Contacts of the helix formed by residues 125 - 139 (chain F) in PDB entry 1Z6Z
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 125 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TRP* 3.6 44.2 - - + +
125E LEU* 4.0 9.9 - - + -
121F TRP* 2.7 45.4 + - + +
123F LEU 3.5 0.2 - - - -
124F ASN* 1.3 79.9 - - + +
126F THR* 1.3 67.4 + - - +
127F SER 3.4 1.1 - - - -
128F MET* 3.3 8.3 - - - +
129F LEU* 3.0 24.2 + - - +
170F GLY* 3.5 28.7 - - - +
173F ALA* 3.5 20.0 - - + -
174F ARG* 3.9 8.3 - - + +
177F LEU* 4.6 5.7 - - + +
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Residues in contact with THR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E SER* 3.7 37.0 - - - +
117E VAL* 3.7 14.5 - - + +
118E ASN* 2.7 29.6 + - - +
121E TRP* 3.1 23.3 + - - +
73F LEU* 4.8 2.5 - - + -
121F TRP 3.0 4.1 + - - -
122F ALA* 3.4 11.0 - - - -
125F LEU* 1.3 76.2 - - - +
127F SER* 1.3 58.7 + - - +
129F LEU* 3.3 1.9 + - - +
130F CYS* 2.9 32.2 + - - +
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F LEU* 3.5 46.1 - - - +
73F LEU* 3.9 21.7 - - - +
98F ALA* 6.1 0.3 - - - +
122F ALA 3.1 7.7 + - - -
123F LEU* 2.7 23.0 + - - +
126F THR* 1.3 76.3 - - - +
128F MET* 1.3 57.4 + - - +
130F CYS* 4.1 0.2 - - - -
131F LEU* 2.9 36.4 + - - +
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Residues in contact with MET 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ASN* 3.7 23.3 - - + +
98F ALA 6.0 0.2 - - - +
123F LEU 4.6 0.4 + - - -
124F ASN 3.6 6.5 - - - +
125F LEU 3.3 10.0 + - - +
127F SER* 1.3 82.2 + - - +
129F LEU* 1.3 60.5 + - - +
131F LEU* 3.7 3.2 - - - +
132F THR* 2.6 37.6 + - - -
151F ASN* 3.6 33.0 - - + +
174F ARG* 3.6 42.0 - - + +
177F LEU* 4.1 17.7 - - - -
178F PHE* 3.7 32.1 - - + -
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E PHE* 3.3 40.6 - - + +
111E LEU* 4.3 21.8 - - + +
117E VAL* 3.9 22.4 - - + -
121E TRP* 4.5 2.5 - - + -
166E LEU* 3.8 29.4 - - + -
125F LEU 3.0 17.7 + - - +
126F THR 3.7 2.7 - - - +
128F MET* 1.3 78.9 - - - +
130F CYS* 1.3 60.9 + - - +
132F THR* 3.3 4.4 + - - -
133F SER* 3.0 28.2 + - - -
177F LEU* 4.1 23.1 - - + -
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Residues in contact with CYS 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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111E LEU 3.8 13.9 - - - -
112E SER* 4.0 11.2 - - - +
113E ASP 4.4 1.3 - - - -
114E SER* 3.9 37.0 - - - -
117E VAL* 4.7 6.3 - - - -
73F LEU* 4.4 12.6 - - + -
77F LEU* 4.0 9.1 - - + +
126F THR* 2.9 25.2 + - - +
127F SER 4.2 1.8 - - - +
129F LEU* 1.3 71.7 - - - +
131F LEU* 1.3 62.3 + - - +
133F SER* 3.2 7.5 + - - -
134F SER* 2.8 31.7 + - - -
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Residues in contact with LEU 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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8F LEU* 4.2 13.5 - - + -
10F THR* 3.5 30.7 - - + -
67F LEU* 5.0 5.6 - - + -
73F LEU* 5.0 2.4 - - + +
76F LEU* 3.8 21.8 - - + -
77F LEU* 4.1 12.0 - - + +
80F LEU* 4.9 6.7 - - + -
94F LEU* 4.1 12.3 - - + -
96F ASN* 3.9 14.8 - - - +
127F SER* 2.9 23.8 + - - +
128F MET* 3.7 4.3 - - - +
130F CYS* 1.3 77.6 - - - +
132F THR* 1.3 62.8 + - - +
134F SER* 3.5 1.2 + - - -
135F VAL* 3.0 45.7 + - + +
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Residues in contact with THR 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E PHE* 4.0 7.6 - - + -
94F LEU* 3.5 8.2 - - + +
96F ASN* 3.1 22.0 + - - -
128F MET 2.6 23.0 + - - -
129F LEU 3.3 3.1 + - - -
