Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 1LIK
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASN 3.5 24.5 - - - -
22A ILE* 3.9 3.8 + - - +
68A GLY* 1.3 70.9 - - - +
70A SER* 1.3 66.2 + - - -
71A ALA 3.5 1.6 - - - -
72A LEU* 3.2 6.6 + - - -
73A ASN* 2.9 27.9 + - - -
699A ADN 2.7 23.8 + - - -
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Residues in contact with SER 70 (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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20A ASN 6.1 0.4 - - - +
69A GLY* 1.3 71.8 - - - +
71A ALA* 1.3 63.7 + - - +
73A ASN* 3.1 11.7 + - - +
74A SER* 3.1 15.5 + - - -
165A TYR* 5.0 2.9 + - - -
167A THR* 4.1 10.9 - - - +
169A TYR* 3.9 20.3 - - - -
196A ASN* 5.1 4.0 + - - -
198A SER* 5.5 0.9 + - - -
318A ASP* 2.7 32.8 + - - -
699A ADN 3.4 32.3 + - - -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 4.8 2.9 - - + -
18A ILE 3.8 22.9 - - - +
19A GLY* 4.2 5.8 - - - -
20A ASN 5.9 0.8 - - - +
69A GLY 3.5 0.2 - - - -
70A SER* 1.3 75.1 + - - +
72A LEU* 1.3 60.6 + - - +
74A SER* 3.0 2.6 + - - -
75A VAL* 2.8 34.7 + - - +
90A TYR* 4.2 9.2 - - + -
165A TYR* 4.0 22.4 - - + -
167A THR* 3.8 18.2 - - + +
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Residues in contact with LEU 72 (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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20A ASN 6.1 0.2 - - - +
21A PRO* 4.1 17.7 - - + -
67A PRO* 5.5 2.7 - - + -
68A GLY 3.5 17.3 - - - +
69A GLY* 3.2 12.6 + - - +
71A ALA* 1.3 77.7 - - - +
73A ASN* 1.3 65.1 + - - +
75A VAL* 3.3 4.2 - - + +
76A ARG* 2.9 42.0 + - + +
90A TYR* 3.8 34.7 + - + +
103A LEU* 3.9 29.2 - - + -
107A CYS* 4.1 11.4 - - - -
112A LEU* 4.0 24.7 - - + -
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 4.2 6.2 - - - +
68A GLY* 4.3 2.0 - - - +
69A GLY 2.9 17.1 + - - +
70A SER 3.2 7.0 - - - +
72A LEU* 1.3 77.7 - - - +
74A SER* 1.3 56.6 + - - +
76A ARG* 3.1 28.3 + - - +
77A VAL* 2.9 31.2 + - - +
315A GLY* 5.4 0.4 - - - -
318A ASP* 3.5 24.3 + - + +
354A PHE* 3.5 35.5 - - + +
699A ADN 3.2 24.0 + - - -
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Residues in contact with SER 74 (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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70A SER* 3.1 5.6 + - - -
71A ALA 3.0 7.6 + - - -
73A ASN* 1.3 74.4 - - - +
75A VAL* 1.3 66.3 + - - +
77A VAL* 3.0 6.5 + - - +
78A VAL* 3.0 25.6 + - - +
165A TYR* 4.2 22.5 + - - -
318A ASP* 2.9 40.0 + - - +
321A VAL* 4.1 8.7 - - - +
322A GLY* 3.9 10.6 - - - -
325A LEU* 5.1 2.9 - - - -
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Residues in contact with VAL 75 (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 VAL* 5.0 11.9 - - + -
17A ALA* 3.4 35.2 - - + +
71A ALA 2.8 19.6 + - - +
72A LEU* 3.3 24.0 - - + +
74A SER* 1.3 72.1 - - - +
76A ARG* 1.3 60.3 + - - +
78A VAL* 3.0 11.2 + - - +
79A GLN* 2.8 31.1 + - - +
88A ALA* 3.8 13.0 - - + +
89A GLY 4.7 4.0 - - - +
90A TYR* 3.9 14.8 - - + -
112A LEU* 4.3 13.7 - - + -
165A TYR* 5.0 4.3 - - + -
325A LEU* 6.1 1.3 - - + -
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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
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66A LEU* 6.0 0.8 - - - +
67A PRO* 3.5 39.5 + - - +
68A GLY 5.2 0.6 + - - -
72A LEU* 2.9 38.5 + - + +
73A ASN* 3.2 27.3 + - - +
74A SER 3.0 0.2 - - - -
75A VAL* 1.3 75.6 - - - +
77A VAL* 1.3 65.7 + - - +
79A GLN* 3.4 5.4 + - - +
80A LYS* 3.1 24.1 + - - +
106A LEU* 6.1 0.4 - - - -
107A CYS* 4.9 7.8 - - - +
110A GLU* 2.8 44.1 + - - +
