Contacts of the helix formed by residues 151 - 163 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LYS* 4.8 1.8 - - - -
112A TYR* 3.5 16.4 - - - -
117A LEU* 3.3 18.2 - - + +
118A PRO 3.1 23.1 - - - +
119A LEU* 3.7 6.5 - - - +
149A LEU 3.1 6.4 + - - +
150A TYR* 1.3 78.5 - - - +
152A ASN* 1.3 66.0 + - - +
154A SER* 3.3 23.7 + - - +
155A ILE* 3.4 11.7 + - - +
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Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 4.2 3.0 + - - -
67A LYS* 2.5 36.4 + - - +
119A LEU* 2.8 31.1 + - - +
120A GLN* 4.6 12.3 - - - +
121A VAL* 5.0 4.7 - - + +
150A TYR* 4.6 3.5 - - - -
151A ALA* 1.3 68.0 - - - +
153A SER* 1.3 57.2 + - - +
154A SER 3.1 5.2 - - - -
156A GLY* 2.9 30.3 + - - -
216A LEU* 5.0 2.1 - - - +
220A ALA* 3.8 20.0 - - + +
221A TYR* 4.1 20.6 - - + -
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.5 7.0 - - - +
118A PRO* 2.6 42.6 + - - +
119A LEU 3.9 0.4 + - - -
121A VAL* 3.8 23.9 - - - +
134A PHE* 4.0 12.3 - - - -
135A TYR* 2.6 39.1 + - - -
152A ASN* 1.3 78.6 - - - +
154A SER* 1.3 61.4 + - - +
156A GLY 4.2 0.9 - - - -
157A LEU* 3.6 5.2 - - - +
216A LEU* 4.9 0.9 - - - -
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A HIS 3.8 0.9 + - - -
109A LEU* 2.5 41.4 + - - +
112A TYR* 3.6 18.9 - - - -
114A ALA* 4.8 1.6 - - - +
117A LEU* 3.9 23.0 - - - +
151A ALA* 3.3 21.2 + - - -
152A ASN 3.1 1.0 - - - -
153A SER* 1.3 78.2 + - - +
155A ILE* 1.3 67.7 + - - +
156A GLY 3.1 1.3 + - - -
157A LEU* 3.2 4.3 + - - +
158A PHE 3.2 15.8 + - - -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS* 3.3 50.3 - - + +
70A THR* 4.2 17.6 - - + +
71A GLY* 5.3 4.3 - - - +
109A LEU 3.3 5.1 + - - +
110A ALA* 3.5 22.4 - - + +
112A TYR* 3.8 13.9 - - + +
151A ALA 3.4 7.3 + - - +
152A ASN* 4.2 2.9 - - - +
154A SER* 1.3 79.3 - - - +
156A GLY* 1.3 66.2 + - - +
158A PHE* 3.2 33.0 + - + +
159A GLY* 3.0 20.6 + - - -
219A GLU 5.2 0.2 - - - -
220A ALA* 4.6 3.8 - - + -
269A LEU* 5.7 0.7 - - + -
270A GLY 5.3 7.9 - - - +
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN 2.9 22.1 + - - -
155A ILE* 1.3 83.0 - - - +
157A LEU* 1.3 60.9 + - - +
159A GLY 3.4 1.4 + - - -
160A ALA* 3.2 19.8 + - - +
216A LEU* 3.7 16.8 - - - +
219A GLU* 3.6 24.3 - - - +
220A ALA* 4.6 3.8 - - - -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A THR* 4.4 6.3 - - + -
93A TRP* 3.3 36.6 - - + -
96A LEU* 4.7 0.7 - - + -
101A TRP* 4.1 15.0 - - + -
109A LEU* 3.8 24.0 - - + -
131A LEU* 5.5 2.5 - - + -
135A TYR* 3.7 33.7 - - + +
