Contacts of the helix formed by residues 72 - 91 (chain A) in PDB entry 1L6N
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 3.9 8.1 + - - +
71A GLY* 1.3 78.2 + - - +
73A GLU* 1.3 58.7 + - - +
74A GLU* 3.8 6.8 + - - +
75A LEU* 3.5 17.3 + - - +
76A ARG* 2.7 34.1 + - - +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 1.3 75.6 - - - +
74A GLU* 1.3 62.4 + - - +
76A ARG* 3.4 18.0 - - - +
77A SER* 3.3 19.2 + - - -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 4.1 29.3 - - + -
40A GLU* 4.1 15.1 - - - +
72A SER* 3.2 7.0 + - - +
73A GLU* 1.3 76.8 - - - +
75A LEU* 1.3 65.8 + - - +
76A ARG 3.1 1.1 - - - -
77A SER* 3.1 18.4 + - - -
78A LEU* 3.2 10.6 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 5.4 13.7 - - + +
44A PHE* 4.9 18.4 - - + -
64A LEU* 4.3 16.6 - - + -
67A SER* 3.6 17.5 - - - +
68A LEU* 3.4 21.4 - - + +
70A THR* 6.1 0.4 - - + -
71A GLY* 3.3 19.1 - - - -
72A SER* 3.2 20.7 + - - +
74A GLU* 1.3 82.2 + - - +
76A ARG* 1.3 61.5 + - - +
78A LEU* 3.1 22.0 + - + +
79A TYR 3.1 9.7 + - - -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.5 25.8 - - + +
72A SER 2.7 18.8 + - - +
73A GLU* 3.4 18.0 - - - +
75A LEU* 1.3 74.0 - - - +
77A SER* 1.3 70.3 + - - +
79A TYR* 2.9 7.8 + - + +
80A ASN* 2.9 33.5 + - + +
101A LEU* 5.5 9.9 - - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 5.4 6.6 + - - +
36A TRP* 5.1 6.3 - - - -
73A GLU 3.3 8.6 + - - -
74A GLU* 3.1 13.5 + - - -
76A ARG* 1.3 81.7 - - - +
78A LEU* 1.3 53.0 + - - +
80A ASN* 3.3 10.6 + - - +
81A THR* 2.8 37.0 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 4.0 18.5 - - + -
37A ALA* 3.4 37.5 - - + +
40A GLU* 3.7 26.5 - - + -
41A LEU* 4.2 7.2 - - + -
64A LEU* 3.5 22.7 - - + -
74A GLU 3.2 4.4 + - - +
75A LEU* 3.1 17.9 + - + +
76A ARG 3.0 0.4 - - - -
77A SER* 1.3 80.0 - - - +
79A TYR* 1.3 64.8 + - - +
81A THR* 3.0 11.9 + - - -
82A ILE* 3.1 35.0 + - + +
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.2 45.5 + - + +
64A LEU* 3.1 35.9 - - + -
65A GLN* 3.8 19.8 - - + +
68A LEU* 2.9 45.1 - - + -
75A LEU 3.1 4.0 + - - -
76A ARG* 2.9 10.0 + - + +
78A LEU* 1.3 74.8 - - - +
80A ASN* 1.3 63.4 + - - +
82A ILE* 3.2 1.9 + - - -
83A ALA* 2.8 31.6 + - + -
101A LEU* 3.8 28.6 - - + +
104A ILE* 5.0 2.6 - - - +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 4.8 0.2 - - - +
76A ARG* 2.9 24.1 + - - +
77A SER* 3.5 14.0 + - - +
79A TYR* 1.3 81.7 - - - +
81A THR* 1.3 62.1 + - - +
83A ALA* 3.6 1.9 - - - +
84A VAL* 3.2 17.5 + - - +
97A THR* 2.8 49.1 - - + +
98A LYS* 4.8 4.6 - - - +
101A LEU* 2.8 36.6 - - - +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.3 40.7 - - + -
29A TYR* 3.3 21.7 + - + -
33A HIS* 4.2 7.4 - - + +
36A TRP* 5.3 4.8 - - + -
37A ALA* 3.6 27.4 - - + -
77A SER* 2.8 17.8 + - - -
78A LEU* 3.0 15.8 + - - -
80A ASN* 1.3 75.3 - - - +
82A ILE* 1.3 62.0 + - - +
84A VAL 3.4 1.0 + - - -
85A LEU* 3.1 19.1 + - + +
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Residues in contact with ILE 82 (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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37A ALA* 4.9 3.8 - - + -
41A LEU* 3.6 26.0 - - + -
51A LEU* 4.6 7.0 - - + -
57A CYS* 3.3 44.2 - - + +
60A ILE* 3.6 10.1 - - + -
61A LEU* 4.1 13.5 - - + -
64A LEU* 3.9 4.0 - - + -
78A LEU* 3.1 50.2 + - + +
79A TYR 3.7 3.8 - - - +
81A THR* 1.3 73.0 - - - +
83A ALA* 1.3 56.3 + - - +
85A LEU* 2.8 9.7 + - - +
86A TYR* 2.7 34.0 + - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.7 15.7 - - + +
79A TYR 2.8 17.3 + - - +
80A ASN 3.6 3.4 - - - +
82A ILE* 1.3 76.8 - - - +
84A VAL* 1.3 63.0 + - - +
86A TYR* 3.0 18.4 + - - +
87A CYS 3.1 5.4 + - - -
100A ALA* 4.1 1.3 - - + -
101A LEU* 3.6 20.2 - - + -
