Contacts of the helix formed by residues 129 - 138 (chain F) in PDB entry 3ZWG
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 ASP 129 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F TYR* 3.7 18.4 - - + +
89F VAL* 5.4 0.5 - - - +
127F ARG 4.1 8.1 - - - +
128F ALA* 1.3 75.4 - - - +
130F GLN* 1.3 69.5 + - - +
131F ARG* 3.4 20.0 - - - +
132F MET* 2.8 31.2 + - - +
133F TYR 3.1 9.5 + - - -
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Residues in contact with GLN 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F TYR* 2.7 47.1 + - + +
53F ARG* 3.4 28.0 + - - +
129F ASP* 1.3 73.4 - - - +
131F ARG* 1.3 65.0 + - - +
133F TYR* 3.2 12.8 + - - +
134F GLU* 2.7 55.8 + - - +
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Residues in contact with ARG 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ASP* 3.4 20.3 - - - +
130F GLN* 1.3 82.2 - - - +
132F MET* 1.3 62.9 + - + +
134F GLU* 3.2 31.2 + - - +
135F GLU* 3.2 40.0 + - - +
139F HIS* 6.2 1.6 - - - -
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Residues in contact with MET 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F VAL* 3.7 23.6 - - + -
91F ALA* 5.0 1.6 - - - -
99F THR* 4.8 1.6 - - + -
101F ALA* 3.8 15.5 - - + -
122F TYR* 4.0 27.1 - - + +
126F LYS* 3.7 31.4 - - + +
127F ARG 3.7 18.8 - - - +
128F ALA* 3.9 9.4 - - - -
129F ASP* 2.8 24.8 + - - +
131F ARG* 1.3 70.7 - - + +
133F TYR* 1.3 68.6 + - - +
135F GLU* 3.2 11.8 + - - +
136F LEU* 2.9 34.3 + - + +
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Residues in contact with TYR 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F TYR* 4.1 10.5 - - + -
53F ARG* 3.8 32.2 + - + +
87F VAL* 3.4 34.0 - - + +
88F GLY 5.4 0.9 - - - -
89F VAL* 3.8 20.7 - - + +
103F LEU* 4.2 11.4 - - + -
105F SER* 5.3 0.2 + - - -
129F ASP 3.1 9.7 + - - +
130F GLN* 3.4 29.4 - - - +
132F MET* 1.3 76.8 - - - +
134F GLU* 1.3 66.8 + - - +
136F LEU* 3.3 1.2 + - - +
137F TYR* 2.9 61.9 + + + +
138F TYR* 4.3 19.6 + + - -
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Residues in contact with GLU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F GLN* 2.7 52.2 + - - +
131F ARG* 3.4 26.0 + - - +
132F MET 3.2 0.2 - - - -
133F TYR* 1.3 80.3 - - + +
135F GLU* 1.3 65.0 + - + +
138F TYR* 2.9 45.9 + - + -
139F HIS* 3.5 12.7 + - + -
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F TYR* 2.7 41.7 + - - +
126F LYS* 5.9 0.9 - - - -
131F ARG* 3.2 46.2 + - - +
132F MET* 3.6 11.0 - - - +
134F GLU* 1.3 79.9 - - - +
136F LEU* 1.3 64.0 + - - +
139F HIS* 3.1 18.2 + - + +
140F ARG* 3.0 37.7 + - + +
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F VAL* 3.8 29.6 - - + -
101F ALA* 3.9 13.5 - - + -
103F LEU* 3.5 32.3 - - + +
118F ASN* 2.8 37.2 + - + +
120F ARG* 3.5 32.1 - - + +
122F TYR* 3.8 15.0 - - + +
132F MET* 2.9 28.4 + - + +
133F TYR* 3.9 3.4 - - - +
135F GLU* 1.3 74.0 - - - +
137F TYR* 1.3 60.7 + - - +
140F ARG* 4.1 5.9 - - + +
142F PRO* 3.5 7.8 - - - +
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LEU* 3.8 14.1 - - + -
105F SER* 3.6 31.8 + - - -
113F TYR* 4.9 15.9 - - - +
114F SER 5.0 1.0 + - - -
116F TRP* 4.0 29.7 + + + -
133F TYR* 2.9 47.2 + + + +
134F GLU 4.3 0.4 - - - +
136F LEU* 1.3 79.1 - - - +
138F TYR* 1.3 92.2 + + + +
142F PRO* 3.5 20.4 - - + +
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Residues in contact with TYR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ARG* 5.5 3.8 + - - -
133F TYR* 4.3 18.0 + + - -
134F GLU* 2.9 46.5 + - + -
137F TYR* 1.3 104.9 - + + +
139F HIS* 1.3 81.8 + + + +
140F ARG 3.4 2.2 + - - -
141F SER* 3.7 9.2 + - - -
142F PRO* 4.7 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