Contacts of the helix formed by residues 130 - 143 (chain B) in PDB entry 1LUA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ALA 4.2 0.4 + - - -
128B GLY 3.3 1.6 - - - -
129B THR* 1.3 81.6 - - - +
131B PRO* 1.4 70.3 - - - +
132B VAL 3.4 2.5 - - - -
133B GLY 3.4 1.9 + - - +
134B MET* 3.0 29.3 + - - +
1456B NAP 3.5 32.6 + - - -
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Residues in contact with PRO 131 (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 MET* 3.7 31.4 - - + +
99B SER* 3.3 25.4 - - - +
130B GLY* 1.4 82.7 - - - +
132B VAL* 1.3 56.8 + - - +
134B MET* 3.8 6.9 - - + +
135B ARG* 3.0 36.3 + - + +
1456B NAP 3.3 25.4 - - - +
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Residues in contact with VAL 132 (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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99B SER* 4.1 18.4 - - - +
102B THR* 4.2 7.9 - - + -
103B ALA* 3.9 9.0 - - + +
131B PRO* 1.3 72.6 - - - +
133B GLY* 1.3 61.3 + - - +
136B SER* 2.8 34.6 + - - +
196B ALA* 4.5 0.7 - - + -
221B TYR* 3.6 48.5 - - + -
1456B NAP 3.1 56.4 + - + +
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Residues in contact with GLY 133 (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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125B VAL* 4.0 8.9 - - - +
128B GLY* 3.4 21.9 - - - +
130B GLY 3.4 4.8 + - - +
132B VAL* 1.3 78.4 - - - +
134B MET* 1.3 56.9 + - - +
136B SER* 3.4 3.0 + - - -
137B ALA* 3.0 29.8 + - - +
196B ALA* 3.6 25.1 - - - +
1456B NAP 4.2 0.8 + - - -
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Residues in contact with MET 134 (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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128B GLY 3.6 11.7 - - - +
129B THR 3.6 18.8 - - - +
130B GLY 3.0 18.2 + - - +
131B PRO* 3.8 6.5 - - + +
133B GLY* 1.3 77.3 - - - +
135B ARG* 1.3 67.8 + - + +
137B ALA* 3.3 6.1 + - - +
138B ALA* 3.0 17.8 + - - +
149B LEU* 4.4 1.8 - - + -
160B ALA* 3.5 36.6 - - + +
163B SER* 3.6 23.8 - - - +
164B VAL* 3.6 24.6 - - + +
168B PHE* 6.0 0.4 - - - -
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Residues in contact with ARG 135 (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 MET* 4.2 12.6 - - + +
74B GLU* 2.9 30.7 + - - +
94B LEU* 4.1 11.1 - - - +
99B SER* 4.5 9.2 - - - +
100B ASN* 2.9 25.4 + - - +
103B ALA* 3.6 20.2 - - + -
131B PRO* 3.0 23.3 + - + +
134B MET* 1.3 80.1 - - + +
136B SER* 1.3 64.6 + - - +
138B ALA* 3.2 4.8 + - - +
139B LEU* 3.0 27.5 + - + +
167B ARG* 5.1 4.8 - - - +
168B PHE* 3.9 29.1 - - - -
276B ASP* 3.0 28.7 + - - -
277B ALA* 3.6 13.8 - - + +
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Residues in contact with SER 136 (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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103B ALA* 3.6 6.3 - - - +
107B VAL* 3.9 14.1 - - - -
125B VAL* 4.8 7.9 - - - -
132B VAL 2.8 22.5 + - - -
133B GLY* 3.6 6.7 - - - -
135B ARG* 1.3 76.7 - - - +
137B ALA* 1.3 63.3 + - - +
139B LEU* 3.2 3.7 + - - +
140B LEU* 3.0 34.3 + - - +
194B PHE* 5.0 2.7 - - - -
221B TYR* 2.8 34.5 + - - -
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Residues in contact with ALA 137 (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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125B VAL* 4.5 5.5 - - + +
133B GLY 3.0 18.0 + - - +
