Contacts of the helix formed by residues 65 - 82 (chain B) in PDB entry 3LMK
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 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 4.7 1.7 - - - +
42B SER 3.8 14.0 + - - -
43B VAL* 3.9 11.7 - - - -
61B ARG 3.5 11.1 + - - -
62B GLU 3.2 4.2 + - - -
64B TYR* 1.3 78.7 - - - +
66B ILE* 1.3 66.3 + - - -
67B GLN 3.1 1.1 - - - -
68B ARG* 2.8 15.9 + - - +
69B VAL* 2.9 19.8 + - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.2 5.1 - - + +
60B VAL* 4.2 6.5 - - + -
61B ARG 3.1 18.2 + - - +
62B GLU* 3.2 4.2 + - - +
65B GLY* 1.3 70.1 - - - +
67B GLN* 1.3 56.6 + - - +
69B VAL* 3.7 5.1 - - + +
70B GLU* 2.9 29.7 + - + +
341B TYR* 3.8 23.1 - - + +
352B ASN* 4.0 10.8 - - - +
354B TRP* 3.7 35.9 - - + +
355B PHE* 3.9 15.0 - - + +
358B PHE* 3.5 44.9 - - + -
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 2.9 43.9 + - + +
63B GLN* 3.5 14.4 - - - +
66B ILE* 1.3 73.3 - - - +
68B ARG* 1.3 53.2 + - - +
70B GLU 3.4 0.5 + - - -
71B ALA* 2.8 34.0 + - - +
337B PHE* 3.4 16.1 - - + -
341B TYR* 3.5 25.0 - - + +
391B HIS* 3.6 17.9 + - - -
392B VAL 3.2 19.0 + - - +
393B GLN* 3.7 1.9 - - - -
394B ASP* 2.9 32.1 + - - +
397B MET* 3.8 13.0 - - + +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.6 35.0 - - + -
42B SER* 5.5 0.6 + - - +
63B GLN 3.5 11.1 + - - +
64B TYR* 3.4 59.9 + - - +
65B GLY 2.8 6.9 + - - +
67B GLN* 1.3 73.9 - - - +
69B VAL* 1.3 65.6 + - - +
71B ALA* 3.2 7.9 + - - +
72B MET* 2.9 23.9 + - - +
100B TRP* 4.7 4.6 - - - -
172B TYR* 3.5 24.7 + - - -
173B SER* 4.6 4.0 + - - -
394B ASP* 2.8 40.8 + - - +
396B LYS* 3.6 18.6 - - - +
397B MET* 4.7 1.1 - - + -
400B VAL* 4.0 16.3 - - + +
507B GLU* 5.0 0.2 + - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 4.7 1.6 - - + -
41B PHE* 3.8 11.8 - - + -
43B VAL* 3.9 17.0 - - + -
65B GLY 2.9 19.8 + - - +
66B ILE* 3.7 10.3 - - - +
68B ARG* 1.3 70.8 - - - +
70B GLU* 1.3 63.0 + - - +
72B MET* 3.0 13.9 + - - +
73B LEU* 3.1 22.2 + - + +
95B ILE* 3.8 25.7 - - + +
352B ASN* 3.9 27.6 - - - +
354B TRP* 3.8 28.0 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.9 25.8 + - + +
67B GLN 3.7 3.6 - - - +
69B VAL* 1.3 69.9 - - - +
71B ALA* 1.3 65.8 - - - +
73B LEU* 3.5 8.4 + - - +
74B HIS* 3.1 26.7 + - - +
337B PHE* 4.4 2.0 - - + -
340B TYR* 2.7 38.3 + - + -
341B TYR* 4.0 20.2 - - + -
344B LEU* 3.4 19.1 - - + -
349B ASN* 2.7 30.0 + - - +
351B ARG* 4.9 0.2 + - - -
352B ASN* 2.9 25.3 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN 2.8 19.5 + - - +
68B ARG* 3.4 8.3 - - - +
70B GLU* 1.3 76.5 - - - +
72B MET* 1.3 54.5 + - - +
74B HIS* 4.1 1.7 - - - +
75B THR* 2.8 38.6 + - - -
336B TRP* 5.3 1.3 - - - -
337B PHE* 3.8 12.7 - - + -
397B MET* 3.4 27.8 - - - -
400B VAL* 4.5 9.6 - - + -
401B ILE* 4.5 7.6 - - + -
404B ILE* 4.6 0.9 - - - -
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.9 26.9 - - + +
38B GLY 4.0 1.1 - - - +
39B ALA* 3.7 26.0 - - + -
41B PHE* 3.9 10.8 - - + -
68B ARG 2.9 12.9 + - - +
69B VAL 3.2 9.9 - - - +
71B ALA* 1.3 76.3 - - - +
73B LEU* 1.3 62.1 + - - +
75B THR* 3.9 1.2 - - - -
76B LEU* 3.2 35.3 + - + +
93B CYS* 3.8 26.0 - - + -
95B ILE* 3.6 23.6 - - + -
147B ILE* 4.3 4.0 - - + -
404B ILE* 3.6 35.6 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 4.8 7.6 - - + -
30B HIS 4.9 4.9 - - - +
31B MET* 3.7 20.3 - - + +
69B VAL* 3.1 28.6 + - + +
70B GLU* 4.0 15.5 - - - +
72B MET* 1.3 76.6 - - - +
74B HIS* 1.3 58.5 + - - +
76B LEU* 3.5 4.8 + - - +
