Contacts of the helix formed by residues 130 - 143 (chain A) in PDB entry 1LU9
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ALA 4.5 4.6 + - - -
128A GLY* 3.3 1.6 - - - -
129A THR* 1.3 83.8 + - - +
131A PRO* 1.4 69.2 - - - +
132A VAL 3.5 2.0 - - - -
133A GLY 3.2 3.6 + - - -
134A MET* 2.9 29.6 + - - +
196A ALA 5.6 3.8 - - - -
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Residues in contact with PRO 131 (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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68A GLY 4.3 14.4 - - - +
70A MET* 3.9 34.0 - - + +
96A SER 4.6 5.4 - - - +
99A SER* 3.7 23.8 - - - -
130A GLY* 1.4 82.0 - - - +
132A VAL* 1.3 60.8 + - + +
134A MET* 3.4 1.4 + - - +
135A ARG* 2.9 33.3 + - - +
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Residues in contact with VAL 132 (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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97A ASN 4.7 6.1 - - - +
98A GLY 3.8 22.9 - - - +
99A SER* 4.1 10.8 - - - -
102A THR* 3.9 17.0 - - + -
103A ALA* 3.7 6.5 - - - +
130A GLY 3.5 0.4 - - - -
131A PRO* 1.3 79.4 - - + +
133A GLY* 1.3 58.3 + - - +
136A SER* 2.8 36.2 + - - +
196A ALA* 5.1 2.9 - - + -
221A TYR* 3.7 43.5 - - + -
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.0 8.7 - - - +
127A ALA 4.9 0.2 - - - -
128A GLY* 3.4 18.8 - - - -
130A GLY* 3.2 7.7 + - - -
132A VAL* 1.3 79.6 - - - +
134A MET* 1.3 56.0 + - - +
136A SER* 3.2 4.5 + - - -
137A ALA* 2.9 28.9 + - - +
196A ALA* 3.7 25.8 + - - +
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Residues in contact with MET 134 (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 MET* 3.9 25.1 - - + -
128A GLY 3.2 14.8 + - - +
129A THR 3.6 17.5 - - - +
130A GLY 2.9 15.2 + - - +
131A PRO 3.9 3.1 - - - +
133A GLY* 1.3 77.3 - - - +
135A ARG* 1.3 62.2 + - - +
137A ALA* 3.2 6.7 + - - +
138A ALA* 3.0 18.9 + - - +
149A LEU* 4.3 1.1 - - + -
160A ALA* 3.5 35.7 - - + +
163A SER* 3.4 28.5 - - - +
164A VAL* 3.5 22.8 - - + +
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Residues in contact with ARG 135 (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 MET* 3.6 26.0 - - - +
74A GLU* 2.8 31.1 + - - +
94A LEU* 3.9 16.8 - - - +
99A SER* 3.4 30.7 + - - +
100A ASN* 2.7 23.3 + - - +
103A ALA* 3.6 8.1 - - + -
131A PRO 2.9 15.9 + - - +
134A MET* 1.3 73.4 - - - +
136A SER* 1.3 66.5 + - - +
138A ALA* 3.3 2.9 + - - +
139A LEU* 3.0 31.6 + - + +
167A ARG* 4.8 2.4 - - - +
168A PHE* 3.7 33.9 - - - -
276A ASP* 3.0 25.5 + - - -
277A ALA* 3.6 9.9 - - + +
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Residues in contact with SER 136 (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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103A ALA* 3.4 10.5 + - - +
107A VAL* 3.8 11.4 - - - +
125A VAL* 5.0 5.6 - - - -
132A VAL 2.8 24.3 + - - -
133A GLY* 3.5 7.2 - - - -
134A MET 3.2 0.2 - - - -
135A ARG* 1.3 78.2 - - - +
137A ALA* 1.3 63.6 + - - +
139A LEU* 3.2 2.4 + - - +
140A LEU* 2.9 32.7 + - - +
194A PHE* 4.7 7.2 - - - -
221A TYR* 2.7 34.1 + - - -
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Residues in contact with ALA 137 (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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125A VAL* 4.3 8.9 - - + +
133A GLY 2.9 13.6 + - - +
134A MET 3.4 9.6 - - - +
