Contacts of the helix formed by residues 64 - 83 (chain F) in PDB entry 4HHM
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 64 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62F GLY 3.5 2.9 + - - -
63F ALA* 1.3 73.4 - - - +
65F ASP* 1.3 66.1 + - - +
66F THR* 3.0 15.3 + - - -
67F GLU* 3.0 28.0 + - - -
68F ARG* 2.6 37.7 + - - +
121F ARG* 5.7 0.2 - - - -
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Residues in contact with ASP 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F ALA 5.4 0.5 - - - +
64F SER* 1.3 78.3 + - - +
66F THR* 1.3 56.4 + - - +
68F ARG* 3.8 7.8 - - - +
69F GLU* 3.1 37.1 + - - +
121F ARG* 2.9 28.1 + - - +
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Residues in contact with THR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F SER* 3.0 10.7 + - - -
65F ASP* 1.3 76.7 - - - +
67F GLU* 1.3 66.0 + - + +
69F GLU* 3.4 7.6 + - - +
70F ALA* 3.1 22.0 + - + +
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F PRO* 5.6 1.0 - - - +
62F GLY 4.5 1.2 - - - +
63F ALA* 3.4 15.6 - - + +
64F SER* 3.0 33.5 + - - +
66F THR* 1.3 77.2 - - + +
68F ARG* 1.3 66.1 + - - +
70F ALA* 3.2 8.1 + - - +
71F HIS* 3.0 39.8 + - + +
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Residues in contact with ARG 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E TYR* 5.0 1.8 + - - -
55F ASP* 5.6 5.9 - - - +
59F ILE* 3.9 43.3 - - + +
63F ALA* 4.4 4.8 + - + +
64F SER 2.6 22.3 + - - +
65F ASP* 3.8 6.5 - - - +
67F GLU* 1.3 73.3 - - - +
69F GLU* 1.3 67.7 + - + +
71F HIS* 3.3 2.4 + - - +
72F VAL* 3.1 31.0 + - + +
121F ARG* 3.2 58.4 + - - +
122F ASN* 5.2 4.8 + - - +
125F LEU* 3.7 31.1 - - - +
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Residues in contact with GLU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASP* 3.1 22.2 + - - +
66F THR* 3.7 7.4 - - - +
68F ARG* 1.3 82.1 - - + +
70F ALA* 1.3 62.6 - - - +
72F VAL* 2.9 11.5 - - + +
73F LYS* 2.9 28.1 + - - +
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F THR* 3.1 14.1 + - + +
67F GLU* 3.2 13.2 + - - +
69F GLU* 1.3 77.1 - - - +
71F HIS* 1.3 66.0 + - + +
73F LYS* 3.3 5.5 + - - +
74F ARG* 3.1 23.4 + - - +
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Residues in contact with HIS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F LEU* 3.5 26.6 + - - +
59F ILE* 4.6 3.6 - - + -
60F PRO* 3.7 31.6 - - + +
63F ALA* 4.9 0.7 - - + -
67F GLU* 3.0 40.3 + - + +
68F ARG* 3.8 5.6 - - - +
70F ALA* 1.3 79.0 - - + +
72F VAL* 1.3 61.2 + - - +
74F ARG* 3.4 9.9 + - - +
75F PHE* 3.1 22.5 + - - +
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Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F LEU* 4.3 6.3 - - + -
59F ILE* 3.7 27.1 - - + -
68F ARG* 3.1 20.7 + - + +
69F GLU* 2.9 32.1 - - + +
71F HIS* 1.3 71.7 - - - +
73F LYS* 1.3 61.0 + - + +
75F PHE* 3.1 7.9 + - - +
76F ARG* 2.9 38.4 + - + +
125F LEU* 4.0 27.4 - - + -
129F LEU* 6.5 0.4 - - + -
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Residues in contact with LYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F GLU 2.9 20.3 + - - +
70F ALA* 3.7 5.8 - - - +
72F VAL* 1.3 77.3 - - + +
74F ARG* 1.3 63.2 + - - +
76F ARG* 3.4 8.8 + - - +
