Contacts of the helix formed by residues 65 - 82 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.5 1.1 - - - +
42A SER 3.3 14.9 + - - -
43A VAL* 3.8 11.4 - - - -
61A ARG 3.4 9.6 + - - -
62A GLU 3.3 3.4 + - - -
64A TYR* 1.3 79.1 - - - +
66A ILE* 1.3 57.7 + - - +
67A GLN 3.2 0.9 - - - -
68A ARG* 3.0 5.9 + - - +
69A VAL* 2.8 39.7 + - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 4.2 5.4 - - + +
60A VAL* 4.1 7.6 - - + -
61A ARG 3.0 17.2 + - - +
62A GLU* 3.9 3.8 - - - +
65A GLY* 1.3 70.5 - - - -
67A GLN* 1.3 58.2 + - - +
69A VAL* 3.4 4.8 + - - +
70A GLU* 2.9 34.2 + - + +
341A TYR* 4.0 9.4 - - + +
352A ASN* 4.0 12.3 - - - +
354A TRP* 3.6 33.7 - - + +
355A PHE* 3.8 19.1 - - + -
358A PHE* 3.6 53.8 - - + -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 2.8 48.7 + - - +
63A GLN* 3.7 14.7 - - - +
66A ILE* 1.3 73.6 - - - +
68A ARG* 1.3 56.5 + - - +
70A GLU 3.4 0.3 + - - -
71A ALA* 2.9 23.9 + - - +
337A PHE* 3.2 27.9 - - + -
341A TYR* 3.4 28.0 + - + +
391A HIS* 3.9 9.0 - - - -
392A VAL 3.1 20.3 + - - -
393A GLN* 3.4 4.9 - - - -
394A ASP* 3.0 27.7 + - - +
397A MET* 3.9 6.1 - - + -
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.7 27.4 - - + -
42A SER* 5.2 0.8 + - - +
63A GLN 3.5 11.1 + - - +
64A TYR* 3.3 59.2 + - - +
65A GLY 3.0 7.4 + - - +
67A GLN* 1.3 74.5 - - - +
69A VAL* 1.3 65.3 + - - +
70A GLU 3.1 1.3 - - - -
71A ALA* 3.1 8.1 + - - +
72A MET* 2.9 24.4 + - - +
100A TRP* 4.9 4.9 - - - -
172A TYR* 3.5 30.1 + - - -
173A SER* 4.9 2.0 + - - -
394A ASP* 2.7 40.9 + - - +
396A LYS* 3.9 17.4 - - - +
397A MET* 4.5 1.6 - - + -
400A VAL* 3.8 20.8 - - + +
506A GLU* 5.2 0.2 + - - -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.5 1.8 - - + -
41A PHE* 3.8 19.7 - - + -
43A VAL* 3.8 17.7 - - + -
65A GLY 2.8 22.3 + - - +
66A ILE* 3.6 9.6 - - - +
68A ARG* 1.3 71.4 - - - +
70A GLU* 1.3 58.7 + - - +
72A MET* 3.2 3.8 + - - +
73A LEU* 3.0 38.4 + - + +
95A ILE* 3.9 10.0 - - + +
352A ASN* 3.7 27.8 - - - +
354A TRP* 3.8 29.6 - - + -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 2.9 22.8 + - + +
67A GLN 3.6 4.9 - - - +
69A VAL* 1.3 74.5 - - - +
71A ALA* 1.3 59.4 + - - +
73A LEU* 3.4 12.0 + - - +
74A HIS* 2.9 32.2 + - - +
337A PHE* 4.1 3.1 - - + -
340A TYR* 2.6 35.7 + - + -
341A TYR* 4.0 21.3 - - + -
344A LEU* 3.5 19.1 - - + -
349A ASN* 3.0 19.9 + - - +
352A ASN* 2.9 29.9 + - - +
355A PHE* 4.1 0.8 - - + -
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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
----------------------------------------------------------
67A GLN 2.9 12.4 + - - +
68A ARG* 3.1 6.7 + - - +
70A GLU* 1.3 72.1 - - - +
72A MET* 1.3 55.9 + - - +
74A HIS* 4.9 1.1 - - - -
75A THR* 2.7 42.4 + - - +
336A TRP* 5.7 0.9 - - - -
337A PHE* 3.5 13.6 - - + -
397A MET* 3.4 33.7 - - + -
400A VAL* 4.6 6.7 - - + -
401A ILE* 4.3 11.4 - - + -
404A ILE* 4.7 1.3 - - - -
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Residues in contact with MET 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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37A ILE* 3.8 27.1 - - + +
39A ALA* 3.7 19.3 - - + -
41A PHE* 3.7 14.1 - - + -
68A ARG 2.9 12.0 + - - +
69A VAL 3.4 9.2 - - - +
71A ALA* 1.3 78.0 - - - +
73A LEU* 1.3 63.2 + - - +
75A THR* 4.0 1.4 - - - -
76A LEU* 3.3 44.0 + - + +
93A CYS* 3.8 24.2 - - + -
95A ILE* 3.5 23.8 - - + -
147A ILE* 4.3 4.3 - - - -
400A VAL* 5.2 0.2 - - - +
404A ILE* 3.8 31.6 - - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.9 5.8 - - + -
30A HIS 4.8 6.1 - - - +
31A MET* 3.9 21.1 - - + +
69A VAL* 3.0 32.2 + - + +
70A GLU* 3.7 28.7 - - - +
72A MET* 1.3 79.4 - - - +
74A HIS* 1.3 60.4 + - - +
76A LEU* 3.5 3.8 + - - +
77A GLU* 3.3 22.3 + - - +