136A SER* 1.3 77.1 - - - +
138A ALA* 1.3 56.1 + - - +
140A LEU* 3.7 2.8 - - - +
141A ALA* 2.9 31.0 + - - +
147A VAL* 3.8 26.2 - - + +
149A LEU* 4.2 20.4 - - + -
164A VAL* 4.8 2.0 - - + -
172A VAL* 3.9 10.4 - - + +
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Residues in contact with ALA 138 (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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134A MET 3.0 16.2 + - - +
135A ARG 3.6 6.5 - - - +
136A SER 3.1 0.4 - - - -
137A ALA* 1.3 78.6 - - - +
139A LEU* 1.3 53.2 + - + +
141A ALA* 3.3 4.7 + - - +
142A GLY* 2.8 31.5 + - - -
164A VAL* 3.8 13.2 - - + -
168A PHE* 3.3 48.8 - - + +
170A VAL* 4.7 3.2 - - - +
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Residues in contact with LEU 139 (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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100A ASN* 5.1 1.1 - - - +
103A ALA* 4.0 7.4 - - + +
104A ALA* 3.5 37.7 - - + +
107A VAL* 3.9 15.9 - - + -
135A ARG* 3.0 22.9 + - + +
136A SER 3.7 2.9 - - - +
138A ALA* 1.3 74.0 - - + +
140A LEU* 1.3 60.9 + - - +
142A GLY* 3.2 3.3 + - - -
143A GLU* 2.9 32.2 + - - +
168A PHE* 5.6 2.5 - - + -
277A ALA* 4.2 24.2 - - + +
278A GLU* 5.1 2.5 - - + +
281A TYR* 3.7 38.9 - - + -
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Residues in contact with LEU 140 (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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107A VAL* 4.0 17.3 - - + -
110A VAL* 5.4 3.8 - - + -
111A VAL* 5.2 2.9 - - + -
118A VAL* 4.9 13.0 - - + -
123A ALA* 4.1 19.1 - - + -
125A VAL* 4.1 12.8 - - + -
136A SER 2.9 25.2 + - - +
137A ALA* 3.7 4.7 - - - +
139A LEU* 1.3 74.2 - - - +
141A ALA* 1.3 62.5 + - - +
143A GLU* 3.1 12.9 + - - +
144A GLY 3.4 0.2 + - - -
145A ALA* 3.0 35.0 + - + +
147A VAL* 3.8 11.0 - - + -
192A PHE* 5.5 1.3 - - + -
194A PHE* 3.5 47.1 - - + -
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Residues in contact with ALA 141 (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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137A ALA 2.9 18.3 + - - +
138A ALA 3.5 3.8 - - - +
140A LEU* 1.3 74.9 - - - +
142A GLY* 1.3 59.9 + - - +
144A GLY* 2.9 21.0 + - - -
145A ALA 3.8 12.6 - - - +
147A VAL* 3.7 4.2 - - + +
170A VAL* 3.7 35.3 - - + +
171A ASN 5.1 1.6 - - - +
172A VAL* 3.9 11.9 - - + +
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Residues in contact with GLY 142 (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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138A ALA 2.8 18.9 + - - -
139A LEU* 3.2 5.3 + - - -
141A ALA* 1.3 74.3 - - - +
143A GLU* 1.3 56.8 + - - +
144A GLY 3.1 3.7 + - - -
170A VAL* 4.1 9.1 - - - +
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Residues in contact with GLU 143 (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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107A VAL* 4.9 0.4 - - + -
111A VAL* 4.0 16.5 - - + +
116A GLY 4.8 3.6 - - - +
117A SER* 5.6 2.1 - - - -
118A VAL* 3.5 17.1 + - + +
119A LYS* 3.7 21.0 + - - +
139A LEU 2.9 17.0 + - - +
140A LEU* 3.1 10.7 + - - +
142A GLY* 1.3 74.7 - - - +
144A GLY* 1.3 60.3 + - - +
145A ALA 3.3 1.2 + - - -
281A TYR* 2.6 34.5 + - + +
285A LYS* 2.6 33.8 + - - -
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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