Contacts of the helix formed by residues 151 - 163 (chain B) in PDB entry 1LL9
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 ALA 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 4.8 2.9 - - - -
112B TYR* 3.6 17.8 - - - -
117B LEU 3.3 19.1 - - - +
118B PRO 3.1 22.9 - - - +
119B LEU* 3.8 6.1 - - - +
149B LEU 3.2 7.0 + - - +
150B TYR* 1.3 81.4 - - - +
152B ASN* 1.3 64.8 + - - +
154B SER* 3.3 19.6 + - - +
155B ILE* 3.5 11.0 + - - +
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 4.1 1.0 + - - -
67B LYS* 2.6 36.4 + - - +
119B LEU* 2.8 20.3 + - - +
120B GLN* 2.9 23.1 + - - +
121B VAL* 5.0 4.9 - - + +
150B TYR* 5.0 1.0 - - - -
151B ALA* 1.3 72.9 - - - +
153B SER* 1.3 58.1 + - - +
156B GLY* 2.8 31.2 + - - -
216B LEU* 5.1 2.1 - - - +
220B ALA* 3.6 20.4 - - + +
221B TYR* 4.1 11.2 - - + -
964B AXL 2.6 34.2 + - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.4 6.6 - - - +
118B PRO* 2.6 49.6 + - - +
119B LEU 4.0 0.4 + - - -
121B VAL* 3.6 27.9 - - - +
134B PHE* 4.3 4.7 - - - -
135B TYR* 2.7 35.5 + - - -
152B ASN* 1.3 80.6 - - - +
154B SER* 1.3 61.4 + - - +
156B GLY 4.2 0.7 - - - -
157B LEU* 3.7 5.4 - - - +
216B LEU* 4.9 0.9 - - - -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B HIS 3.7 0.9 + - - -
109B LEU* 2.6 39.5 + - - +
112B TYR* 3.5 21.7 - - - -
113B THR 4.6 0.2 + - - -
114B ALA* 4.7 1.0 - - - +
117B LEU* 3.8 22.6 - - - +
149B LEU 5.3 0.2 - - - -
151B ALA* 3.3 19.7 + - - -
152B ASN 3.1 1.0 - - - -
153B SER* 1.3 78.8 + - - +
155B ILE* 1.3 67.0 + - - +
156B GLY 3.2 0.7 - - - -
157B LEU* 3.3 5.2 + - - +
158B PHE 3.2 15.4 + - - -
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Residues in contact with ILE 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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67B LYS* 3.4 66.6 - - + +
70B THR* 4.2 16.0 - - + +
71B GLY* 4.9 3.1 - - - +
109B LEU 3.2 8.2 + - - +
110B ALA* 4.0 15.9 - - + +
112B TYR* 3.8 16.4 - - + +
151B ALA 3.5 8.0 + - - +
152B ASN 4.1 2.2 - - - +
154B SER* 1.3 76.4 - - - +
156B GLY* 1.3 69.8 + - - +
157B LEU 3.3 0.2 - - - -
158B PHE* 3.2 11.8 + - + -
159B GLY* 2.9 21.1 + - - -
220B ALA* 4.7 3.8 - - + -
269B LEU 5.1 0.2 - - - -
270B GLY* 4.2 10.8 - - - +
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Residues in contact with GLY 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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152B ASN 2.8 21.2 + - - -
155B ILE* 1.3 81.0 - - - +
157B LEU* 1.3 60.7 + - - +
159B GLY 3.4 0.3 + - - -
160B ALA* 3.2 19.1 + - - +
216B LEU* 3.8 16.0 - - - +
219B GLU* 3.4 24.7 - - - +
220B ALA* 4.4 6.3 - - - -
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Residues in contact with LEU 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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89B THR* 4.5 1.3 - - + -
93B TRP* 3.4 35.4 - - + -
96B LEU* 4.9 0.2 - - + -
101B TRP* 4.2 9.4 - - + -
109B LEU* 3.9 22.4 - - + -
131B LEU* 6.0 1.1 - - + -
135B TYR* 3.7 36.3 - - + +
153B SER 3.7 16.8 + - - +
154B SER 3.3 4.8 + - - +