112A LEU* 4.2 20.2 - - + -
354A PHE* 3.8 11.7 - - - -
356A LEU* 3.2 29.4 - - + +
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Residues in contact with VAL 77 (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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73A ASN 2.9 19.3 + - - +
74A SER 3.0 7.2 + - - +
76A ARG* 1.3 75.3 - - - +
78A VAL* 1.3 67.6 + - - +
80A LYS* 3.5 5.5 + - - +
81A LEU* 3.2 34.5 + - + +
318A ASP 4.5 0.4 - - - +
319A ALA* 4.5 14.6 - - - -
322A GLY* 3.8 26.0 - - - +
323A GLY 4.0 2.9 - - - +
344A CYS* 4.4 5.8 - - - -
354A PHE* 4.0 22.4 - - + -
356A LEU* 4.8 3.8 - - + +
358A PHE* 4.3 24.9 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.6 25.6 - - + -
74A SER 3.0 17.4 + - - +
75A VAL* 3.0 14.3 + - - +
77A VAL* 1.3 77.8 - - - +
79A GLN* 1.3 63.9 + - - +
81A LEU* 2.9 7.2 + - - +
82A LEU* 2.8 47.3 + - + +
88A ALA* 4.5 5.2 - - + -
322A GLY* 3.9 20.9 - - - +
325A LEU* 4.4 15.5 - - + -
326A TYR* 4.6 11.4 - - - +
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Residues in contact with GLN 79 (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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75A VAL 2.8 18.5 + - - +
76A ARG* 3.7 5.8 - - - +
78A VAL* 1.3 71.4 - - - +
80A LYS* 1.3 54.0 + - - +
82A LEU* 3.0 4.0 + - - +
83A ARG* 2.7 45.0 + - - +
84A LYS 2.6 20.7 + - - +
85A PRO* 4.0 0.2 - - - +
86A GLY* 3.4 5.7 - - - +
87A SER* 2.6 36.5 - - - +
88A ALA* 2.9 21.6 + - + +
110A GLU* 4.0 15.3 - - + +
111A GLY* 3.5 13.0 + - - +
112A LEU* 3.6 29.8 - - + +
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Residues in contact with LYS 80 (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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76A ARG 3.1 17.1 + - - +
77A VAL* 3.8 6.7 - - - +
79A GLN* 1.3 76.0 - - - +
81A LEU* 1.3 68.6 + - + +
83A ARG* 3.6 16.0 + - - +
110A GLU* 6.4 2.5 - - + -
356A LEU* 3.6 37.4 + - + +
357A SER* 3.1 24.7 + - - +
358A PHE* 5.2 9.0 - - + +
899A CL 3.3 27.5 - - + +
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Residues in contact with LEU 81 (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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77A VAL* 3.2 24.2 + - + +
78A VAL 2.9 5.7 + - - +
80A LYS* 1.3 83.0 - - + +
82A LEU* 1.3 63.5 + - - +
83A ARG* 3.6 7.8 + - - +
323A GLY* 4.9 0.4 - - - -
326A TYR* 3.2 64.2 + - + -
340A CYS* 4.7 3.4 - - - -
344A CYS* 4.6 13.7 - - - -
358A PHE* 4.4 23.8 - - + +
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Residues in contact with LEU 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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14A ARG* 4.2 38.9 + - + +
78A VAL* 2.8 48.1 + - + +
79A GLN 3.9 0.2 - - - +
81A LEU* 1.3 71.9 - - - +
83A ARG* 1.3 65.6 + - - +
84A LYS* 2.9 18.4 + - - +
87A SER* 3.4 27.2 + - - +
326A TYR* 3.4 30.3 - - + -
329A SER* 4.3 14.6 - - - +
330A GLN* 4.5 8.7 - - - +
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Residues in contact with ARG 83 (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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79A GLN* 2.7 24.0 + - - +
80A LYS* 3.6 13.9 + - - +
81A LEU 3.3 6.9 - - - +
82A LEU* 1.3 73.5 - - - +
84A LYS* 1.3 71.4 + - + +
85A PRO* 3.5 3.3 - - - +
110A GLU 5.4 1.4 - - - +
111A GLY* 6.0 0.3 - - - -
899A CL 4.1 18.3 - - - +
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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
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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