Contacts of the helix formed by residues 64 - 83 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ALA* 1.3 77.2 - - - +
65G ASP* 1.3 64.7 + - - +
66G THR* 3.9 8.5 + - - -
67G GLU* 2.6 45.0 + - - +
68G ARG* 3.0 18.9 + - - +
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Residues in contact with ASP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ALA 3.7 1.0 + - - -
64G SER* 1.3 73.5 - - - +
66G THR* 1.3 59.0 + - - +
68G ARG* 3.1 14.0 + - - +
69G GLU* 2.9 36.4 + - - +
121G ARG* 3.2 26.8 + - - +
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Residues in contact with THR 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G SER* 3.2 7.9 + - - -
65G ASP* 1.3 79.8 - - - +
67G GLU* 1.3 59.4 + - - +
69G GLU* 4.0 3.9 + - - +
70G ALA* 3.2 25.2 + - + +
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ALA* 3.7 15.6 - - + +
64G SER* 2.6 45.7 + - - +
65G ASP 3.2 0.4 - - - -
66G THR* 1.3 77.8 - - - +
68G ARG* 1.3 59.9 + - - +
70G ALA* 3.5 5.8 - - - +
71G HIS* 3.0 42.8 + - + +
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Residues in contact with ARG 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ILE* 3.6 43.8 - - + +
63G ALA* 4.9 3.3 - - - +
64G SER 3.0 13.2 + - - +
65G ASP* 3.1 18.6 + - - +
67G GLU* 1.3 73.3 - - - +
69G GLU* 1.3 71.4 + - - +
70G ALA 2.9 3.8 - - - -
71G HIS* 2.9 16.0 + - - +
72G VAL* 3.0 17.8 + - + +
121G ARG* 3.4 71.3 + - - +
122G ASN* 4.9 3.0 + - - +
125G LEU* 4.0 29.2 - - - +
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Residues in contact with GLU 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ASP* 2.9 23.0 + - - +
66G THR* 4.6 3.6 - - - +
68G ARG* 1.3 82.3 + - - +
70G ALA* 1.3 55.4 + - - +
72G VAL* 2.9 42.5 - - - +
73G LYS* 3.2 13.7 + - - +
76G ARG* 5.5 1.0 + - - -
125G LEU* 6.2 0.3 - - - +
128G GLU* 4.0 17.9 - - - +
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Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G THR 3.2 20.5 + - - +
67G GLU* 3.5 9.0 - - - +
68G ARG 2.9 0.6 - - - -
69G GLU* 1.3 78.3 - - - +
71G HIS* 1.3 64.7 + - - +
72G VAL 3.2 0.2 - - - -
73G LYS* 3.2 15.6 + - - +
74G ARG* 3.2 23.0 + - - +
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Residues in contact with HIS 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G VAL* 5.5 0.5 - - - +
58G LEU* 4.1 20.4 + - - +
59G ILE* 4.5 6.3 - - + -
60G PRO* 3.5 38.0 - - + +
63G ALA* 5.7 1.9 - - + +
67G GLU* 3.0 33.5 + - + +
68G ARG* 2.9 11.3 + - - +
70G ALA* 1.3 78.1 - - - +
72G VAL* 1.3 59.9 + - - +
74G ARG* 3.6 23.6 + - - +
75G PHE* 3.4 19.1 + - - +
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Residues in contact with VAL 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G LEU* 4.3 6.7 - - + -
59G ILE* 3.9 26.7 - - + -
68G ARG* 3.0 16.7 + - + +
69G GLU* 2.9 49.4 - - - +
71G HIS* 1.3 74.0 - - - +
73G LYS* 1.3 65.5 + - - +
75G PHE* 3.2 10.5 + - + +
76G ARG* 3.1 29.0 + - - +
125G LEU* 4.3 22.0 - - + -
128G GLU* 5.1 5.4 - - - +
129G LEU* 5.6 5.1 - - + +
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Residues in contact with LYS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G GLU* 3.2 11.6 + - - +
70G ALA* 3.2 14.3 + - - +
72G VAL* 1.3 84.2 - - - +
74G ARG* 1.3 62.1 + - + +
76G ARG* 3.5 9.3 + - - +
77G GLN* 3.3 32.6 + - - +
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Residues in contact with ARG 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ASP* 3.1 38.0 + - - -
36G PRO* 5.3 2.0 - - - +
37G VAL* 3.1 37.9 - - + +
70G ALA 3.2 18.2 - - - +
71G HIS* 4.0 22.9 + - - +
72G VAL 3.3 0.2 - - - -
73G LYS* 1.3 73.9 - - + +
75G PHE* 1.3 65.1 + - - +
