Contacts of the helix formed by residues 151 - 162 (chain H) in PDB entry 1LP9
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 HIS 151 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H TRP 3.1 3.9 + - - -
148H GLU* 3.1 14.1 + - - +
149H ALA 3.7 13.4 + - - -
150H ALA* 1.3 82.7 - - - +
152H VAL* 1.3 65.4 + - - +
153H ALA 3.3 2.7 - - - -
154H GLU* 3.4 15.3 + - + +
155H GLN* 3.1 20.4 + - - +
48L LYS* 5.3 6.2 - - + +
50L PHE* 3.4 63.8 - + + +
51L THR* 4.5 13.4 + - + -
100M TYR* 3.8 4.3 - - - -
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Residues in contact with VAL 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H HIS* 5.1 1.3 - - + -
133H TRP* 3.7 21.1 - - + -
147H TRP* 3.0 49.6 + - + +
148H GLU* 5.1 0.4 - - - +
150H ALA* 4.0 3.1 - - + -
151H HIS* 1.3 76.6 - - - +
153H ALA* 1.3 58.8 + - - +
155H GLN* 3.2 5.9 + - - +
156H LEU* 2.8 32.2 + - + +
3J TRP* 4.2 17.8 - - + -
5J PHE* 4.2 8.7 - - + -
7J PRO* 4.2 7.6 - - + -
97M TRP* 3.6 27.4 - - + -
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Residues in contact with ALA 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H LEU* 4.2 6.1 - - + +
130H LEU 4.0 7.1 - - - +
131H ARG 3.9 17.9 - - - +
133H TRP* 3.9 32.4 - - + +
147H TRP 4.9 0.2 + - - -
151H HIS 3.3 1.0 - - - -
152H VAL* 1.3 78.7 - - - +
154H GLU* 1.3 57.0 + - - +
156H LEU* 3.3 5.4 + - - +
157H ARG* 2.9 43.8 + - - +
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Residues in contact with GLU 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H HIS* 3.4 20.5 + - + +
152H VAL 3.2 0.6 - - - -
153H ALA* 1.3 79.6 - - - +
155H GLN* 1.3 61.7 + - - +
157H ARG* 3.3 35.4 + - - +
158H ALA* 3.4 8.7 + - - +
31L PHE* 3.7 28.8 - - + -
50L PHE* 3.5 20.3 - - - +
52L ASP* 3.4 35.6 + - - +
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Residues in contact with GLN 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H ALA 3.0 25.9 + - - -
151H HIS 3.1 12.0 + - - +
152H VAL 3.8 3.6 - - - +
154H GLU* 1.3 74.9 - - - +
156H LEU* 1.3 61.9 + - - +
158H ALA* 3.2 14.2 + - - +
159H TYR 3.4 7.8 + - - -
3J TRP* 3.9 19.1 + - + +
5J PHE* 3.4 31.8 - - + +
31L PHE* 3.8 29.2 - - + -
50L PHE* 4.3 8.3 - - + -
93L PHE* 3.3 30.0 - - - -
97L ALA* 4.6 2.6 - - - +
98L SER* 4.6 1.6 + - - -
100M TYR* 3.6 13.5 - - - -
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Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 5.4 1.6 - - + -
114H HIS* 3.5 40.8 - - + +
126H LEU* 3.7 20.6 - - + -
133H TRP* 3.9 15.7 - - + -
152H VAL* 2.8 16.9 + - + +
153H ALA* 3.5 3.1 - - - +
155H GLN* 1.3 78.7 - - - +
157H ARG* 1.3 58.1 + - - +
159H TYR* 3.0 8.3 + - + +
160H LEU* 2.8 50.4 + - + +
3J TRP* 3.6 35.8 - - + -
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Residues in contact with ARG 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H LEU* 5.8 1.1 - - + -
130H LEU* 2.9 40.4 + - + +
131H ARG* 3.2 53.8 - - - +
153H ALA* 2.9 27.1 + - - +
154H GLU* 3.3 35.6 + - - +
156H LEU* 1.3 76.6 - - - +
158H ALA* 1.3 58.1 + - - +
160H LEU* 4.3 7.9 - - + +
161H GLU* 2.8 56.8 + - + +
52L ASP* 3.7 21.8 + - - -
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Residues in contact with ALA 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H GLU 3.4 4.1 + - - +
155H GLN 3.2 12.3 + - - +
157H ARG* 1.3 77.8 - - - +
159H TYR* 1.3 57.3 + - - +
161H GLU* 5.4 0.2 - - - -
162H GLY* 3.1 25.6 + - - +
163H THR* 3.5 4.2 + - - -
28L TYR* 4.5 4.5 - - - +
29L SER* 3.7 34.3 + - - +
31L PHE* 4.0 15.7 - - + -
98L SER* 3.7 16.4 + - - +
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Residues in contact with TYR 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H MET* 4.3 2.4 - - - +
7H TYR* 3.7 9.0 - - - -
99H TYR* 3.4 31.7 - + - -
100H GLY* 5.2 0.2 - - - -
155H GLN 3.4 2.4 + - - -
156H LEU* 3.0 12.8 + - + +
158H ALA* 1.3 77.5 - - - +
160H LEU* 1.3 78.8 + - + +
163H THR* 3.1 28.0 + - + -
164H CYS* 2.7 51.5 + - + +
1J ALA 2.7 29.4 + - - -
2J LEU 3.7 1.3 - - - -
3J TRP* 3.4 47.6 - + + +
98L SER* 3.4 21.7 + - - +
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Residues in contact with LEU 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 5.1 0.9 - - + -
100H GLY 3.5 29.4 - - - +
101H CYS* 3.7 2.6 - - + +
109H PHE* 3.5 24.7 - - + -
112H GLY* 4.0 14.8 - - - -
113H TYR 3.8 13.5 - - - +
126H LEU* 3.7 21.3 - - + -
130H LEU* 4.5 5.6 - - + -
156H LEU* 2.8 44.5 + - + +
157H ARG* 4.1 7.0 - - + +
159H TYR* 1.3 92.6 - - + +
161H GLU* 1.3 59.5 + - + +
164H CYS* 3.6 9.9 - - + +
165H VAL* 3.5 12.5 - - - +
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Residues in contact with GLU 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H PHE* 3.9 42.1 - - + +
130H LEU* 4.0 9.3 - - + +
131H ARG* 5.1 1.2 + - - -
157H ARG* 2.8 49.2 + - - +
158H ALA* 5.4 0.4 - - - -
160H LEU* 1.3 74.3 - - + +
162H GLY* 1.3 60.8 + - - +
165H VAL* 3.9 14.1 - - - +
166H GLU* 5.6 0.2 - - - +
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Residues in contact with GLY 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H ALA 3.1 16.6 + - - -
159H TYR 3.3 0.4 + - - -
161H GLU* 1.3 78.0 - - - +
163H THR* 1.3 60.3 + - - +
164H CYS 3.4 0.7 - - - -
165H VAL* 3.2 3.6 + - - +
166H GLU* 2.9 37.8 + - - +
28L TYR* 3.7 15.7 - - - -
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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