Contacts of the helix formed by residues 148 - 162 (chain B) in PDB entry 4L28
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 GLY 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B THR* 2.9 13.5 + - - -
147B SER* 1.3 81.3 - - - +
149B ASN* 1.3 54.5 + - - +
150B THR 3.4 1.6 - - - -
151B GLY* 3.1 2.6 + - - -
152B ILE* 2.7 43.2 + - - +
169B MET* 3.5 18.4 - - - -
177B LYS* 4.0 7.6 - - - -
181B LEU* 4.7 2.6 - - - +
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.4 23.2 + - - +
119B LYS* 3.3 25.4 - - + +
147B SER* 3.7 3.2 + - - -
148B GLY* 1.3 73.2 - - - +
150B THR* 1.3 61.8 + - - +
152B ILE* 3.2 11.3 + - - +
153B GLY* 2.9 22.9 + - - -
177B LYS* 4.8 4.6 - - - +
376B ASP* 3.3 15.2 + - - +
379B ARG* 5.5 0.9 + - - -
380B ASN* 2.9 25.6 + - - +
381B TYR* 4.6 0.8 + - - -
601B PLP 2.8 41.3 + - - +
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 2.9 30.9 - - - +
122B ILE* 3.9 12.7 - - + +
123B SER* 3.1 11.1 + - - +
126B MET* 5.0 4.0 - - + -
144B GLU* 4.5 5.4 - - + -
146B THR* 3.3 13.1 + - - -
148B GLY 3.4 0.4 - - - -
149B ASN* 1.3 77.7 - - - +
151B GLY* 1.3 58.8 + - - +
154B LEU* 2.9 43.1 + - + +
222B GLN* 2.6 35.7 + - + +
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU* 5.5 0.4 - - - -
146B THR* 3.4 16.1 + - - -
148B GLY 3.1 7.9 + - - -
150B THR* 1.3 80.9 - - - +
152B ILE* 1.3 55.8 + - - +
154B LEU* 3.8 3.1 - - - -
155B ALA* 2.9 30.5 + - - +
167B ILE* 3.5 25.9 - - - +
181B LEU* 3.3 9.2 - - - +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY* 4.1 25.4 - - - +
117B SER* 5.6 0.9 - - - +
120B ASP* 5.0 0.9 - - - +
148B GLY 2.7 22.6 + - - +
149B ASN* 3.6 17.0 - - - +
151B GLY* 1.3 72.6 - - - +
153B GLY* 1.3 67.4 + - - +
155B ALA* 3.8 1.5 - - - +
156B LEU* 2.9 23.2 + - + +
177B LYS* 4.3 17.9 - - + -
180B VAL* 4.2 20.0 - - + -
181B LEU* 3.7 23.1 - - + -
184B LEU* 3.8 13.0 - - + +
379B ARG* 4.3 7.0 - - - +
380B ASN* 4.2 17.9 - - - +
345D LEU* 5.6 1.6 - - + -
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 5.5 0.5 - - - +
120B ASP* 3.8 20.8 + - - -
123B SER* 3.4 21.4 - - - -
149B ASN 2.9 11.8 + - - -
150B THR 3.2 0.2 + - - -
152B ILE* 1.3 76.7 - - - +
154B LEU* 1.3 57.8 + - - +
156B LEU* 3.3 8.7 + - - +
157B ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER* 3.7 19.3 - - - +
126B MET* 4.8 3.4 - - + -
127B ILE* 3.6 32.2 - - + +
142B ILE* 4.4 14.6 - - + +
144B GLU* 3.6 43.7 - - + +
150B THR* 2.9 24.9 + - + +
151B GLY* 3.9 4.0 - - - +
153B GLY* 1.3 78.9 - - - +
155B ALA* 1.3 57.1 + - - +
157B ALA* 3.5 3.0 + - - +
158B ALA* 2.8 30.3 + - - +
165B CYS* 4.1 9.8 - - - -
167B ILE* 5.4 0.7 - - + -
220B LEU* 3.8 13.5 - - + -
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Residues in contact with ALA 155 (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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151B GLY 2.9 19.3 + - - +
152B ILE 3.8 3.6 - - - +
154B LEU* 1.3 75.1 - - - +
156B LEU* 1.3 60.2 + - - +
158B ALA* 3.7 1.9 - - - +
159B ALA* 2.9 29.1 + - - +
165B CYS* 3.6 12.9 - - - +
181B LEU* 3.8 17.0 - - + -
184B LEU* 4.0 17.4 - - + +
186B ALA* 3.8 20.2 - - + -
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Residues in contact with LEU 156 (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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80B ILE* 4.4 5.8 - - + -