153A SER 3.6 17.4 + - - +
154A SER 3.2 5.2 + - - +
156A GLY* 1.3 72.6 - - - +
158A PHE* 1.3 67.3 + - - +
160A ALA* 3.2 7.8 + - + +
161A LEU* 2.9 40.9 + - + +
216A LEU* 3.7 7.5 - - + +
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 4.2 9.9 - - + -
71A GLY* 4.9 6.1 - - - -
74A GLY* 3.9 31.2 - - - -
83A ILE* 4.4 11.7 - - + -
85A LEU* 3.7 31.2 - - + -
106A LEU* 3.5 32.8 - - + -
109A LEU* 3.9 8.9 - - + +
110A ALA* 3.6 22.0 - - + +
154A SER 3.2 12.3 + - - +
155A ILE* 3.4 30.3 - - + +
157A LEU* 1.3 77.6 - - - +
159A GLY* 1.3 60.9 + - - +
161A LEU* 3.3 3.1 + - - +
162A ALA* 2.8 38.1 + - + +
269A LEU* 5.2 4.7 - - + -
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 3.7 24.7 - - - -
155A ILE 3.0 11.1 + - - -
156A GLY 3.4 2.9 + - - -
157A LEU 3.2 0.2 - - - -
158A PHE* 1.3 82.3 - - - +
160A ALA* 1.3 62.2 + - - +
162A ALA* 3.4 10.7 + - - +
163A VAL* 3.5 10.4 + - - +
170A PHE* 3.6 24.2 - - - -
219A GLU* 4.1 1.3 - - - -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 6.2 0.2 - - + -
156A GLY 3.2 13.6 + - - +
157A LEU* 3.2 13.6 + - + +
159A GLY* 1.3 74.6 - - - +
161A LEU* 1.3 65.0 + - + +
163A VAL* 3.4 20.0 - - - +
164A LYS* 3.7 14.1 - - - +
170A PHE* 4.9 0.9 - - - -
216A LEU* 4.1 19.1 - - + -
219A GLU* 3.9 13.7 - - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 4.6 0.6 - - - +
89A THR* 3.4 38.8 - - + +
92A TYR* 4.1 16.4 - - + +
93A TRP* 4.0 19.3 - - + -
106A LEU* 3.9 23.8 - - + -
109A LEU* 4.0 1.1 - - + -
157A LEU* 2.9 39.0 + - + +
158A PHE 3.9 2.0 - - - +
160A ALA* 1.3 78.0 - - + +
162A ALA* 1.3 66.7 + - - +
163A VAL 3.2 0.4 - - - -
164A LYS* 3.1 45.1 + - - +
165A PRO* 3.6 4.2 - - - +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 5.6 1.1 - - + +
74A GLY* 4.3 18.2 - - - -
77A ALA* 3.9 13.5 - - + +
82A GLU* 4.7 3.5 - - - +
83A ILE* 3.7 36.6 - - + +
106A LEU* 5.5 1.3 - - - +
158A PHE* 2.8 24.4 + - + +
159A GLY* 3.8 7.4 - - - +
160A ALA 3.4 0.2 - - - -
161A LEU* 1.3 77.9 - - - +
163A VAL* 1.3 63.3 + - + +
165A PRO* 3.7 9.5 - - - +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.9 22.9 - - + -
77A ALA* 5.9 1.1 - - + -
82A GLU* 5.7 0.4 - - - -
159A GLY 3.5 12.3 + - - +
160A ALA* 3.4 16.8 - - - +
162A ALA* 1.3 79.0 - - + +
164A LYS* 1.3 65.7 + - - +
165A PRO 3.4 1.8 - - - -
166A SER* 2.8 31.7 + - - +
167A GLY 3.4 2.1 + - - -
168A LEU 3.7 20.8 - - - +
169A SER* 5.2 0.2 - - - -
170A PHE* 4.1 19.5 - - + +
173A ALA* 3.8 23.1 - - + -
177A ARG* 6.0 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