93A CYS* 4.2 11.9 - - - -
95A ILE* 3.9 18.6 - - + -
351A ARG* 4.0 38.8 - - + +
352A ASN* 4.3 11.7 - - + -
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU 2.9 17.5 + - - +
71A ALA* 4.3 1.8 - - - +
73A LEU* 1.3 75.5 - - - +
75A THR* 1.3 66.5 + - - +
77A GLU* 3.0 29.9 + - + +
78A ARG* 2.9 45.6 + - + +
336A TRP* 3.5 35.0 + + + +
337A PHE* 5.8 0.4 - - + -
340A TYR* 3.2 52.4 - + + +
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Residues in contact with THR 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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71A ALA 2.7 30.3 + - - -
72A MET 4.0 2.9 - - - -
74A HIS* 1.3 73.0 - - - +
76A LEU* 1.3 56.9 + - - +
78A ARG* 3.1 7.2 + - - +
79A ILE* 2.9 38.6 + - + +
336A TRP* 3.5 20.5 - - + -
401A ILE* 3.7 13.3 - - + +
404A ILE* 3.8 23.0 - - + +
405A TYR* 3.8 31.4 - - + -
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Residues in contact with LEU 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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31A MET* 4.0 11.0 - - + -
37A ILE* 5.5 3.8 - - + -
72A MET* 3.3 25.1 + - + +
73A LEU 3.8 4.9 - - - +
74A HIS 3.2 0.4 - - - -
75A THR* 1.3 74.4 - - - +
77A GLU* 1.3 58.7 + - - +
79A ILE* 3.3 4.1 + - + +
80A ASN* 2.8 38.5 + - - +
91A LEU* 3.7 43.1 - - + +
92A GLY* 3.5 30.1 - - - +
93A CYS* 3.7 19.1 - - + -
404A ILE* 3.9 22.2 - - + -
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Residues in contact with GLU 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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31A MET* 3.7 17.7 - - + +
73A LEU 3.3 8.9 + - - +
74A HIS* 3.0 32.1 + - + +
76A LEU* 1.3 76.3 - - - +
78A ARG* 1.3 56.7 + - - +
80A ASN* 3.4 6.6 + - - +
81A SER* 3.0 32.4 + - - -
340A TYR* 4.0 2.4 - - - -
351A ARG* 2.8 40.9 + - - -
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Residues in contact with ARG 78 (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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74A HIS* 2.9 40.0 + - + +
75A THR* 3.1 8.0 + - - +
77A GLU* 1.3 72.7 - - - +
79A ILE* 1.3 61.6 + - - +
81A SER* 3.3 7.9 + - - -
82A ASP* 3.0 28.0 + - - +
336A TRP* 3.1 72.9 - - - +
405A TYR* 4.4 17.1 + - - +
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Residues in contact with ILE 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 THR* 2.9 37.5 + - + +
76A LEU* 3.6 11.2 - - + +
78A ARG* 1.3 77.2 - - - +
80A ASN* 1.3 57.2 + - - +
82A ASP* 3.0 18.3 + - - +
85A LEU* 3.7 25.7 - - + +
86A LEU* 4.6 3.8 - - + -
91A LEU* 3.8 20.4 - - + -
404A ILE* 4.1 12.1 - - + -
405A TYR* 3.7 28.7 - - + -
408A ALA* 3.9 20.0 - - + -
507A MG 2.6 23.7 - - - -
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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
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31A MET* 4.2 9.9 - - - +
76A LEU 2.8 25.0 + - - +
77A GLU* 3.8 6.3 - - - +
79A ILE* 1.3 75.0 - - - +
81A SER* 1.3 58.9 + - - +
82A ASP 4.6 0.5 - - - +
86A LEU* 6.2 0.2 - - - +
89A ILE 3.7 8.7 - - - +
90A THR* 3.5 21.4 - - + +
91A LEU* 3.0 49.2 + - - +
507A MG 3.7 10.1 - - - -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 3.0 17.6 + - - -
78A ARG* 3.6 7.9 - - - -
79A ILE 3.1 0.2 - - - -
80A ASN* 1.3 76.9 - - - +
82A ASP* 1.3 63.0 + - - +
83A PRO* 3.4 10.0 - - - +
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG 3.0 14.9 + - - +
79A ILE* 3.0 10.1 + - - +
80A ASN 4.9 0.2 - - - -
81A SER* 1.3 76.0 - - - +
83A PRO* 1.3 64.6 - - - +
84A THR* 2.5 35.1 + - - +
85A LEU* 3.1 22.4 - - + +
405A TYR* 5.4 6.8 + - - +
409A TYR* 5.5 2.6 + - - -
507A MG 2.7 26.5 - - - -
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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