Contacts of the helix formed by residues 86 - 102 (chain L) in PDB entry 1LWU
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 GLN 86 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR* 3.7 27.5 + - - +
102A SER* 4.7 5.7 + - - -
105A LEU* 5.5 2.3 - - - +
163B ALA* 5.8 7.7 - - + +
83L LYS* 3.4 28.7 - - - +
84L THR 3.0 1.2 - - - +
85L VAL* 1.3 80.7 - - - +
87L LYS* 1.3 72.7 + - + +
89L LEU* 3.8 8.1 + - - +
90L GLU* 3.7 22.9 + - - +
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Residues in contact with LYS 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K GLU* 5.4 3.4 - - - +
83L LYS* 4.6 11.4 - - - +
84L THR 3.7 6.0 + - - +
86L GLN* 1.3 84.7 - - + +
88L ILE* 1.3 53.7 + - + +
89L LEU 2.7 16.3 + - - -
90L GLU* 2.6 34.3 + - + +
91L GLU* 2.7 48.7 + - + +
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Residues in contact with ILE 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J LEU* 3.9 9.8 - - + +
163K ALA 3.2 25.4 - - - +
164K GLN* 3.4 19.3 - - - +
167K ILE* 3.1 49.6 - - + +
168K GLU* 4.5 11.9 - - + -
84L THR* 3.0 22.4 - - + +
85L VAL* 3.4 27.4 - - + +
86L GLN 3.4 0.2 - - - -
87L LYS* 1.3 76.4 - - + +
89L LEU* 1.3 54.9 + - - +
91L GLU* 4.6 6.3 - - - +
92L VAL* 3.7 17.6 - - - +
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 2.7 46.7 - - + +
98A GLU* 3.2 30.7 - - + -
101A TYR* 4.9 14.8 - - + -
108J LEU* 4.0 14.6 - - + -
111J ARG* 5.6 0.7 - - - +
85L VAL* 3.8 13.8 + - + +
86L GLN* 3.8 9.8 + - - +
87L LYS 2.7 1.2 + - - -
88L ILE* 1.3 82.1 - - - +
90L GLU* 1.3 65.2 + - + +
91L GLU 3.5 0.4 - - - -
92L VAL* 3.5 16.9 - - + +
93L ARG* 3.6 11.7 + - + +
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Residues in contact with GLU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L GLN* 3.7 18.3 + - - +
87L LYS* 2.6 45.2 + - + +
89L LEU* 1.3 83.2 - - + +
91L GLU* 1.3 60.6 + - + +
92L VAL 3.0 1.8 - - - -
93L ARG* 2.8 37.9 + - + +
94L ILE* 3.1 14.4 + - + +
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Residues in contact with GLU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 4.2 6.6 - - + +
168K GLU* 2.6 45.1 - - - +
171K TYR* 3.1 41.1 - - + +
87L LYS* 2.7 41.3 + - + +
88L ILE* 4.6 5.4 - - - +
90L GLU* 1.3 72.9 - - + +
92L VAL* 1.3 61.7 + - + +
94L ILE* 3.0 20.5 + - - +
95L LEU* 3.0 19.7 + - - +
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Residues in contact with VAL 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J LEU* 3.8 11.7 - - + -
111J ARG* 3.7 24.2 - - + +
112J ILE* 3.3 32.8 - - + -
115J LEU* 4.1 7.4 - - + +
167K ILE* 5.3 1.6 - - + -
88L ILE 3.7 20.6 - - - +
89L LEU* 3.5 11.2 + - + +
90L GLU 3.0 0.4 - - - -
91L GLU* 1.3 78.7 - - + +
93L ARG* 1.3 51.8 + - - +
95L LEU* 4.6 1.1 - - - +
96L GLU* 2.6 66.9 + - + +
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Residues in contact with ARG 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASN* 3.4 48.3 - - - +
98A GLU* 4.3 10.3 - - - +
89L LEU* 3.6 8.8 + - + +
90L GLU* 2.8 26.0 + - + +
92L VAL* 1.3 79.3 - - - +
94L ILE* 1.3 52.4 + - + +
96L GLU* 4.0 11.2 - - - +
97L GLN* 2.7 36.3 + - - +
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Residues in contact with ILE 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K TYR* 4.4 9.2 - - - +
90L GLU* 3.1 17.7 + - + +
91L GLU* 3.0 14.1 + - - +
92L VAL 2.9 1.6 + - - -
93L ARG* 1.3 76.3 - - + +