104A ILE* 2.9 39.1 - - + +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.0 28.9 - - + -
19A ILE* 3.3 26.2 - - + -
29A TYR* 3.6 9.4 - - + -
80A ASN 3.2 15.1 + - - +
81A THR 3.6 3.8 - - - +
82A ILE 3.2 0.2 - - - -
83A ALA* 1.3 78.9 - - - +
85A LEU* 1.3 62.9 + - - +
87A CYS* 2.9 14.4 + - - +
88A VAL* 3.0 11.6 + - - +
97A THR* 3.4 28.7 - - + -
100A ALA* 3.1 28.0 - - + -
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Residues in contact with LEU 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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7A VAL* 5.7 0.4 - - + -
8A LEU* 3.3 38.8 - - + -
16A TRP* 3.0 47.3 - - + -
34A ILE* 3.6 16.4 - - + -
37A ALA* 6.0 0.2 - - + -
51A LEU* 3.8 24.9 - - + +
57A CYS* 4.4 4.5 - - - -
81A THR* 3.1 12.1 + - + +
82A ILE* 2.8 16.0 + - - +
84A VAL* 1.3 76.0 - - - +
86A TYR* 1.3 55.6 + - - +
88A VAL* 3.0 9.8 + - + +
89A HIS* 2.9 41.6 + - + -
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Residues in contact with TYR 86 (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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54A SER* 3.9 24.2 + - - -
57A CYS* 4.7 6.5 - - + -
58A ARG* 3.4 40.8 + - + +
61A LEU* 4.6 8.3 - - + -
82A ILE* 2.7 14.4 + - + +
83A ALA* 3.0 17.3 - - - +
85A LEU* 1.3 73.7 - - - +
87A CYS* 1.3 59.8 + - - +
89A HIS* 3.3 10.6 + - - +
90A GLN* 3.1 26.7 + - + +
92A ILE* 5.4 0.9 - - + -
104A ILE* 4.0 19.7 - - + -
107A GLU* 4.6 21.9 - - + +
108A GLN* 3.1 35.4 + - - -
111A SER* 5.2 5.2 + - - -
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Residues in contact with CYS 87 (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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15A LYS* 5.3 0.2 - - - -
83A ALA 3.1 4.0 + - - +
84A VAL 2.9 10.8 + - - +
86A TYR* 1.3 74.8 - - - +
88A VAL* 1.3 58.1 + - - +
90A GLN 3.1 0.7 + - - -
91A ARG 2.5 32.2 + - - -
92A ILE* 2.9 55.3 + - + -
94A VAL* 3.0 36.1 - - + -
100A ALA* 4.2 3.1 - - + -
104A ILE* 3.6 19.5 - - + +
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Residues in contact with VAL 88 (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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8A LEU* 4.4 9.4 - - + -
12A GLU* 2.7 62.5 - - + +
15A LYS* 4.1 13.3 - - + +
16A TRP* 3.6 32.1 - - + +
19A ILE* 4.1 13.7 - - + -
84A VAL 3.0 17.3 + - - +
85A LEU* 3.0 10.7 + - + +
87A CYS* 1.3 78.4 - - - +
89A HIS* 1.3 59.1 + - - +
91A ARG* 3.3 14.0 + - - +
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Residues in contact with HIS 89 (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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7A VAL 5.4 1.0 + - - -
8A LEU* 4.6 5.3 - - - +
12A GLU* 3.1 28.3 + - - +
51A LEU 4.0 12.0 + - - -
52A GLU 4.4 6.5 + - - -
53A THR* 3.9 8.7 - - - -
54A SER* 2.7 56.4 + - - +
57A CYS* 4.4 6.8 - - + +
85A LEU* 2.9 41.2 + - + +
86A TYR* 3.4 8.3 - - - +
87A CYS 3.1 0.4 - - - -
88A VAL* 1.3 80.9 - - - +
90A GLN* 1.3 60.2 + - - +
91A ARG* 4.8 1.2 - - - +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 5.7 1.8 - - - +
86A TYR* 3.1 18.2 + - + +
89A HIS* 1.3 76.7 - - + +
91A ARG* 1.3 71.4 + - - +
92A ILE* 2.9 24.4 - - + +
107A GLU* 2.4 44.7 + - + +
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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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15A LYS* 3.6 26.9 + - + +
87A CYS 2.5 14.0 + - - -
88A VAL 3.3 10.0 + - - +
89A HIS 3.3 3.3 - - - +
90A GLN* 1.3 79.8 - - - +
92A ILE* 1.3 62.3 + - - +
93A ASP 3.9 1.0 + - - -
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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
------------------------------------------------------------
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