Contacts of the helix formed by residues 98 - 114 (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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP* 5.8 2.1 + - - -
95B ASP* 2.9 29.7 + - - -
97B ASN* 1.3 78.0 - - - +
99B SER* 1.3 57.9 + - - +
100B ASN 3.4 2.5 - - - -
101B THR* 3.5 3.0 + - - -
102B THR* 2.8 36.6 + - - -
256B LYS* 4.5 9.4 - - - -
1456B NAP 4.2 4.3 - - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B MET* 4.2 13.6 - - - +
95B ASP* 3.7 0.4 + - - -
96B SER 3.0 15.8 + - - -
97B ASN* 3.2 10.1 + - - +
98B GLY* 1.3 78.8 - - - +
100B ASN* 1.3 62.4 + - - +
102B THR* 4.2 0.3 - - - -
103B ALA* 3.2 26.3 + - - +
131B PRO* 3.3 35.1 - - - +
132B VAL* 4.1 19.4 - - - +
135B ARG* 4.4 5.3 - - - +
1456B NAP 4.6 2.1 + - - -
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Residues in contact with ASN 100 (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* 5.3 3.2 - - - +
94B LEU* 2.8 31.3 + - - +
95B ASP* 3.0 12.3 + - - +
99B SER* 1.3 76.7 - - - +
101B THR* 1.3 62.5 + - - +
103B ALA* 4.1 1.8 - - - +
104B ALA* 2.9 31.9 + - - +
135B ARG* 2.9 32.2 + - - +
139B LEU* 5.4 0.7 - - - +
276B ASP* 3.1 23.0 + - - +
277B ALA* 3.5 21.5 - - - +
280B ILE* 3.7 16.3 - - + +
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Residues in contact with THR 101 (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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93B MET* 3.9 20.0 - - + -
95B ASP* 2.8 29.1 + - - +
98B GLY 3.5 2.3 + - - -
100B ASN* 1.3 75.3 - - - +
102B THR* 1.3 59.1 + - - +
105B ALA* 3.1 30.3 + - - +
256B LYS* 2.8 42.7 + - - +
259B LEU* 3.8 12.9 - - + +
260B HIS* 4.0 16.8 - - + +
263B CYS* 5.0 0.2 - - - -
280B ILE* 4.1 13.9 - - + -
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Residues in contact with THR 102 (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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98B GLY 2.8 22.4 + - - -
99B SER* 4.2 2.9 - - - -
101B THR* 1.3 75.6 + - - +
103B ALA* 1.3 65.4 + - - +
105B ALA* 3.4 2.9 + - - +
106B GLY 3.0 19.1 + - - -
132B VAL* 4.2 12.3 - - + -
221B TYR* 3.4 31.3 - - + -
252B ILE* 3.9 6.4 - - + +
256B LYS* 3.8 15.1 - - + +
1456B NAP 3.5 36.5 + - + -
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Residues in contact with ALA 103 (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 3.2 18.1 + - - +
100B ASN 4.1 1.3 - - - +
102B THR* 1.3 80.5 - - - +
104B ALA* 1.3 57.3 + - - +
106B GLY 3.5 0.2 + - - -
107B VAL* 3.1 35.3 + - - +
132B VAL* 3.9 6.5 - - + +
135B ARG* 3.6 26.7 - - + -
136B SER* 3.6 17.3 - - - +
139B LEU* 4.2 4.0 - - + -
221B TYR* 3.6 11.5 + - - -
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Residues in contact with ALA 104 (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 2.9 19.2 + - - +
103B ALA* 1.3 74.7 - - - +
105B ALA* 1.3 60.0 + - - +
108B ALA* 3.0 32.1 + - - +
139B LEU* 3.8 13.8 - - + +
259B LEU* 4.0 6.7 - - + -
277B ALA 5.0 1.3 - - - +
280B ILE* 3.8 22.9 - - + -
281B TYR* 3.6 24.5 - - + +
284B ALA* 3.6 2.8 - - + +
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Residues in contact with ALA 105 (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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101B THR 3.1 19.0 + - - +
102B THR 3.9 2.9 - - - +
104B ALA* 1.3 77.1 - - - +
106B GLY* 1.3 64.2 + - - +
108B ALA* 3.4 1.2 + - - +
109B LEU* 3.0 32.2 + - - +
252B ILE* 3.8 12.3 - - + +
255B LEU* 3.7 20.6 - - + +
256B LYS* 3.7 27.1 - - + +
259B LEU* 4.3 2.6 - - + +
284B ALA* 4.7 2.9 - - - -
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Residues in contact with GLY 106 (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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102B THR 3.0 10.9 + - - -
105B ALA* 1.3 80.2 - - - +
107B VAL* 1.3 60.9 + - - +
109B LEU* 3.8 2.2 - - - +
110B VAL* 3.1 27.2 + - - +
194B PHE* 4.2 4.0 - - - -
219B ALA* 5.3 0.2 - - - +
221B TYR* 3.7 17.9 - - - -
252B ILE* 3.6 25.6 - - - +
