Contacts of the helix formed by residues 125 - 139 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TRP* 3.6 42.0 - - + +
125C LEU* 3.9 10.1 - - + -
121D TRP* 2.6 45.8 + - + +
124D ASN* 1.3 80.8 - - + +
126D THR* 1.3 64.9 + - - +
127D SER 3.4 1.3 - - - -
128D MET* 3.3 8.0 - - - +
129D LEU* 3.0 25.1 + - - +
170D GLY* 3.4 29.2 - - - +
173D ALA* 3.5 21.5 - - + -
174D ARG* 3.9 8.7 - - + +
177D LEU* 4.7 5.2 - - + +
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Residues in contact with THR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C SER* 3.6 37.2 - - - +
117C VAL* 3.6 15.6 - - + +
118C ASN* 2.7 31.5 + - - +
121C TRP* 3.0 23.9 + - - +
73D LEU* 4.8 2.7 - - + -
121D TRP 3.0 4.1 + - - -
122D ALA 3.5 8.5 - - - -
125D LEU* 1.3 76.8 - - - +
127D SER* 1.3 59.0 + - - +
129D LEU* 3.2 1.8 + - - +
130D CYS* 2.9 31.7 + - - +
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Residues in contact with SER 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 3.5 46.9 - - - +
73D LEU* 3.9 22.6 - - - +
98D ALA* 6.0 0.3 - - - +
122D ALA 3.1 8.3 + - - -
123D LEU* 2.7 22.3 + - - +
126D THR* 1.3 75.3 - - - +
128D MET* 1.3 57.8 + - - +
130D CYS* 4.0 0.2 - - - -
131D LEU* 2.9 35.6 + - - +
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Residues in contact with MET 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASN* 3.7 24.7 - - + +
123D LEU 4.5 0.4 + - - +
124D ASN 3.6 18.2 - - - +
125D LEU 3.3 12.5 + - - +
127D SER* 1.3 81.6 + - - +
129D LEU* 1.3 57.7 + - - +
131D LEU* 3.7 2.9 - - - +
132D THR* 2.6 37.8 + - - -
151D ASN* 3.5 33.7 - - + +
174D ARG* 3.6 28.5 - - + +
177D LEU* 4.1 17.3 - - - -
178D PHE* 3.6 32.8 - - + -
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE* 3.5 37.5 - - + -
111C LEU* 4.1 24.7 - - + +
117C VAL* 3.9 21.3 - - + -
121C TRP* 4.4 4.5 - - + -
166C LEU* 3.6 31.2 - - + -
125D LEU 3.0 17.7 + - - +
126D THR 3.6 2.7 - - - +
128D MET* 1.3 81.2 - - - +
130D CYS* 1.3 58.9 + - - +
132D THR* 3.3 4.2 + - - -
133D SER* 3.0 28.5 + - - -
177D LEU* 4.1 22.7 - - + -
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Residues in contact with CYS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU 3.7 21.3 - - - +
112C SER* 4.0 11.1 - - - +
113C ASP 4.3 1.1 - - - -
114C SER* 3.8 37.2 - - - -
117C VAL* 4.5 7.6 - - - -
73D LEU* 4.4 12.6 - - + -
77D LEU* 3.9 9.1 - - + +
126D THR* 2.9 26.9 + - - +
127D SER 4.1 1.8 - - - +
129D LEU* 1.3 71.0 - - - +
131D LEU* 1.3 58.4 + - - +
133D SER* 3.3 1.2 + - - -
134D SER* 2.7 36.3 + - - -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.2 13.2 - - + -
10D THR* 3.5 30.1 - - + -
67D LEU* 4.9 5.8 - - + -
73D LEU* 5.3 2.7 - - + -
76D LEU* 3.8 22.2 - - + -
77D LEU* 4.1 9.3 - - + +
80D LEU* 4.9 5.8 - - + -
94D LEU* 4.0 13.0 - - + -
96D ASN* 3.8 14.8 - - - +
127D SER* 2.9 22.7 + - - +
128D MET* 3.7 4.3 - - - +
130D CYS* 1.3 78.4 - - - +
132D THR* 1.3 62.4 - - - +
134D SER* 3.5 4.6 + - - -
135D VAL* 3.0 45.4 + - + +