134B MET 3.6 4.7 - - - +
136B SER* 1.3 75.4 - - - +
138B ALA* 1.3 64.2 + - - +
140B LEU* 3.8 4.6 - - - +
141B ALA* 2.9 26.2 + - - +
147B VAL* 4.0 27.4 - - + +
149B LEU* 4.3 18.4 - - + -
164B VAL* 4.9 2.0 - - + -
172B VAL* 4.1 13.6 - - + +
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Residues in contact with ALA 138 (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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134B MET 3.0 12.4 + - - +
135B ARG 3.2 9.6 + - - +
137B ALA* 1.3 76.9 - - - +
139B LEU* 1.3 60.6 + - + +
141B ALA* 3.3 5.0 + - - +
142B GLY* 3.0 25.3 + - - -
164B VAL* 3.7 12.3 - - + +
168B PHE* 3.4 48.8 - - + +
170B VAL* 4.5 5.3 - - - +
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Residues in contact with LEU 139 (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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100B ASN 5.4 0.7 - - - +
103B ALA* 4.1 9.4 - - + +
104B ALA* 3.8 34.5 - - + +
107B VAL* 4.1 14.1 - - + -
135B ARG* 3.0 16.6 + - + +
136B SER 3.8 2.9 - - - +
138B ALA* 1.3 77.2 - - + +
140B LEU* 1.3 66.0 + - - +
142B GLY* 3.3 2.8 + - - -
143B GLU* 3.2 25.6 + - - +
168B PHE* 5.6 2.2 - - + -
277B ALA* 3.9 26.2 - - + +
278B GLU* 4.6 8.1 - - + +
281B TYR* 3.7 38.4 - - + -
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Residues in contact with LEU 140 (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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107B VAL* 3.9 22.4 - - + -
110B VAL* 5.5 2.9 - - + -
111B VAL* 5.0 9.0 - - + -
118B VAL* 5.2 4.9 - - + -
123B ALA* 4.4 15.9 - - + -
125B VAL* 4.1 14.4 - - + -
136B SER* 3.0 27.6 + - - +
137B ALA* 3.8 1.1 - - - +
139B LEU* 1.3 75.3 - - - +
141B ALA* 1.3 58.8 + - - +
143B GLU* 2.9 22.4 + - - +
144B GLY 3.3 0.2 + - - -
145B ALA* 3.2 24.0 + - + +
147B VAL* 3.7 16.8 - - + -
192B PHE* 5.7 3.8 - - + -
194B PHE* 3.8 38.4 - - + -
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Residues in contact with ALA 141 (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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137B ALA 2.9 17.5 + - - +
138B ALA 3.6 2.9 - - - +
140B LEU* 1.3 76.8 - - - +
142B GLY* 1.3 58.0 + - - +
144B GLY* 3.0 18.7 + - - -
145B ALA 4.0 12.5 - - - +
147B VAL* 3.8 6.2 - - + +
170B VAL* 3.6 33.8 - - + +
171B ASN 4.9 3.1 - - - +
172B VAL* 4.0 11.7 - - + +
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Residues in contact with GLY 142 (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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119B LYS* 5.1 2.9 + - - -
138B ALA 3.0 15.3 + - - -
139B LEU* 3.8 4.5 - - - -
140B LEU 3.2 0.4 - - - -
141B ALA* 1.3 77.3 - - - +
143B GLU* 1.3 60.7 + - - +
144B GLY 3.1 1.5 + - - -
170B VAL* 4.1 9.6 - - - +
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Residues in contact with GLU 143 (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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111B VAL* 4.1 15.5 - - + +
116B GLY 5.1 3.1 - - - +
117B SER* 5.6 1.2 + - - -
118B VAL* 3.7 18.3 + - + +
119B LYS* 3.4 25.3 + - - +
139B LEU 3.2 13.6 + - - +
140B LEU* 2.9 12.7 + - - +
142B GLY* 1.3 77.2 - - - +
144B GLY* 1.3 58.8 + - - +
145B ALA 3.5 1.0 + - - -
281B TYR* 2.6 36.7 + - + +
285B LYS* 2.8 29.8 + - - -
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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