Contacts of the helix formed by residues 126 - 139 (chain Z) in PDB entry 5UZV
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 126 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124Z ASN* 2.8 33.7 + - + +
125Z ILE* 1.3 79.8 - - - +
127Z HIS* 1.3 66.6 + - - +
128Z ALA* 3.6 9.8 + - - +
129Z MET* 3.2 32.9 + - - +
130Z ALA* 3.5 18.0 + - - +
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Residues in contact with HIS 127 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Z ASP 4.7 9.5 + - - -
79Z GLY 4.4 7.1 + - - -
125Z ILE 5.3 2.9 - - - -
126Z THR* 1.3 78.3 - - - +
128Z ALA* 1.3 59.9 + - - +
130Z ALA* 3.8 9.0 - - + +
131Z HIS* 2.9 29.3 + - - +
146Z VAL* 6.2 0.2 - - + -
331Z ASP* 4.7 15.5 + - - +
332Z ILE* 3.5 41.5 - - + +
333Z ASN* 3.7 25.4 + - - -
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Residues in contact with ALA 128 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Z THR* 3.6 9.8 + - - +
127Z HIS* 1.3 76.3 - - - +
129Z MET* 1.3 61.5 + - + +
131Z HIS* 3.2 7.6 + - - +
132Z LYS* 2.9 41.9 + - - +
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Residues in contact with MET 129 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z LEU* 4.5 6.3 - - + -
39Z ALA* 4.1 17.5 - - + -
46Z LEU* 3.7 37.9 - - + -
55Z TYR* 3.3 46.2 - - + +
123Z ILE* 5.8 0.2 - - + -
124Z ASN 4.0 9.0 - - - +
125Z ILE* 4.3 11.4 - - + -
126Z THR* 3.2 35.0 - - - +
127Z HIS 3.4 0.4 - - - -
128Z ALA* 1.3 73.6 - - + +
130Z ALA* 1.3 66.1 + - - +
132Z LYS* 3.0 7.1 + - + +
133Z VAL* 2.9 26.2 + - - +
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Residues in contact with ALA 130 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z LEU* 3.9 18.8 - - + +
77Z PHE* 3.8 26.8 - - + -
125Z ILE* 5.4 0.9 - - + -
126Z THR 3.5 12.5 + - - +
127Z HIS* 3.8 12.6 - - + +
128Z ALA 3.3 0.2 - - - -
129Z MET* 1.3 79.3 - - - +
131Z HIS* 1.3 57.8 + - - +
133Z VAL* 3.2 5.7 + - - +
134Z ILE* 2.9 33.2 + - + +
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Residues in contact with HIS 131 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127Z HIS 2.9 19.8 + - - +
128Z ALA* 3.6 7.8 + - - +
130Z ALA* 1.3 73.6 - - - +
132Z LYS* 1.3 61.1 + - - +
134Z ILE* 3.2 16.5 + - + +
135Z LYS* 2.9 52.6 + - + +
138Z ARG* 4.5 6.2 + - - -
328Z GLY* 3.3 29.4 + - - -
338Z ILE* 4.7 15.8 - - + +
339Z ASP* 3.4 41.5 - - + +
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Residues in contact with LYS 132 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Z PRO* 5.7 3.2 - - - +
52Z THR* 4.0 15.6 + - - +
53Z ASP* 4.4 12.9 + - - +
55Z TYR* 3.3 24.1 + - + +
56Z VAL* 4.1 14.0 - - + +
128Z ALA* 2.9 27.1 + - - +
129Z MET* 3.0 8.2 + - - +
131Z HIS* 1.3 78.4 - - - +
133Z VAL* 1.3 57.2 + - - +
135Z LYS* 3.3 8.0 + - + +
136Z ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z THR* 4.4 7.6 - - + -
35Z LEU* 3.7 27.1 - - + -
55Z TYR* 4.2 11.0 - - + -
56Z VAL* 4.5 10.1 - - + +
59Z CYS* 4.1 25.6 - - + -
60Z MET* 4.9 4.1 - - - +
75Z LEU* 4.5 8.5 - - + -
77Z PHE* 4.1 18.4 - - + -
129Z MET 2.9 14.2 + - - +
130Z ALA 3.2 7.8 + - - +
132Z LYS* 1.3 75.3 - - - +
134Z ILE* 1.3 55.6 + - - +
136Z ALA* 3.4 5.8 + - - +
137Z ALA* 2.9 29.5 + - + +
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Residues in contact with ILE 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Z PHE* 3.5 24.7 - - + -
130Z ALA* 2.9 21.6 + - + +
131Z HIS* 3.2 20.8 + - + +
133Z VAL* 1.3 77.4 - - - +
135Z LYS* 1.3 57.6 + - - +
137Z ALA* 3.3 2.1 + - - +
138Z ARG* 2.9 65.9 + - - +
144Z CYS* 3.8 19.4 - - + -
146Z VAL* 3.9 28.0 - - + -
327Z LEU 4.5 1.8 - - - +
328Z GLY* 4.5 11.7 - - - -
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Residues in contact with LYS 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Z HIS* 2.9 49.0 + - + +
132Z LYS* 3.8 7.2 - - + +
134Z ILE* 1.3 75.5 - - - +
136Z ALA* 1.3 58.7 + - - +
138Z ARG* 3.2 13.7 + - - +
139Z SER* 2.9 31.1 + - - -
339Z ASP* 4.6 9.0 + - - +
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Residues in contact with ALA 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Z VAL* 3.6 26.7 - - + -
60Z MET* 3.8 14.6 - - + +
132Z LYS 2.9 17.5 + - - +
133Z VAL 3.8 3.8 - - - +
135Z LYS* 1.3 77.0 - - - +
137Z ALA* 1.3 59.0 + - - +
139Z SER* 2.6 22.4 + - - -
140Z GLN* 3.7 12.1 - - - +
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Residues in contact with ALA 137 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Z MET* 4.1 15.5 - - - -
63Z VAL* 5.3 0.4 - - + -
75Z LEU* 3.7 27.8 - - + -
133Z VAL 2.9 18.4 + - - +
134Z ILE 3.7 3.8 - - - +
136Z ALA* 1.3 76.9 - - - +
138Z ARG* 1.3 58.6 + - - +
139Z SER 3.2 0.4 - - - -
140Z GLN* 3.0 13.3 + - - +
142Z VAL* 2.9 34.1 + - + +
144Z CYS* 3.9 8.7 - - - -
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Residues in contact with ARG 138 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Z HIS* 4.5 8.3 + - - -
134Z ILE* 2.9 42.6 + - + +
135Z LYS* 3.8 12.0 - - - +
137Z ALA* 1.3 73.5 - - - +
139Z SER* 1.3 57.8 + - - +
140Z GLN 3.0 4.9 - - - -
141Z GLY* 3.0 17.7 + - - +
142Z VAL 3.7 17.3 - - - +
143Z ASP* 5.4 0.9 - - - +
144Z CYS* 4.4 14.8 + - + +
327Z LEU* 3.2 26.3 + - - +
329Z ASN* 4.4 0.8 + - - -
339Z ASP* 4.1 8.1 + - - -
341Z TYR* 3.4 70.3 - - + +
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Residues in contact with SER 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Z LYS 2.9 11.2 + - - -
136Z ALA* 2.6 29.9 + - - -
138Z ARG* 1.3 77.0 - - - +
140Z GLN* 1.3 66.3 + - - +
141Z GLY 3.4 0.2 - - - -
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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