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Residues in contact with THR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 3.7 19.7 - - + -
94D LEU* 3.5 8.1 - - + -
96D ASN* 3.1 21.3 + - - -
128D MET 2.6 23.5 + - - -
129D LEU 3.7 3.4 - - - -
131D LEU* 1.3 77.9 - - - +
133D SER* 1.3 63.1 + - - +
135D VAL* 3.3 1.7 + - - +
136D LEU* 3.1 25.5 + - + +
149D VAL* 4.0 16.6 - - + -
178D PHE* 3.6 17.3 - - + -
181D LEU* 3.9 17.9 - - + -
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Residues in contact with SER 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE* 3.0 39.5 - - - -
109C VAL* 3.2 20.9 + - - +
111C LEU* 3.0 27.0 + - - -
112C SER* 3.8 2.9 + - - -
129D LEU 3.0 12.8 + - - -
130D CYS 3.3 7.4 + - - -
132D THR* 1.3 78.2 - - - +
134D SER* 1.3 59.8 + - - +
136D LEU* 3.5 4.1 + - - +
137D LYS* 3.1 21.1 + - - +
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Residues in contact with SER 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL 4.9 0.7 - - - -
112C SER* 4.5 15.3 - - - -
77D LEU* 3.2 23.8 - - - +
80D LEU* 3.7 10.3 - - - +
130D CYS 2.7 19.7 + - - -
131D LEU 3.5 2.3 + - - -
133D SER* 1.3 80.1 + - - +
135D VAL* 1.3 61.4 + - - +
137D LYS* 3.8 8.4 - - - +
138D ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.0 11.0 - - + -
80D LEU* 3.7 31.0 - - + -
92D LEU* 3.9 31.4 - - + -
94D LEU* 4.5 20.6 - - + -
131D LEU* 3.0 35.2 + - + +
132D THR 3.7 4.5 - - - +
134D SER* 1.3 75.8 - - - +
136D LEU* 1.3 63.1 + - + +
138D ALA* 3.3 2.8 + - - -
139D PHE* 2.9 32.5 + - + +
149D VAL* 5.6 0.4 - - + -
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 4.9 2.0 - - + -
109C VAL* 4.1 20.3 - - + +
92D LEU* 4.3 16.2 - - + -
132D THR* 3.1 26.0 + - + +
133D SER 3.9 3.8 - - - +
135D VAL* 1.3 74.8 - - + +
137D LYS* 1.3 63.1 + - - +
139D PHE 3.2 17.3 - - - +
140D PRO* 3.8 3.8 - - - +
147D ARG* 3.3 27.1 + - + +
149D VAL* 4.0 20.0 - - + -
181D LEU* 3.9 38.6 - - + -
185D GLU* 5.2 0.2 - - + -
188D VAL* 4.1 20.4 - - + -
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 3.4 26.4 - - + +
110C ASP* 3.0 32.5 - - - +
112C SER* 5.3 7.6 - - - -
133D SER 3.1 15.2 + - - +
134D SER* 4.0 8.7 - - - +
135D VAL 3.3 0.2 - - - -
136D LEU* 1.3 79.8 - - - +
138D ALA* 1.3 60.7 + - - +
140D PRO* 4.1 10.7 - - - +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 5.2 12.1 - - + +
81D ARG* 6.3 0.4 - - - -
85D ARG* 3.4 36.6 + - - +
134D SER 3.0 19.7 + - - +
135D VAL* 3.8 4.7 - - - +
137D LYS* 1.3 78.3 - - - +
139D PHE* 1.3 69.1 + - + +
140D PRO* 3.3 9.2 - - - +
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.9 34.8 - - + -
8D LEU* 5.5 0.4 - - + -
80D LEU* 4.9 7.6 - - + -
83D LEU* 4.5 13.7 - - + -
84D PRO 4.4 4.7 - - - -
85D ARG* 3.5 46.0 - - - -
89D LEU* 4.1 20.6 - - + -
92D LEU* 3.6 36.3 - - + +
135D VAL* 2.9 18.4 + - + +
136D LEU* 3.2 6.6 - - - +
138D ALA* 1.3 84.2 - - + +
140D PRO* 1.3 65.8 - - - +
145D LEU* 5.1 4.3 - - + -
147D ARG* 2.8 25.2 + - - -
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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