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Residues in contact with VAL 107 (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 3.1 17.4 + - - +
106B GLY* 1.3 75.4 - - - +
108B ALA* 1.3 57.4 + - - +
110B VAL* 3.2 1.2 + - - +
111B VAL* 2.8 33.3 + - + +
136B SER* 3.9 34.8 - - - +
139B LEU* 4.1 14.1 - - + +
140B LEU* 3.9 29.8 - - + +
194B PHE* 4.4 10.5 - - + -
221B TYR* 4.2 1.8 - - - +
281B TYR* 3.7 26.7 - - + +
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Residues in contact with ALA 108 (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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104B ALA 3.0 21.5 + - - +
105B ALA* 3.8 3.8 - - - +
107B VAL* 1.3 75.1 - - - +
109B LEU* 1.3 57.6 + - - +
111B VAL* 4.0 1.4 - - - +
112B LYS* 3.0 29.3 + - - +
255B LEU* 4.7 0.7 - - + -
281B TYR* 3.5 16.7 - - + -
284B ALA* 3.7 33.4 - - + +
285B LYS* 4.1 6.6 - - - +
288B ALA* 4.2 9.9 - - + +
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Residues in contact with LEU 109 (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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105B ALA 3.0 21.7 + - - +
106B GLY 3.8 3.6 - - - +
108B ALA* 1.3 74.4 - - - +
110B VAL* 1.3 59.0 + - - +
112B LYS* 3.5 6.4 + - + +
113B ALA* 3.0 30.1 + - - +
237B LYS* 3.9 24.7 - - - +
247B PHE* 3.9 32.9 - - + -
251B GLY 4.3 6.1 - - - +
252B ILE* 3.9 31.4 - - + -
255B LEU* 3.5 26.9 - - + -
288B ALA* 4.2 14.8 - - + +
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Residues in contact with VAL 110 (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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106B GLY 3.1 17.5 + - - +
107B VAL 3.7 2.2 - - - +
109B LEU* 1.3 73.4 - - - +
111B VAL* 1.3 69.0 + - + +
113B ALA* 3.3 1.4 + - - -
114B ALA* 3.0 22.8 + - + +
118B VAL* 5.7 1.1 - - + -
140B LEU* 5.5 2.9 - - + -
192B PHE* 4.2 22.7 - - + -
194B PHE* 3.4 36.3 - - + -
217B ILE* 3.7 31.0 - - + +
218B VAL 5.5 0.2 - - - -
219B ALA* 3.9 17.3 - - + -
247B PHE* 4.5 6.5 - - + -
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Residues in contact with VAL 111 (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* 2.8 33.3 + - + +
108B ALA* 4.1 2.9 - - - +
110B VAL* 1.3 72.8 - - + +
112B LYS* 1.3 61.3 + - - +
114B ALA* 3.3 12.2 + - - +
115B GLY 3.5 0.2 + - - -
116B GLY* 2.9 48.3 + - - +
117B SER* 4.3 2.5 - - - +
118B VAL* 4.3 25.1 - - + -
140B LEU* 5.0 5.4 - - + -
143B GLU* 4.1 19.5 - - + +
281B TYR* 3.5 17.7 - - - +
285B LYS* 4.6 8.7 - - - -
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Residues in contact with LYS 112 (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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108B ALA 3.0 19.8 + - - +
109B LEU* 3.8 7.0 - - + +
111B VAL* 1.3 79.5 - - - +
113B ALA* 1.3 59.5 + - - +
115B GLY* 3.0 20.6 + - - -
116B GLY* 3.8 5.6 + - - +
285B LYS 5.9 0.7 - - - +
288B ALA* 3.1 43.9 + - + +
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Residues in contact with ALA 113 (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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109B LEU 3.0 18.4 + - - +
110B VAL 3.3 0.2 + - - -
112B LYS* 1.3 76.7 - - - +
114B ALA* 1.3 59.1 + - - +
115B GLY 3.1 1.6 + - - -
217B ILE* 3.8 19.1 - - + +
245B ARG* 4.7 23.0 + - - +
247B PHE* 3.9 21.3 - - + -
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Residues in contact with ALA 114 (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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110B VAL 3.0 16.7 + - - +
111B VAL 3.6 6.3 - - - +
112B LYS 3.1 0.4 - - - -
113B ALA* 1.3 77.0 - - - +
115B GLY* 1.3 57.9 + - - +
116B GLY 3.6 0.2 - - - -
117B SER 4.3 8.6 - - - +
118B VAL* 4.0 11.4 - - + -
121B LYS* 4.9 7.9 + - - +
192B PHE* 3.8 33.4 - - + -
216B GLU* 4.8 6.8 - - - +
217B ILE* 3.8 5.8 - - + -
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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