155B ILE 3.3 0.2 - - - -
156B GLY* 1.3 72.4 - - - +
158B PHE* 1.3 67.9 + - - +
160B ALA* 3.2 8.3 + - + -
161B LEU* 2.9 47.8 + - + +
216B LEU* 3.9 8.5 - - + +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 4.2 15.5 - - + -
71B GLY* 4.9 6.3 - - - -
74B GLY* 3.9 31.9 - - - -
83B ILE* 4.4 11.0 - - + -
85B LEU* 3.8 29.2 - - + -
106B LEU* 3.5 32.5 - - + -
109B LEU* 3.9 11.6 - - + +
110B ALA* 3.6 34.3 - - + +
154B SER 3.2 7.3 + - - +
155B ILE* 3.3 15.0 - - + +
157B LEU* 1.3 78.6 - - - +
159B GLY* 1.3 61.0 + - - +
161B LEU* 3.3 2.6 + - - +
162B ALA* 2.8 38.1 + - + +
269B LEU* 5.1 4.5 - - + -
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Residues in contact with GLY 159 (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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70B THR* 3.7 25.1 - - - -
155B ILE 2.9 11.5 + - - -
156B GLY 3.8 3.1 - - - -
157B LEU 3.2 0.2 - - - -
158B PHE* 1.3 82.1 - - - +
160B ALA* 1.3 61.4 + - - +
162B ALA* 3.4 11.3 + - - +
163B VAL* 3.5 8.5 + - - +
170B PHE* 3.6 24.1 - - - -
219B GLU* 4.2 1.1 - - - -
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Residues in contact with ALA 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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156B GLY 3.2 11.0 + - - +
157B LEU* 3.2 15.1 + - + +
159B GLY* 1.3 73.7 - - - +
161B LEU* 1.3 65.9 + - + +
163B VAL* 3.3 20.3 - - - +
164B LYS* 3.6 17.2 - - - +
170B PHE* 4.9 0.9 - - - -
216B LEU* 4.0 11.9 - - + -
219B GLU* 3.6 23.3 - - - +
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Residues in contact with LEU 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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89B THR* 3.4 39.9 - - + +
92B TYR* 3.8 34.8 - - + +
93B TRP* 3.9 17.7 - - + -
106B LEU* 4.4 12.6 - - + -
109B LEU* 4.0 6.7 - - + -
157B LEU* 2.9 41.8 + - + +
158B PHE 3.9 2.2 - - - +
160B ALA* 1.3 77.4 - - + +
162B ALA* 1.3 67.0 + - - +
163B VAL 3.2 0.7 - - - -
164B LYS* 3.1 31.5 + - + +
165B PRO* 3.6 4.9 - - - +
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Residues in contact with ALA 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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73B LEU* 5.6 1.6 - - + +
74B GLY* 4.4 11.2 - - - -
77B ALA* 3.9 14.1 - - + +
82B GLU* 4.8 2.4 - - - +
83B ILE* 3.6 41.8 - - + +
106B LEU* 5.4 2.4 - - - +
158B PHE* 2.8 35.8 + - + +
159B GLY* 3.4 8.5 + - - +
161B LEU* 1.3 72.7 - - - +
163B VAL* 1.3 63.2 + - + +
164B LYS 3.7 0.5 + - - -
165B PRO* 3.7 2.8 - - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.8 23.6 - - + -
77B ALA* 5.9 0.4 - - - -
82B GLU* 5.7 0.2 - - - -
159B GLY 3.8 11.7 - - - +
160B ALA* 3.3 17.9 - - - +
162B ALA* 1.3 79.8 - - + +
164B LYS* 1.3 65.2 + - + +
165B PRO* 3.4 1.8 - - - -
166B SER* 2.7 30.3 + - - +
167B GLY 3.4 2.8 + - - -
168B LEU 3.6 19.3 - - - +
170B PHE* 4.0 20.2 - - + +
173B ALA* 3.7 24.5 - - + -
177B ARG* 6.0 2.2 - - - +
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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