81B LEU* 4.2 15.9 - - + -
84B ILE* 5.6 2.7 - - + -
114B ALA* 4.4 12.1 - - + +
115B GLY* 3.9 32.8 - - - +
120B ASP* 5.2 2.7 - - - -
152B ILE* 2.9 17.2 + - + +
153B GLY* 3.4 8.3 - - - +
154B LEU 3.2 0.2 - - - -
155B ALA* 1.3 75.3 - - - +
157B ALA* 1.3 66.7 + - - +
159B ALA* 3.0 5.2 + - - +
160B VAL* 3.0 25.1 + - + +
184B LEU* 3.9 19.7 - - + +
343D GLY* 3.4 41.3 - - - +
345D LEU* 5.8 3.4 - - + -
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Residues in contact with ALA 157 (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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81B LEU* 3.9 28.5 - - + -
123B SER* 5.2 2.7 - - - +
124B LEU* 5.2 9.2 - - + -
127B ILE* 3.6 27.8 - - + -
153B GLY 3.0 13.8 + - - +
154B LEU* 4.0 0.4 - - - +
156B LEU* 1.3 80.7 - - - +
158B ALA* 1.3 58.4 + - - +
160B VAL* 3.3 0.7 + - - -
161B ARG* 2.9 36.2 + - + +
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Residues in contact with ALA 158 (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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127B ILE* 4.8 0.6 - - - +
142B ILE* 4.8 4.0 - - + -
154B LEU 2.8 20.4 + - - +
155B ALA 3.7 4.3 - - - +
157B ALA* 1.3 74.9 - - - +
159B ALA* 1.3 61.8 + - - +
162B GLY* 2.9 25.3 + - - -
163B TYR* 3.0 47.8 + - + +
165B CYS* 3.9 17.5 - - + -
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 2.9 19.1 + - - +
156B LEU* 3.0 8.0 + - - +
158B ALA* 1.3 76.9 - - - +
160B VAL* 1.3 61.4 + - + +
162B GLY* 4.1 2.6 + - - -
163B TYR 5.2 0.4 - - - -
184B LEU* 3.5 26.5 - - + +
94D LYS* 2.8 20.4 + - - -
339D ILE 4.9 1.6 - - - +
340D ALA 3.8 18.8 - - - +
341D GLN 4.0 4.4 - - - +
343D GLY* 5.6 1.3 - - - -
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Residues in contact with VAL 160 (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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79B ASP* 4.2 23.3 - - + +
80B ILE* 4.5 13.5 - - + -
81B LEU* 4.1 22.2 - - + -
156B LEU 3.0 15.1 + - - +
157B ALA 3.8 5.2 - - - +
159B ALA* 1.3 80.7 - - - +
161B ARG* 1.3 64.6 + - + +
93D ASN* 5.9 1.3 - - - +
94D LYS* 3.1 24.8 + - - +
341D GLN 4.5 1.8 - - - +
342D GLU* 3.8 28.5 - - - +
343D GLY* 4.6 2.2 - - - +
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Residues in contact with ARG 161 (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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79B ASP* 5.5 2.0 + - - -
81B LEU* 3.9 19.9 - - + +
82B LYS* 3.9 19.0 - - - +
124B LEU* 4.1 10.3 - - - +
127B ILE* 4.8 6.2 - - - +
128B GLU* 3.1 34.5 + - - +
131B GLU* 2.7 41.0 + - - -
138B PRO* 6.1 0.7 - - - +
139B GLY 5.8 0.5 + - - -
157B ALA* 2.9 20.3 + - - +
160B VAL* 1.3 81.3 - - + +
162B GLY* 1.3 60.3 + - - +
163B TYR* 3.7 21.5 - - + -
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Residues in contact with GLY 162 (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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139B GLY* 3.8 22.2 + - - -
158B ALA 2.9 10.9 + - - -
159B ALA 4.1 3.3 + - - -
160B VAL 3.3 4.2 + - - -
161B ARG* 1.3 80.2 - - - +
163B TYR* 1.3 60.1 + - - -
164B ARG 4.2 0.2 + - - -
94D LYS* 5.5 2.0 - - - -
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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