77F GLN* 3.1 42.0 + - - +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ASP* 2.9 41.6 + - - -
37F VAL* 3.8 23.6 - - + +
70F ALA 3.1 14.7 + - - +
71F HIS* 3.6 10.7 + - - +
73F LYS* 1.3 80.5 - - - +
75F PHE* 1.3 61.2 + - - +
77F GLN* 3.3 22.4 - - + +
78F ALA* 3.5 4.5 + - - +
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Residues in contact with PHE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 4.2 19.7 - - + -
36F PRO* 4.2 16.2 - - + -
37F VAL* 4.8 7.4 - - - +
40F VAL* 3.3 29.4 - - + -
51F VAL* 3.9 24.0 - - + -
53F PHE* 5.0 6.5 - + - -
58F LEU* 3.4 43.7 - - + -
71F HIS 3.1 7.3 + - - +
72F VAL* 3.1 8.9 + - - +
74F ARG* 1.3 75.2 - - - +
76F ARG* 1.3 64.3 + - - +
78F ALA* 3.3 4.6 + - + +
79F LEU* 3.2 40.8 + - + +
86F VAL* 4.4 9.4 - - + -
129F LEU* 4.7 10.1 - - + -
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F VAL* 2.9 26.7 + - + +
73F LYS* 3.6 8.1 - - - +
74F ARG 3.3 0.2 - - - -
75F PHE* 1.3 73.8 - - + +
77F GLN* 1.3 66.0 + - - +
79F LEU* 3.2 10.6 + - - +
80F ASP* 3.1 34.1 + - - +
125F LEU* 6.5 0.4 - - - -
128F GLU* 3.1 45.2 + - - +
129F LEU* 3.4 29.7 - - + +
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Residues in contact with GLN 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LYS* 3.1 46.5 + - - +
74F ARG* 3.3 16.2 - - + +
75F PHE 3.2 0.2 - - - -
76F ARG* 1.3 78.0 - - - +
78F ALA* 1.3 62.2 + - - +
80F ASP* 3.4 8.0 + - - +
81F ALA* 3.2 21.4 + - - +
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 3.9 31.2 - - + +
40F VAL* 4.3 19.3 - - + -
41F GLN* 5.3 2.5 - - + -
74F ARG 3.5 4.9 + - - +
75F PHE* 3.3 9.9 + - - +
77F GLN* 1.3 78.3 - - - +
79F LEU* 1.3 57.4 + - - +
81F ALA* 3.3 5.8 + - - +
82F THR* 2.7 41.8 + - + +
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Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F VAL* 4.2 6.7 - - + -
51F VAL* 4.4 4.0 - - + -
75F PHE* 3.2 36.0 + - + +
76F ARG* 3.2 13.0 + - - +
78F ALA* 1.3 78.9 - - - +
80F ASP* 1.3 61.6 + - - +
82F THR* 3.8 3.1 - - - -
83F GLY* 2.8 28.8 + - - -
84F MET* 3.2 41.0 + - + +
85F THR* 5.6 0.4 - - - -
86F VAL* 3.6 31.9 - - + -
129F LEU* 3.9 20.4 - - + +
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ARG* 3.1 21.8 + - - +
77F GLN* 3.8 8.3 - - - +
78F ALA 3.3 0.2 - - - -
79F LEU* 1.3 78.8 - - - +
81F ALA* 1.3 65.4 + - - +
83F GLY* 3.5 7.0 + - - -
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F GLN 3.2 11.9 + - - +
78F ALA* 3.6 9.9 - - - +
80F ASP* 1.3 81.6 - - - +
82F THR* 1.3 67.2 + - + +
83F GLY* 4.2 0.5 - - - -
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Residues in contact with THR 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F VAL* 3.4 20.7 - - + +
41F GLN* 4.0 21.8 - - + +
44F ALA* 3.9 13.1 - - + +
78F ALA* 2.7 26.9 + - - +
79F LEU 3.4 0.5 + - - -
81F ALA* 1.3 77.9 - - + +
83F GLY* 1.3 60.2 + - - +
84F MET* 3.3 32.5 + - - +
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Residues in contact with GLY 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F TYR* 4.4 3.5 - - - +
79F LEU 2.8 14.8 + - - -
80F ASP* 3.9 7.2 - - - -
81F ALA 3.2 3.2 - - - -
82F THR* 1.3 73.5 - - - +
84F MET* 1.3 68.3 + - - +
85F THR* 3.7 9.4 + - - +
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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