77B GLU* 3.2 27.7 + - - +
93B CYS* 3.8 15.3 - - - -
95B ILE* 3.7 18.2 - - + -
351B ARG* 4.0 46.9 - - + +
352B ASN* 4.3 8.7 - - + -
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU 3.1 17.7 + - - +
71B ALA* 4.1 2.2 - - - +
73B LEU* 1.3 74.0 - - - +
75B THR* 1.3 67.6 + - - +
77B GLU* 3.1 25.6 + - + +
78B ARG* 2.9 39.6 + - + +
336B TRP* 3.7 31.3 + + + +
337B PHE* 6.1 0.4 - + + -
340B TYR* 3.4 53.2 - + + +
351B ARG* 4.6 0.2 - - - +
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 2.8 25.5 + - - -
72B MET 3.9 3.1 - - - -
74B HIS* 1.3 74.3 - - - +
76B LEU* 1.3 57.5 + - - +
78B ARG* 3.1 5.9 + - - +
79B ILE* 2.9 31.9 + - + +
336B TRP* 3.7 12.4 - - + -
401B ILE* 3.6 23.0 - - + +
404B ILE* 3.7 30.4 - - + +
405B TYR* 3.5 33.9 - - + +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B MET* 4.0 10.1 - - + -
37B ILE* 4.3 7.4 - - + -
72B MET* 3.2 18.0 + - + +
73B LEU 3.6 9.0 - - - +
74B HIS 3.2 0.2 - - - -
75B THR* 1.3 78.4 - - - +
77B GLU* 1.3 53.7 + - - +
79B ILE* 3.8 4.7 - - + +
80B ASN* 2.7 43.5 + - - +
91B LEU* 4.1 28.7 - - + +
92B GLY* 3.8 17.9 - - - +
93B CYS* 3.4 37.9 - - + -
404B ILE* 3.7 25.1 - - + -
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Residues in contact with GLU 77 (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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31B MET* 3.5 22.4 - - + -
73B LEU 3.2 6.6 + - - +
74B HIS* 3.1 30.3 + - + +
76B LEU* 1.3 73.4 - - - +
78B ARG* 1.3 60.1 + - - +
80B ASN* 3.2 7.0 + - - +
81B SER* 2.9 33.0 + - - +
340B TYR* 4.2 1.9 - - - -
351B ARG* 3.0 38.3 + - - -
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Residues in contact with ARG 78 (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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74B HIS* 2.9 28.1 + - + +
75B THR* 3.1 6.7 + - - +
77B GLU* 1.3 75.8 - - - +
79B ILE* 1.3 58.0 + - - +
81B SER* 3.2 8.7 + - - -
82B ASP* 3.0 29.0 + - - +
336B TRP* 3.3 77.7 - - - +
405B TYR* 3.9 17.4 + - - +
449B VAL* 5.5 1.0 - - - +
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Residues in contact with ILE 79 (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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75B THR* 2.9 31.2 + - + +
76B LEU* 3.9 5.4 - - + +
78B ARG* 1.3 76.1 - - - +
80B ASN* 1.3 53.1 + - - +
82B ASP* 3.0 20.6 + - - +
85B LEU* 4.0 22.0 - - + -
86B LEU* 4.5 4.7 - - + -
91B LEU* 4.0 23.3 - - + -
404B ILE* 4.4 10.8 - - + -
405B TYR* 3.6 37.5 - - + -
408B ALA* 3.7 22.2 - - + -
506B MG 2.5 28.0 - - - -
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B MET* 4.3 9.5 - - - +
76B LEU* 2.7 29.6 + - - +
77B GLU* 3.7 6.4 - - - +
79B ILE* 1.3 76.2 - - - +
81B SER* 1.3 59.0 + - - +
82B ASP 3.4 0.4 - - - -
89B ILE 3.8 4.3 - - - +
90B THR* 3.2 22.2 - - + +
91B LEU* 2.7 53.0 + - - +
506B MG 3.6 9.0 - - - -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU 2.9 17.4 + - - -
78B ARG* 3.6 9.0 - - - -
79B ILE 3.1 0.4 - - - -
80B ASN* 1.3 76.3 - - - +
82B ASP* 1.3 58.4 + - - +
83B PRO* 3.4 11.1 - - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG 3.0 14.5 + - - +
79B ILE* 3.0 8.9 + - - +
80B ASN 5.0 0.2 - - - -
81B SER* 1.3 77.7 - - - +
83B PRO* 1.3 64.5 - - - +
84B THR* 2.7 39.3 + - - +
85B LEU* 2.8 36.8 + - + +
405B TYR* 5.8 1.9 - - - -
409B TYR* 5.7 0.7 + - - -
506B MG 2.9 9.0 - - - -
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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