Contacts of the helix formed by residues 84 - 103 (chain A) in PDB entry 1LI5
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 SER 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 1.3 78.5 - - - +
85A PHE* 1.3 60.3 + - - +
86A VAL* 3.5 20.4 - - - +
87A ALA* 3.6 16.1 - - - +
88A MET* 2.9 30.1 + - - +
62B LYS* 4.2 24.6 + - - +
110B MET* 5.7 9.6 - - - +
216B GLN* 5.8 4.2 - - - +
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Residues in contact with PHE 85 (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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69A ASP* 3.1 24.7 - - + -
70A ILE* 3.5 23.1 - - + -
74A ILE* 3.9 15.7 - - + -
75A ILE* 4.9 4.9 - - + -
78A ALA* 4.2 14.3 - - + +
83A GLU 3.5 3.0 + - - -
84A SER* 1.3 71.0 + - - +
86A VAL* 1.3 86.4 + - + +
88A MET* 3.1 12.5 + - - +
89A VAL* 3.2 22.8 + - + +
115A THR* 4.0 17.3 - - + -
192A PRO* 3.3 36.3 - - + -
194A TRP* 4.5 8.7 - + - -
110B MET* 6.2 1.0 - - - -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 3.5 13.0 - - - +
85A PHE* 1.3 95.1 - - + +
87A ALA* 1.3 69.0 + - + +
89A VAL* 3.1 25.4 - - + +
90A ASP* 3.2 18.7 + - - +
60B LYS* 5.2 13.9 - - - -
62B LYS* 5.8 6.3 - - + -
109B ASP* 5.9 2.7 - - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 4.0 11.4 - - + +
84A SER* 3.6 24.9 + - - +
85A PHE 3.2 0.6 - - - -
86A VAL* 1.3 83.9 - - + +
88A MET* 1.3 62.4 + - - +
90A ASP* 3.8 6.0 + - - +
91A ARG* 3.3 22.3 + - - +
60B LYS* 6.2 0.4 - - - +
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL 4.3 4.5 - - - +
33A TYR* 4.0 25.6 - - - +
74A ILE* 3.8 32.8 - - + +
77A ARG* 3.7 30.1 - - + -
78A ALA* 3.8 18.4 - - + -
81A ASN* 6.4 0.4 - - - -
83A GLU* 3.6 26.7 + - + +
84A SER 2.9 17.7 + - - +
85A PHE* 3.1 6.0 + - - +
87A ALA* 1.3 75.4 - - - +
89A VAL* 1.3 60.2 + - + +
91A ARG* 3.2 10.6 + - - +
92A MET* 2.9 39.1 + - + +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 4.7 8.5 - - + +
69A ASP* 3.7 35.2 - - - +
74A ILE* 4.0 17.9 - - + -
85A PHE* 3.5 23.3 - - + +
86A VAL* 3.1 19.7 - - - +
88A MET* 1.3 73.9 - - + +
90A ASP* 1.3 59.7 + - - +
92A MET* 3.1 6.1 + - - +
93A ILE* 2.7 42.8 + - + +
113A ARG* 3.8 23.8 - - - +
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.2 19.8 + - - +
87A ALA* 4.1 6.2 - - - +
89A VAL* 1.3 81.7 - - - +
91A ARG* 1.3 61.4 + - - +
93A ILE* 3.6 6.9 + - - +
94A ALA* 3.2 23.0 + - - +
113A ARG* 3.5 29.1 + - - -
60B LYS* 3.1 30.0 + - - -
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Residues in contact with ARG 91 (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 GLU* 3.5 31.3 + - - -
87A ALA 3.3 10.5 + - - +
88A MET* 3.2 13.6 + - - +
89A VAL 3.1 0.6 - - - -
90A ASP* 1.3 79.6 - - - +
92A MET* 1.3 91.3 + - - +
94A ALA* 3.3 7.1 + - - +
95A GLU* 3.0 36.7 + - - +
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.2 38.8 - - + +
33A TYR 4.2 16.6 - - - +
34A ASP* 4.4 16.4 - - - +
35A LEU* 4.8 12.3 - - + -
88A MET* 2.9 30.4 + - + +
91A ARG* 1.3 113.1 - - - +
93A ILE* 1.3 54.5 + - - +
95A GLU* 3.2 18.2 + - + +
96A MET* 2.7 34.8 + - - +
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Residues in contact with ILE 93 (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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32A VAL* 3.6 16.6 - - + -
67A ILE* 3.9 24.9 - - + -
69A ASP* 3.9 13.2 - - - +
89A VAL 2.7 28.4 + - - +
90A ASP* 3.8 6.7 - - - +
92A MET* 1.3 72.8 - - - +
94A ALA* 1.3 57.0 + - - +
96A MET* 3.2 7.7 + - + +
97A HIS* 2.9 50.8 + - + +
113A ARG* 3.7 39.0 - - - +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP 3.2 13.8 + - - +
91A ARG* 3.6 9.9 - - - +
93A ILE* 1.3 78.6 - - - +
95A GLU* 1.3 65.7 + - - +
97A HIS* 3.4 8.8 + - - +
98A LYS* 3.0 23.4 + - - +
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Residues in contact with GLU 95 (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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35A LEU* 3.2 27.4 - - + -
91A ARG* 3.0 25.1 + - - +