95L LEU* 1.3 70.8 + - + +
96L GLU 3.1 1.1 - - - -
97L GLN* 2.8 20.8 + - - +
98L ILE* 2.5 51.0 + - + +
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Residues in contact with LEU 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ILE* 6.5 0.7 - - + -
115J LEU* 3.3 23.9 - - + +
119J ILE* 4.4 1.2 - - + +
171K TYR* 3.5 33.9 - - + +
174K VAL* 3.2 37.0 - - + +
175K LYS* 5.7 4.5 - - + -
178K ILE* 3.6 31.5 - - + +
91L GLU 3.0 15.3 + - - +
92L VAL* 5.3 0.4 - - - -
94L ILE* 1.3 84.4 - - + +
96L GLU* 1.3 57.0 + - - +
97L GLN 3.0 4.9 - - - -
98L ILE* 4.2 2.5 - - + +
99L GLY* 3.0 25.5 + - - -
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Residues in contact with GLU 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J ARG* 3.1 43.3 + - - +
114J HIS* 4.9 4.3 - - - -
115J LEU* 3.1 20.4 - - + +
118J ARG* 3.2 34.6 + - - +
92L VAL* 2.6 44.5 + - - +
93L ARG* 4.0 8.1 - - - +
95L LEU* 1.3 71.9 - - - +
97L GLN* 1.3 56.6 + - - +
99L GLY 4.4 1.1 - - - -
100L VAL* 3.5 9.0 - - - +
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Residues in contact with GLN 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L ARG 2.7 19.0 + - - +
94L ILE* 2.8 28.6 + - - +
96L GLU* 1.3 79.2 - - - +
98L ILE* 1.3 59.9 + - + +
99L GLY 3.1 1.1 - - - -
100L VAL* 2.8 28.0 + - - +
101L SER* 3.2 10.1 + - - -
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Residues in contact with ILE 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178K ILE* 3.1 48.7 - - + -
179K GLU* 6.3 0.7 - - + -
94L ILE* 2.5 40.0 + - + +
95L LEU* 4.3 2.2 - - + -
97L GLN* 1.3 77.1 - - + +
99L GLY* 1.3 54.6 + - - +
101L SER* 2.9 9.4 + - - -
102L HIS* 2.5 48.8 + - + +
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Residues in contact with GLY 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU* 5.4 3.4 - - - -
118J ARG* 5.0 9.4 - - - -
119J ILE* 5.2 6.1 - - - -
122J GLN* 2.8 30.8 + - - -
178K ILE* 5.1 3.4 - - - -
95L LEU 3.0 18.9 + - - -
96L GLU 5.0 0.9 - - - -
97L GLN 3.1 0.6 - - - -
98L ILE* 1.3 78.4 - - - +
100L VAL* 1.3 60.2 + - - +
102L HIS* 3.9 8.5 - - - -
103L ASP* 2.9 7.5 - - - +
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Residues in contact with VAL 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J ARG* 4.0 11.4 - - - +
96L GLU 3.5 22.7 - - - +
97L GLN* 2.8 10.1 + - - +
99L GLY* 1.3 80.1 - - - +
101L SER* 1.3 59.9 + - - +
102L HIS 3.3 1.1 - - - -
103L ASP* 3.5 8.5 - - + -
104L ALA* 3.1 24.4 + - - +
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Residues in contact with SER 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L GLN* 3.2 9.8 + - - -
98L ILE* 2.9 13.7 + - - -
100L VAL* 1.3 73.9 - - - +
102L HIS* 1.3 64.8 + - - +
103L ASP 3.1 1.8 - - - -
104L ALA* 3.3 15.3 + - - +
105L GLN* 3.3 24.3 + - - +
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Residues in contact with HIS 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J ILE* 6.0 1.1 - - + -
122J GLN* 3.2 25.6 - - + +
126J LEU* 5.4 0.9 - - + -
178K ILE* 3.0 33.7 + - + -
182K VAL* 2.8 54.9 + - + +
183K ALA* 3.7 7.6 - - + -
186K LEU* 4.1 16.4 - - + +
98L ILE* 2.5 32.9 + - + +
99L GLY* 3.9 2.2 - - - -
101L SER* 1.3 75.7 - - - +
103L ASP* 1.3 55.0 - - - +
104L ALA 3.3 1.5 + - - -
105L GLN* 4.2 3.6 + - - -
106L ILE* 3.1 28.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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