Contacts of the helix formed by residues 65 - 79 (chain B) in PDB entry 3LX9
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 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B CYS* 4.5 1.3 - - - -
60B PRO 4.5 5.0 + - - -
63B CYS* 3.1 25.6 + - - -
64B ILE* 1.3 76.6 - - - +
66B GLU* 1.3 64.9 + - - +
67B LYS* 3.6 10.4 + - - +
68B LEU* 3.2 22.7 + - - +
69B PHE* 3.2 17.8 - - - -
112B ARG* 3.3 19.5 - - - -
113B PHE* 3.7 9.2 - - - -
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Residues in contact with GLU 66 (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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65B SER* 1.3 71.7 - - - +
67B LYS* 1.3 63.0 + - + +
69B PHE* 3.3 3.5 + - - +
70B MET* 2.9 48.1 + - - +
112B ARG 2.9 15.8 + - - +
113B PHE* 3.5 24.7 - - + +
114B PRO* 3.4 19.4 - - + +
115B HIS* 2.7 56.6 + - - +
116B GLY 4.1 3.3 + - - +
120B LEU* 4.1 13.0 - - + +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO* 4.9 13.5 + - + +
61B ASP* 3.6 21.5 + - - +
65B SER* 3.2 9.5 + - - +
66B GLU* 1.3 83.8 - - + +
68B LEU* 1.3 64.0 + - - +
70B MET* 3.4 9.5 + - + +
71B GLU* 2.9 54.1 + - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 4.8 6.7 - - + -
46B HIS* 4.9 1.1 - - + -
50B PHE* 3.9 31.9 - - + -
60B PRO 6.2 0.2 - - - +
61B ASP 3.9 9.0 - - - +
63B CYS 3.8 22.7 - - - +
64B ILE* 4.2 15.7 - - + -
65B SER* 3.2 13.5 + - - +
67B LYS* 1.3 80.3 - - - +
69B PHE* 1.3 67.6 + - + +
71B GLU* 3.4 7.3 + - - +
72B MET* 3.0 52.0 + - + +
301B ARG* 3.8 28.9 - - - +
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Residues in contact with PHE 69 (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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44B TRP* 3.7 22.0 - + - -
46B HIS* 3.4 28.0 - + + -
64B ILE* 4.1 10.8 - - + -
65B SER 3.2 24.0 - - - -
66B GLU 3.3 5.0 + - - +
67B LYS 3.3 0.4 - - - -
68B LEU* 1.3 80.1 - - + +
70B MET* 1.3 61.0 + - - +
72B MET* 3.4 3.5 + - - -
73B ALA* 2.9 23.8 + - - +
89B LEU* 3.2 29.7 - - + +
90B CYS 3.5 22.0 - - - -
91B ILE* 3.6 29.2 - - + -
113B PHE* 3.9 22.7 - + - -
120B LEU* 4.1 16.2 - - + -
131B LEU* 5.8 0.9 - - + -
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Residues in contact with MET 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 2.9 41.8 + - - +
67B LYS* 3.7 8.3 - - + +
69B PHE* 1.3 76.8 - - - +
71B GLU* 1.3 61.3 + - + +
73B ALA* 3.4 2.8 + - - +
74B GLU* 3.1 36.3 + - - +
120B LEU* 3.8 17.9 - - + -
123B TYR* 3.8 49.4 - - + +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASP* 5.2 2.6 - - - +
67B LYS* 2.9 50.2 + - + +
68B LEU* 3.6 8.3 - - - +
70B MET* 1.3 74.3 - - + +
72B MET* 1.3 64.9 + - - +
74B GLU* 3.2 19.5 + - - +
75B LEU* 3.0 28.9 + - + +
301B ARG* 2.8 46.1 + - + -
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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
----------------------------------------------------------
44B TRP* 3.8 24.0 - - + -
50B PHE* 3.8 26.9 - - + -
68B LEU* 3.0 33.7 + - + +
69B PHE* 3.7 4.7 - - - +
