Contacts of the helix formed by residues 66 - 81 (chain G) in PDB entry 4E45
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 ASP 66 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F SER* 3.5 7.0 + - - -
45F GLN* 5.3 0.7 - - - +
46F THR* 3.2 9.0 + - - -
64G ARG* 3.1 51.7 + - - +
65G VAL* 1.3 74.6 - - - +
67G VAL* 1.3 63.0 + - + +
68G ASP* 3.2 7.2 - - + +
69G GLN* 2.7 37.0 + - - +
70G LEU* 3.4 7.3 + - - +
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Residues in contact with VAL 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F SER* 4.4 0.4 - - - +
45F GLN* 3.5 46.2 - - + +
46F THR* 3.7 6.3 - - - +
49F ALA* 4.7 4.5 - - + -
66G ASP* 1.3 74.1 + - + +
68G ASP* 1.3 62.4 + - + +
70G LEU* 3.1 8.8 + - + +
71G GLU* 2.9 33.1 + - - +
765J ILE* 4.1 21.6 - - + +
768J MET* 4.4 10.1 - - + +
769J ARG* 4.0 35.4 - - + +
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Residues in contact with ASP 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G GLU* 5.8 0.4 - - - +
66G ASP* 4.4 4.0 - - + +
67G VAL* 1.3 82.9 - - + +
69G GLN* 1.3 71.1 + - - +
71G GLU* 3.3 27.4 + - - +
72G LYS* 3.4 25.9 + - - +
737J ARG* 4.6 11.7 - - - +
769J ARG* 4.6 6.1 - - + +
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Residues in contact with GLN 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G GLY* 4.2 2.0 - - - +
56G GLN* 3.5 27.9 - - + +
57G ALA* 3.7 23.6 - - - +
60G GLU* 3.1 28.0 + - - +
62G ALA* 4.0 19.1 - - - +
64G ARG 3.5 6.2 - - - +
65G VAL* 3.6 12.1 - - + -
66G ASP* 2.7 46.9 + - - +
68G ASP* 1.3 85.4 - - - +
70G LEU* 1.3 62.4 + - - +
72G LYS 3.3 8.1 + - - -
73G VAL* 3.5 11.8 + - - +
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F THR* 4.3 12.3 - - + +
49F ALA* 3.4 34.1 - - + +
50F ILE* 3.7 36.6 - - + +
53F LEU* 5.6 0.2 - - + -
49G ALA* 4.2 12.6 - - + +
53G GLY* 5.0 6.3 - - - -
65G VAL* 4.8 1.2 - - + +
66G ASP 3.4 5.4 + - - +
67G VAL* 3.1 13.0 + - - +
69G GLN* 1.3 76.6 - - - +
71G GLU* 1.3 65.7 + - - +
72G LYS 3.0 1.8 - - - -
73G VAL* 3.1 25.4 + - + +
74G LEU* 3.2 31.8 + - + +
761J LEU* 6.2 0.4 - - + -
765J ILE* 4.4 7.4 - - + -
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Residues in contact with GLU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G VAL 2.9 9.7 + - - +
68G ASP* 3.3 11.4 + - - +
70G LEU* 1.3 77.5 - - - +
72G LYS* 1.3 61.9 + - - +
73G VAL 3.5 0.3 + - - -
74G LEU* 3.5 18.5 + - - +
75G PRO* 3.7 10.9 - - - +
734J SER* 5.0 1.0 - - - -
737J ARG* 2.7 46.5 + - - +
738J LEU* 4.6 1.2 - - - +
762J MET* 3.4 31.7 - - + +
765J ILE* 3.4 29.6 - - + +
769J ARG* 2.7 35.7 + - - -
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Residues in contact with LYS 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G GLN* 3.5 19.4 - - - +
60G GLU* 2.9 36.2 + - - +
68G ASP* 3.7 19.7 - - - +
69G GLN 3.3 8.8 + - - +
70G LEU 3.0 1.0 - - - -
71G GLU* 1.3 79.7 - - - +
73G VAL* 1.3 60.3 + - - +
74G LEU 3.7 0.2 + - - -
75G PRO* 3.9 5.9 - - - +
76G GLN* 5.6 0.5 + - - +
733J LEU* 5.2 0.7 - - - +
734J SER* 3.4 38.1 - - - +
737J ARG* 4.1 28.6 - - - +
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Residues in contact with VAL 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ALA 4.6 2.0 - - - +
52G ARG* 3.8 46.4 + - + +
53G GLY 4.3 4.9 - - - +
56G GLN* 3.9 16.2 - - + +
69G GLN 3.5 8.7 + - - +
70G LEU* 3.1 33.4 + - + +
72G LYS* 1.3 79.7 - - - +
74G LEU* 1.3 66.2 + - + +
75G PRO* 3.5 1.9 - - - -
76G GLN* 3.6 6.8 + - - +
77G LEU* 3.3 24.1 + - + +
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Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 4.1 24.0 - - + -
70G LEU* 3.2 43.9 + - + +
71G GLU* 3.8 7.4 - - - +
