Contacts of the helix formed by residues 125 - 139 (chain B) in PDB entry 5ZF6
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B SER* 1.3 71.7 + - - +
126B LYS* 1.3 62.0 + - - +
128B ILE* 3.4 12.6 + - - +
129B LEU* 3.1 36.8 + - + +
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 3.9 28.3 - - + +
124B SER* 2.8 9.1 + - - +
125B ASP* 1.3 77.8 - - - +
127B GLU* 1.3 55.0 + - + +
129B LEU* 3.9 6.2 - - - +
130B THR* 2.7 50.1 + - - +
164B GLU* 5.0 9.4 + - - -
166B ASP* 4.2 19.8 + - - -
192B ARG* 5.3 2.8 - - - +
209B MET* 5.7 6.1 - - - +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 3.5 25.4 - - + +
103B ARG* 3.3 13.3 + - - +
104B GLN* 2.8 41.7 + - + +
124B SER* 2.8 31.5 + - - +
126B LYS* 1.3 76.9 - - - +
128B ILE* 1.3 61.4 + - + +
130B THR* 3.4 1.9 + - - -
131B SER* 2.8 35.3 + - - -
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER 3.1 40.4 - - - +
125B ASP* 3.8 12.1 - - - +
126B LYS 3.3 0.4 - - - -
127B GLU* 1.3 81.6 - - + +
129B LEU* 1.3 67.9 + - + +
131B SER* 3.3 6.1 + - - -
132B ARG* 3.0 35.7 + - + +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 3.1 26.7 + - + +
126B LYS* 4.1 5.8 - - - +
128B ILE* 1.3 81.4 - - + +
130B THR* 1.3 57.4 + - - +
132B ARG* 3.5 4.9 + - + +
133B ILE* 3.0 37.1 + - + +
449B GLY* 4.9 14.1 - - - +
452B ALA* 4.5 25.8 - - + -
456B LYS* 6.2 2.7 - - + -
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 3.6 39.4 - - + -
126B LYS* 2.7 40.4 + - - -
129B LEU* 1.3 75.4 - - - +
131B SER* 1.3 65.9 + - - +
133B ILE* 3.1 11.3 + - + +
134B ILE* 2.9 33.9 + - + +
166B ASP* 3.8 25.1 + - + +
170B ILE* 5.8 0.4 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.6 33.6 + - - +
102B TYR* 3.2 28.7 + - - +
127B GLU 2.8 28.3 + - - -
128B ILE* 3.6 8.0 - - - -
130B THR* 1.3 73.1 - - - +
132B ARG* 1.3 70.1 + - - +
134B ILE* 3.5 0.8 + - - -
135B ASP* 2.9 25.6 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU 4.6 5.3 + - - -
99B VAL* 4.5 9.3 - - - +
100B VAL 3.3 32.8 + - - +
128B ILE* 3.0 26.1 + - + +
129B LEU* 4.1 5.4 - - + +
131B SER* 1.3 85.4 - - - +
133B ILE* 1.3 60.5 + - - +
135B ASP* 3.0 33.5 + - + +
136B ARG* 2.9 44.5 + - + +
139B ARG* 4.8 1.6 - - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 3.0 27.8 + - + +
130B THR* 3.1 10.3 + - + +
132B ARG* 1.3 76.9 - - + +
134B ILE* 1.3 59.4 + - - +
136B ARG* 3.5 10.2 + - - +
137B SER* 2.8 26.9 + - - -
170B ILE* 3.6 27.8 - - + -
192B ARG* 5.9 2.5 - - - +
217B VAL* 4.5 12.1 - - + -
228B MET* 3.9 15.6 - - + +
230B GLU* 4.1 37.5 - - + +
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.6 28.0 - - + -
102B TYR* 4.1 10.1 - - + -
130B THR* 2.9 27.6 + - + +
131B SER 3.7 5.2 - - - +
133B ILE* 1.3 74.4 - - - +
135B ASP* 1.3 65.0 + - - +
137B SER* 3.0 16.4 + - - -
138B ILE* 3.3 13.8 + - + +
154B CYS* 4.2 5.4 - - - -
169B ALA* 3.7 24.7 - - + -
170B ILE* 3.6 27.6 - - + +
173B ALA* 3.6 31.6 - - + -
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.9 7.7 - - - +
100B VAL* 3.7 19.5 - - + +
131B SER 2.9 18.4 + - - +
132B ARG* 3.0 37.6 + - - +
134B ILE* 1.3 77.8 - - - +
136B ARG* 1.3 60.2 + - + +
137B SER 3.2 0.3 + - - -
138B ILE* 3.3 3.2 + - - +
139B ARG* 2.5 74.1 + - - +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 2.9 35.7 + - + +
133B ILE* 4.0 10.0 - - - +
135B ASP* 1.3 78.2 - - + +
137B SER* 1.3 60.8 + - - +
139B ARG* 4.8 4.3 - - - +
140B PRO* 3.4 18.2 - - - +
227B VAL* 3.5 12.4 - - - +
228B MET* 3.5 31.2 - - + +
229B LEU 3.6 15.0 + - - -
230B GLU* 2.5 30.8 + - - -
558B GLN* 3.6 13.1 - - - +
559B ALA 3.7 8.5 + - - -
560B ASP* 2.7 33.4 + - - +
561B ILE 5.1 0.9 - - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE 2.8 18.1 + - - -
134B ILE 3.0 9.9 + - - -
136B ARG* 1.3 78.1 - - - +
138B ILE* 1.3 60.2 + - - +
141B LEU* 4.9 0.9 - - - +
170B ILE* 3.4 26.0 - - - +
188B VAL* 3.5 20.8 - - - +
219B ALA* 3.5 10.4 - - - +
227B VAL* 3.3 22.3 - - - +
228B MET* 3.3 22.5 - - - +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.9 18.8 - - + -
100B VAL* 4.4 9.2 - - + -
134B ILE* 3.6 16.6 - - + +
135B ASP 3.8 3.8 - - - +
137B SER* 1.3 83.6 - - - +
139B ARG* 1.3 69.2 + - - +
140B PRO* 3.5 2.2 - - - -
141B LEU 3.5 3.0 + - - -
142B PHE* 3.3 5.9 - - + -
152B VAL* 4.0 22.2 - - + -
170B ILE 4.9 2.2 - - - +
173B ALA* 4.1 26.2 - - + -
174B SER* 4.8 1.8 - - - +
177B LEU* 3.7 20.4 - - + -
184B TRP* 2.7 50.6 + - + +
188B VAL* 5.5 1.3 - - + -
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B MET* 3.8 34.0 + - + +
98B LEU* 3.2 32.1 + - + +
132B ARG* 4.8 2.0 - - - +
135B ASP* 2.5 55.6 + - - +
136B ARG* 4.8 2.2 - - - +
138B ILE* 1.3 76.3 - - - +
140B PRO* 1.3 66.3 - - + +
141B LEU 2.9 6.4 + - - -
142B PHE* 3.4 24.3 + - - +
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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