4 + - - +
115C LYS 3.0 12.9 + - - +
116C GLU 3.6 9.4 - - - +
118C ALA* 1.3 79.8 - - - +
120C LEU* 1.3 62.7 + - + +
122C PRO* 4.1 6.1 - - - +
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Residues in contact with LEU 120 (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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1C ALA* 4.7 10.8 - - + -
2C GLN* 3.0 61.5 - - + +
3C GLY 4.1 3.6 - - - +
4C THR* 4.3 15.5 - - - +
50C GLY* 4.0 25.4 - - - +
116C GLU 3.3 12.7 + - - +
117C CYS* 2.9 7.4 + - - +
119C ASP* 1.3 77.5 - - - +
121C TRP* 1.3 78.8 + - + +
122C PRO* 3.3 8.8 - - - +
123C ARG* 5.0 0.5 + - - -
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Residues in contact with TRP 121 (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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36C GLY* 5.9 2.7 - - - -
50C GLY 4.4 8.8 + - - -
52C MET* 3.7 37.3 - - + +
72C ILE* 2.8 45.3 - - + +
101C LYS 4.9 2.2 - - - -
102C GLY* 3.5 30.5 - - - +
117C CYS* 2.9 12.3 + - - -
118C ALA 3.1 4.0 - - - +
120C LEU* 1.3 93.6 - - + +
122C PRO* 1.3 68.8 - - - +
123C ARG* 3.2 14.6 - - - -
124C VAL* 2.7 39.5 - - + +
125C ALA 3.0 2.6 + - - -
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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