92A MET* 3.3 22.1 - - + +
94A ALA* 1.3 79.7 - - - +
96A MET* 1.3 63.2 + - - +
98A LYS* 3.1 14.0 + - - +
99A ASP* 3.1 19.5 + - - +
278A ARG* 2.8 35.8 + - - +
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.2 38.8 - - + -
32A VAL* 4.7 8.7 - - + -
35A LEU* 6.5 0.9 - - - +
36A CYS* 5.0 8.7 - - + +
65A ARG* 4.4 1.8 - - - +
67A ILE* 4.7 11.0 - - + -
92A MET 2.7 20.8 + - - +
93A ILE* 3.3 8.3 - - - +
95A GLU* 1.3 73.5 - - - +
97A HIS* 1.3 101.6 + - + +
99A ASP* 3.1 8.5 + - - +
100A PHE* 3.0 64.4 + - + -
111A GLU* 3.8 10.1 - - - +
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Residues in contact with HIS 97 (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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65A ARG* 5.3 0.4 + - - -
67A ILE* 4.6 1.5 - - + +
93A ILE* 2.9 35.9 + - + +
94A ALA* 3.8 8.5 - - - +
95A GLU 3.3 0.2 - - - -
96A MET* 1.3 92.9 - - + +
98A LYS* 1.3 57.5 + - - +
100A PHE* 4.5 4.4 - - - +
101A ASP* 2.9 38.4 + - - +
107A ARG* 3.3 41.9 + - - +
111A GLU* 2.9 40.8 + - - -
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Residues in contact with LYS 98 (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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94A ALA 3.0 14.5 + - - +
95A GLU* 3.1 12.5 + - - +
97A HIS* 1.3 77.8 - - - +
99A ASP* 1.3 62.0 + - - +
101A ASP* 4.0 4.4 - - - +
102A ALA* 3.2 23.2 + - - +
278A ARG* 4.5 10.3 - - - +
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Residues in contact with ASP 99 (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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35A LEU* 4.5 10.0 - - - +
36A CYS* 3.7 30.4 + - - +
95A GLU 3.1 16.3 + - - +
96A MET* 3.7 6.2 - - - +
98A LYS* 1.3 74.7 - - - +
100A PHE* 1.3 66.0 + - - +
102A ALA* 3.3 7.8 + - - +
103A LEU* 3.2 25.8 + - - +
277A VAL* 4.1 18.6 - - + +
278A ARG* 3.1 45.8 + - - +
281A LEU* 4.6 4.3 - - - +
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Residues in contact with PHE 100 (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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30A ILE* 4.9 5.2 - - + -
36A CYS* 3.7 28.3 - - + -
40A HIS* 5.2 2.7 - - + -
41A GLY* 5.6 2.2 - - - -
44A PHE* 3.4 40.8 - + + -
65A ARG* 3.8 32.3 - - - -
96A MET* 3.0 48.1 + - + +
97A HIS* 4.0 6.7 - - - +
99A ASP* 1.3 77.3 - - - +
101A ASP* 1.3 66.1 + - - +
103A LEU* 3.0 10.8 + - + -
105A ILE* 3.0 54.2 + - + +
107A ARG* 6.3 1.3 - - - -
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Residues in contact with ASP 101 (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 HIS* 2.9 24.9 + - - +
98A LYS* 4.0 5.4 - - - +
100A PHE* 1.3 77.7 - - - +
102A ALA* 1.3 58.9 + - - +
104A ASN* 3.0 19.2 + - - +
105A ILE 4.0 12.2 - - - +
107A ARG* 2.5 44.4 + - - -
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Residues in contact with ALA 102 (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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98A LYS 3.2 19.0 + - - +
99A ASP 3.5 6.3 - - - +
100A PHE 3.2 0.4 - - - -
101A ASP* 1.3 77.2 - - - +
103A LEU* 1.3 57.1 + - - +
104A ASN* 3.0 5.1 + - - +
281A LEU* 3.9 23.6 - - + -
286A ALA* 3.1 28.7 - - + +
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Residues in contact with LEU 103 (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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41A GLY* 4.2 16.4 - - - -
45A VAL* 4.3 6.7 - - + -
99A ASP 3.2 12.0 + - - +
100A PHE* 3.0 11.0 + - + +
102A ALA* 1.3 77.7 - - + +
104A ASN* 1.3 61.4 + - - +
105A ILE* 3.1 15.0 + - + -
277A VAL* 4.0 26.2 - - + -
281A LEU* 4.8 8.1 - - + -
286A ALA 3.9 19.1 - - - +
289A VAL* 4.0 22.9 - - + -
290A ARG* 2.8 36.8 + - - +
293A LEU* 4.1 20.0 - - + -
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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
------------------------------------------------------------
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