70B MET 3.4 0.2 - - - -
71B GLU* 1.3 75.9 - - - +
73B ALA* 1.3 57.9 + - - +
75B LEU* 3.3 3.8 + - - +
76B MET* 2.8 35.7 + - - +
89B LEU* 3.9 16.4 - - + -
299B ASP* 3.4 23.6 - - - +
300B LEU* 3.7 36.8 - - + +
301B ARG* 3.8 12.6 - - - +
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Residues in contact with ALA 73 (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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69B PHE 2.9 17.6 + - - +
70B MET* 3.6 7.2 - - - +
72B MET* 1.3 75.8 - - - +
74B GLU* 1.3 63.4 + - - +
76B MET* 3.4 1.1 + - - -
77B VAL* 3.4 19.6 + - - +
89B LEU* 3.4 18.1 - - + +
123B TYR* 4.5 9.2 - - + -
124B VAL* 4.4 10.1 - - + -
127B LYS* 4.4 8.5 - - + +
129B LEU* 3.6 27.4 - - + +
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Residues in contact with GLU 74 (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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70B MET* 3.1 29.3 + - - +
71B GLU* 3.2 18.4 + - - +
73B ALA* 1.3 76.9 - - - +
75B LEU* 1.3 59.1 + - + +
77B VAL* 3.3 6.1 + - - +
78B SER* 3.0 29.9 + - - -
123B TYR* 2.7 30.4 + - + +
127B LYS* 4.0 16.2 - - - +
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Residues in contact with LEU 75 (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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71B GLU* 3.0 21.5 + - + +
72B MET* 3.9 4.3 - - - +
74B GLU* 1.3 76.3 - - + +
76B MET* 1.3 60.0 + - - +
78B SER* 3.4 13.9 - - - +
79B GLU* 2.8 49.1 + - + +
81B TRP* 3.4 3.4 - - - -
300B LEU* 3.7 17.9 - - + +
301B ARG* 3.2 50.9 - - + +
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 4.1 12.8 - - + -
72B MET 2.8 21.2 + - - +
73B ALA 3.7 5.8 - - - +
74B GLU 3.3 0.4 - - - -
75B LEU* 1.3 75.8 - - - +
77B VAL* 1.3 59.3 + - - +
81B TRP* 3.0 21.9 + - + -
82B LYS* 2.9 26.6 + - - +
86B TYR* 3.2 41.3 - - + +
87B GLU 4.3 2.7 - - - -
88B TYR 4.2 16.2 - - - +
89B LEU* 3.9 34.1 - - - -
129B LEU* 3.9 21.8 - - + -
296B MET* 5.4 0.9 - - + -
300B LEU* 3.6 16.6 - - + -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA 3.4 12.8 + - - +
74B GLU* 3.3 7.5 + - - +
75B LEU 3.2 0.4 - - - -
76B MET* 1.3 77.8 - - - +
78B SER* 1.3 66.0 + - - +
80B GLY* 3.4 12.1 + - - -
82B LYS* 4.4 18.2 + - + +
83B ASP* 5.2 4.7 - - - +
127B LYS* 3.5 42.8 - - + +
129B LEU* 4.6 3.1 - - + -
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Residues in contact with SER 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 GLU 3.0 19.0 + - - -
75B LEU* 3.4 20.1 - - - +
77B VAL* 1.3 79.1 - - - +
79B GLU* 1.3 70.0 + - - +
80B GLY 3.3 1.0 + - - -
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Residues in contact with GLU 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 LEU* 2.8 37.2 + - + +
78B SER* 1.3 86.8 + - - +
80B GLY* 1.3 56.9 + - - +
81B TRP* 3.3 17.7 - - - +
300B LEU 5.2 5.4 - - - +
308B LYS* 3.1 38.0 + - - +
312B GLN* 2.8 21.1 + - - +
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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