Contacts of the helix formed by residues 115 - 120 (chain G) in PDB entry 2ZHX
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 LEU 115 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G LEU* 4.8 0.2 - - - -
80G SER 3.4 24.9 - - - +
81G PHE* 4.1 10.5 - - + -
82G SER* 2.8 25.0 + - - +
94G LEU* 4.0 6.1 - - + -
97G ILE* 6.2 0.2 - - + -
98G PHE* 3.6 35.9 - - + -
113G GLY 3.7 8.1 - - - +
114G ASP* 1.3 74.3 - - - +
116G THR* 1.3 67.7 + - - +
117G PRO* 3.2 4.0 - - - -
118G TRP* 2.7 49.2 + - + +
119G ALA 3.4 2.4 + - - -
125G LEU* 3.6 19.9 - - + +
226G LEU* 4.4 7.2 - - + -
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Residues in contact with THR 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G ARG* 3.2 33.4 + - - +
55G PHE* 4.9 7.0 - - + -
77G VAL* 5.6 0.2 - - - +
79G LEU* 4.2 11.8 - - - +
82G SER* 3.9 2.5 + - - -
114G ASP* 2.6 27.7 + - - -
115G LEU* 1.3 74.6 - - - +
117G PRO* 1.4 65.1 - - - +
119G ALA* 2.9 22.5 + - - +
120G GLN* 3.1 26.7 + - + +
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Residues in contact with PRO 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G ASP* 3.7 18.6 - - - +
115G LEU 3.4 2.9 - - - +
116G THR* 1.4 89.9 - - + +
118G TRP* 1.3 66.7 + - - +
119G ALA 3.2 0.5 + - - -
120G GLN* 3.3 27.5 + - + +
121G ARG* 3.2 45.0 + - - +
226G LEU* 4.3 21.3 - - + +
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Residues in contact with TRP 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G ILE* 4.7 6.7 - - + -
97G ILE* 4.5 9.9 - - + -
98G PHE* 4.3 15.3 - + - -
101G TYR* 3.9 22.7 - + - -
115G LEU* 2.7 47.8 + - + +
117G PRO* 1.3 73.6 - - + +
119G ALA* 1.3 57.5 + - - +
121G ARG* 3.1 14.9 + - - +
123G VAL* 3.0 40.2 + - + +
125G LEU* 4.4 13.0 - - + -
168G TRP* 5.7 1.3 - + - -
207G PHE* 3.7 24.7 - + - -
222G ILE* 5.2 0.2 - - + -
224G TRP* 3.3 60.1 - + - +
226G LEU* 3.5 28.2 - - + +
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Residues in contact with ALA 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G PHE* 3.7 38.4 - - + +
79G LEU* 4.1 22.4 - - + -
115G LEU 3.4 1.5 + - - +
116G THR 2.9 13.3 + - - +
118G TRP* 1.3 75.7 - - - +
120G GLN* 1.3 56.0 + - - +
121G ARG 3.0 8.9 + - - -
122G GLY* 3.5 8.8 + - - -
123G VAL 3.1 19.9 + - - +
124G LEU* 5.9 0.2 - - - -
125G LEU* 4.6 7.1 - - + +
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Residues in contact with GLN 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G PHE* 3.7 27.5 - - + -
56G PRO* 6.0 2.7 - - - +
59G ASN* 4.7 5.7 - - - +
116G THR* 3.1 19.0 + - - +
117G PRO* 3.4 34.1 - - + +
119G ALA* 1.3 76.0 - - - +
121G ARG* 1.3 63.2 + - + +
122G GLY 3.6 0.9 - - - -
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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