77G GLN* 3.2 28.4 - - - +
78G ALA 3.3 4.0 + - - -
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Residues in contact with PHE 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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15G LEU* 4.1 16.8 - - + -
36G PRO* 4.4 11.0 - - + -
37G VAL* 3.7 6.5 - - + +
40G VAL* 3.9 25.8 - - + -
51G VAL* 4.0 21.5 - - + -
53G PHE* 4.7 6.5 - + - -
58G LEU* 3.4 46.0 - - + -
71G HIS 3.4 12.1 + - - +
72G VAL* 3.3 11.2 - - - +
74G ARG* 1.3 80.1 - - - +
76G ARG* 1.3 61.9 + - - +
77G GLN 3.3 0.3 + - - -
78G ALA* 3.4 4.5 + - - +
79G LEU* 3.2 45.0 + - + +
86G VAL* 4.3 4.9 - - + -
129G LEU* 3.9 23.3 - - + -
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Residues in contact with ARG 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G GLU* 5.5 1.0 + - - -
72G VAL* 3.1 24.0 + - - +
73G LYS* 3.5 7.2 + - - +
75G PHE* 1.3 73.7 - - - +
77G GLN* 1.3 55.7 + - - +
79G LEU* 3.7 15.7 - - + +
80G ASP* 2.7 75.2 + - - +
128G GLU* 3.3 51.9 + - - +
129G LEU* 4.0 16.9 - - + +
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Residues in contact with GLN 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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73G LYS* 3.3 30.6 + - - +
74G ARG* 3.2 18.7 - - - +
76G ARG* 1.3 77.3 - - - +
78G ALA* 1.3 57.5 + - - +
80G ASP* 3.9 5.9 - - - +
81G ALA* 2.9 32.8 + - + +
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Residues in contact with ALA 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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37G VAL* 4.0 27.4 - - + +
40G VAL* 3.9 25.1 - - + -
41G GLN* 4.9 7.9 - - + +
74G ARG 3.3 1.9 + - - +
75G PHE 3.7 7.2 - - - +
77G GLN* 1.3 79.5 - - - +
79G LEU* 1.3 52.9 + - - +
81G ALA* 3.1 5.1 + - - -
82G THR* 2.6 46.4 + - - +
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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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40G VAL* 4.2 8.3 - - + -
51G VAL* 4.5 7.9 - - + -
75G PHE* 3.2 34.5 + - + +
76G ARG* 3.5 18.2 - - + +
78G ALA* 1.3 78.4 - - - +
80G ASP* 1.3 57.8 + - - +
82G THR* 3.8 3.6 - - - -
83G GLY* 2.6 36.4 + - - -
84G MET* 3.3 37.0 + - + +
85G THR* 3.8 12.1 - - - +
86G VAL* 3.8 22.4 - - + -
129G LEU* 4.8 7.6 - - + +
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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
----------------------------------------------------------
76G ARG* 2.7 57.5 + - - +
77G GLN* 4.0 4.3 + - - +
79G LEU* 1.3 75.8 - - - +
81G ALA* 1.3 60.7 + - - +
83G GLY* 3.9 5.9 + - - -
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Residues in contact with ALA 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G GLN* 2.9 21.6 + - + +
78G ALA* 3.5 6.1 - - - +
80G ASP* 1.3 79.5 - - - +
82G THR* 1.3 63.9 - - + +
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Residues in contact with THR 82 (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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40G VAL* 3.4 4.5 - - + +
41G GLN* 4.2 26.7 - - + -
44G ALA* 3.7 29.7 - - + +
78G ALA* 2.6 29.9 + - - +
81G ALA* 1.3 77.1 - - + +
83G GLY* 1.3 57.9 + - - +
84G MET* 3.1 23.8 + - - +
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Residues in contact with GLY 83 (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 TYR* 4.2 4.5 - - - +
79G LEU 2.6 15.9 + - - -
80G ASP* 3.9 5.5 + - - -
81G ALA 3.4 3.0 + - - -
82G THR* 1.3 73.2 - - - +
84G MET* 1.3 63.7 + - - -
85G THR* 3.6 9.5 + - - +
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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