73G VAL* 1.3 74.8 - - + +
75G PRO* 1.3 74.7 - - + +
77G LEU* 3.1 8.5 + - + +
78G LEU* 3.0 27.1 + - + +
758J PHE* 4.3 11.4 - - + -
761J LEU* 3.9 26.2 - - + -
762J MET* 4.2 10.5 - - - -
765J ILE* 3.6 30.5 - - + -
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Residues in contact with PRO 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G GLU 3.7 11.9 - - - +
72G LYS 3.9 7.2 - - - +
73G VAL 3.6 3.8 - - - -
74G LEU* 1.3 94.8 - - + +
76G GLN* 1.3 56.0 + - - +
78G LEU* 3.4 6.7 + - + +
79G LEU* 2.9 35.4 + - + +
75I PRO* 4.5 11.4 - - + -
79I LEU* 4.5 5.6 - - + +
733J LEU* 3.5 38.8 - - + +
758J PHE* 3.8 27.8 - - + -
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Residues in contact with GLN 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ARG* 3.9 7.6 - - - +
72G LYS 6.1 0.2 - - - +
73G VAL* 3.6 7.0 + - - +
74G LEU 3.3 0.4 - - - -
75G PRO* 1.3 81.4 - - - +
77G LEU* 1.3 58.7 + - - +
79G LEU* 3.2 15.7 + - - +
80G ASP* 2.7 67.2 + - - +
706J PRO* 4.4 25.9 + - + +
707J GLN 5.5 3.6 - - - +
708J VAL* 4.2 14.4 - - - +
709J GLN 6.1 0.4 - - - +
733J LEU* 3.5 23.7 - - + +
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.7 20.2 - - + -
45G PHE* 4.1 14.1 - - + +
48G GLU* 4.2 2.0 - - + -
49G ALA* 3.4 44.2 - - + +
52G ARG* 3.6 28.7 - - - +
70G LEU* 5.8 0.2 - - + -
73G VAL* 3.3 16.9 + - + +
74G LEU* 3.1 17.4 + - + +
76G GLN* 1.3 76.0 - - - +
78G LEU* 1.3 66.5 + - + +
80G ASP* 3.1 10.7 + - - -
81G PHE* 3.2 45.9 + - + +
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Residues in contact with LEU 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.8 29.6 - - + +
57F GLN* 3.6 25.6 - - + +
60F ASN* 4.8 7.0 - - - +
45G PHE* 5.1 2.7 - - + -
74G LEU* 3.0 16.1 + - + +
75G PRO* 3.8 6.1 - - + +
77G LEU* 1.3 79.2 - - - +
79G LEU* 1.3 60.0 + - - +
81G PHE* 3.4 20.0 + - - +
79I LEU* 3.8 16.4 - - + -
754J ARG* 3.7 20.5 + - + +
757J HIS* 5.9 3.4 - - + -
758J PHE* 3.7 45.1 - - + +
761J LEU* 5.5 1.3 - - + -
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Residues in contact with LEU 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F ARG* 3.6 20.8 - - - +
75G PRO* 2.9 22.7 + - + +
76G GLN* 3.7 16.2 - - - +
77G LEU 3.2 0.2 - - - -
78G LEU* 1.3 77.1 - - - +
80G ASP* 1.3 61.5 + - - +
81G PHE* 3.5 4.9 + - - +
75I PRO* 5.7 2.0 - - + +
78I LEU* 3.7 47.6 - - + +
79I LEU* 3.8 19.7 - - + -
733J LEU* 3.8 27.8 - - + -
754J ARG* 4.0 14.4 + - - +
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Residues in contact with ASP 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU 4.9 1.9 - - - +
88F ARG* 3.5 23.8 + - - +
92F LEU* 4.4 6.1 - - - +
52G ARG* 2.8 33.7 + - - +
76G GLN* 2.7 48.1 + - - +
77G LEU 3.1 5.3 + - - +
79G LEU* 1.3 75.7 - - - +
81G PHE* 1.3 64.7 + - + +
708J VAL* 3.5 24.9 - - + +
709J GLN 4.3 3.1 + - - +
710J PHE* 3.8 24.3 - - + -
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Residues in contact with PHE 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN* 3.0 31.7 + - - +
60F ASN* 5.7 1.2 - - - +
61F PHE* 4.1 18.2 - + + -
64F ASP* 5.7 1.2 - - - +
85F LEU* 4.6 15.5 - - - +
87F ARG* 5.9 0.9 + - - -
88F ARG* 4.4 6.9 - - - +
92F LEU* 3.8 23.1 - - + -
41G LEU* 4.2 16.2 - - + -
44G VAL 4.6 3.6 - - - -
45G PHE* 3.4 50.7 - + + -
48G GLU* 4.5 2.5 - - + -
77G LEU* 3.2 38.2 + - + +
78G LEU* 3.6 10.8 - - - +
79G LEU 3.2 9.1 - - - +
80G ASP* 1.3 83.0 - - + +
88H ARG* 4.7 8.0 + - - -
710J PHE* 3.6 30.7 - + - -
754J ARG* 4.2 9.8 + - - -
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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
------------------------------------------------------------
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