131F LEU* 1.3 75.7 - - - +
133F SER* 1.3 62.9 + - - +
135F VAL* 3.4 2.4 + - - +
136F LEU* 3.1 31.6 + - + +
149F VAL* 4.0 11.9 - - + -
178F PHE* 3.6 17.6 - - + -
181F LEU* 3.9 28.3 - - + -
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Residues in contact with SER 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E PHE* 3.3 36.8 - - - -
109E VAL* 3.6 17.8 + - - +
111E LEU* 3.2 24.5 + - - -
112E SER* 4.1 3.6 - - - -
129F LEU 3.0 13.3 + - - -
130F CYS* 3.2 8.5 + - - -
132F THR* 1.3 77.4 - - - +
134F SER* 1.3 59.5 + - - +
136F LEU* 3.5 5.3 + - - +
137F LYS* 3.1 26.0 + - - +
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Residues in contact with SER 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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109E VAL 5.3 0.2 - - - -
112E SER* 4.8 13.5 - - - -
77F LEU* 3.2 25.4 - - - +
80F LEU* 3.8 10.8 - - - +
130F CYS 2.8 19.8 + - - -
131F LEU 3.5 1.7 + - - -
133F SER* 1.3 78.9 + - - +
135F VAL* 1.3 62.1 + - - +
137F LYS* 3.8 6.9 - - - +
138F ALA* 3.0 28.8 + - - +
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Residues in contact with VAL 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LEU* 4.0 10.3 - - + -
80F LEU* 3.6 30.7 - - + -
92F LEU* 3.9 30.7 - - + -
94F LEU* 4.5 21.5 - - + -
131F LEU* 3.0 34.9 + - + +
132F THR 3.4 4.9 + - - +
134F SER* 1.3 77.7 - - - +
136F LEU* 1.3 60.1 + - + +
138F ALA* 3.4 2.6 + - - -
139F PHE* 2.9 32.6 + - + +
149F VAL* 5.6 0.7 - - + -
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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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108E PHE* 5.1 0.2 - - + -
109E VAL* 4.5 17.4 - - + +
92F LEU* 4.3 15.5 - - + -
132F THR* 3.1 26.5 + - + +
133F SER* 3.9 5.8 - - - +
135F VAL* 1.3 75.0 - - + +
137F LYS* 1.3 62.3 + - - +
139F PHE 3.2 18.8 - - - +
140F PRO* 3.8 3.6 - - - +
147F ARG* 3.2 28.0 + - + +
149F VAL* 4.1 19.7 - - + -
181F LEU* 3.9 39.0 - - + -
185F GLU* 5.3 0.9 - - + -
188F VAL* 4.1 21.5 - - + -
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Residues in contact with LYS 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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109E VAL* 4.1 25.5 - - + +
110E ASP* 5.4 2.9 - - - +
133F SER 3.1 17.5 + - - +
134F SER* 4.0 7.4 - - - +
135F VAL 3.3 0.2 - - - -
136F LEU* 1.3 77.7 - - - +
138F ALA* 1.3 63.4 + - - +
139F PHE 3.6 0.2 + - - -
140F PRO* 4.0 11.3 - - - +
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Residues in contact with ALA 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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80F LEU* 5.1 15.3 - - + +
81F ARG* 6.3 1.1 - - - -
134F SER 3.0 18.6 + - - +
135F VAL* 3.4 5.4 + - - +
137F LYS* 1.3 79.0 - - - +
139F PHE* 1.3 75.6 + - + +
140F PRO* 3.3 9.2 - - - +
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Residues in contact with PHE 139 (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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6F VAL* 3.9 35.2 - - + -
8F LEU* 5.6 0.7 - - + -
80F LEU* 4.6 21.1 - - + -
83F LEU* 5.5 9.9 - - + -
84F PRO 5.4 3.8 - - - -
85F ARG* 5.0 14.8 - - + -
89F LEU* 4.2 13.5 - - + -
92F LEU* 3.7 32.8 - - + -
135F VAL* 2.9 21.2 + - + +
136F LEU* 3.2 6.8 - - - +
138F ALA* 1.3 92.4 - - + +
140F PRO* 1.3 57.7 - - - +
145F LEU* 5.1 5.4 - - + -
147F ARG* 2.8 31.7 + - - -
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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