Contacts of the helix formed by residues 60 - 78 (chain G) in PDB entry 4ZZ7
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 PRO 60 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASN* 3.5 17.9 - - + +
126F VAL 4.7 5.6 - - - +
127F GLY* 4.1 5.4 - - - +
128F PRO* 4.0 36.6 - - + -
58G ASN 3.5 7.2 - - - +
59G THR* 1.3 90.6 - - + +
61G PRO* 1.3 71.9 - - + +
62G LEU* 4.3 6.5 - - + +
63G LYS* 3.0 28.2 + - + +
64G ARG* 3.1 10.6 + - - +
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Residues in contact with PRO 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446E TYR* 5.5 3.1 - - - +
124F ARG* 3.8 17.9 - - + +
125F ASN* 3.4 20.4 - - + +
59G THR 3.4 4.9 - - - +
60G PRO* 1.3 81.6 - - + +
62G LEU* 1.3 57.0 + - - +
64G ARG* 3.3 19.0 + - + +
65G ALA* 2.9 31.2 + - - +
114G ALA* 4.5 3.0 - - + +
115G PRO* 4.2 24.7 - - + +
118G LEU* 3.9 31.2 - - + -
164G VAL 4.9 0.9 - - - +
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Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E GLU* 4.0 18.4 - - + +
109E GLU* 3.3 28.7 - - + +
444E VAL* 3.8 29.2 - - + -
445E ALA* 6.4 0.4 - - + -
446E TYR* 3.8 24.3 + - + +
125F ASN 5.4 0.4 + - - +
126F VAL 4.3 11.0 - - - +
60G PRO* 3.1 6.6 + - + +
61G PRO* 1.3 76.9 - - - +
63G LYS* 1.3 58.1 + - - +
65G ALA* 3.2 7.1 + - + +
66G ARG* 3.0 49.2 + - + +
69G PHE* 6.2 1.1 - - + -
115G PRO* 4.1 13.1 - - + +
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TRP* 5.5 0.8 - - + -
59G THR* 3.9 21.3 - - + +
60G PRO* 3.0 23.0 + - + +
62G LEU* 1.3 76.3 - - - +
64G ARG* 1.3 65.4 + - - +
66G ARG* 3.4 26.2 + - + +
67G VAL* 3.7 10.4 + - - +
70G ARG* 5.2 2.8 + - - +
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Residues in contact with ARG 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ARG* 4.9 6.1 - - - +
56G TRP* 3.4 62.2 + - + +
57G ARG 3.3 20.0 + - - -
59G THR* 2.8 35.2 + - + -
60G PRO 3.1 14.9 + - - +
61G PRO* 3.7 17.6 - - - +
63G LYS* 1.3 75.7 - - - +
65G ALA* 1.3 64.7 + - - +
67G VAL* 3.1 21.5 + - - +
68G MET* 3.7 4.0 + - - +
118G LEU* 3.6 17.4 - - - +
138G PRO* 4.9 1.8 - - - +
163G ILE* 3.8 1.7 - - - +
164G VAL* 2.8 38.8 + - + +
165G CYS 3.3 14.3 + - - -
166G GLY* 3.3 13.7 - - - +
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Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G PRO 2.9 18.8 + - - +
62G LEU* 3.5 9.0 - - + +
64G ARG* 1.3 76.6 - - - +
66G ARG* 1.3 58.2 + - - +
68G MET* 2.8 24.2 + - - +
69G PHE* 2.8 18.0 + - + -
111G ALA 4.3 0.2 - - - +
112G CYS* 3.4 30.2 - - - +
114G ALA* 4.5 3.8 - - + -
115G PRO* 4.5 2.7 - - + -
164G VAL* 3.7 16.5 - - + +
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Residues in contact with ARG 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS* 4.6 9.6 + - - +
76E GLU* 5.9 0.4 - - - -
102E GLN* 4.3 17.6 - - - +
106E GLU* 3.4 25.9 + - - +
109E GLU* 2.5 50.1 + - - +
62G LEU* 3.0 38.7 + - - +
63G LYS* 3.7 13.5 - - + +
64G ARG 3.2 0.8 - - - -
65G ALA* 1.3 73.5 - - - +
67G VAL* 1.3 56.3 + - - +
69G PHE* 3.2 14.8 + - + +
70G ARG* 3.0 53.5 + - - +
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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
----------------------------------------------------------
56G TRP* 4.2 17.5 - - + -
63G LYS* 3.7 10.0 + - + +
64G ARG 3.3 12.6 - - - +
65G ALA 3.1 0.4 + - - -
66G ARG* 1.3 76.2 - - - +
68G MET* 1.3 61.7 + - - +
70G ARG* 3.2 18.8 + - - +
71G PHE* 2.8 26.2 + - - +
163G ILE* 6.4 0.2 - - + -
188G LEU* 4.4 11.0 - - + +
191G ALA* 3.7 18.3 - - + +
192G GLY 4.0 16.2 - - - +
193G LEU* 3.9 29.2 - - + +
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Residues in contact with MET 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ARG 4.2 2.7 - - - +
65G ALA 2.8 14.7 + - - +
67G VAL* 1.3 76.9 - - - +
69G PHE* 1.3 64.9 + - - +
71G PHE* 3.5 28.3 - - + -
72G LYS* 2.9 22.2 + - - +
108G VAL* 3.3 21.7 - - + +
111G ALA* 4.2 13.7 - - + -
112G CYS* 3.7 11.7 - - - +
159G PHE* 5.6 0.7 - - + -
160G PRO* 3.4 43.3 - - + +
163G ILE* 5.1 14.6 - - - -
164G VAL* 4.2 18.2 - - + -
188G LEU* 4.6 11.9 - - + -
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Residues in contact with PHE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E PHE* 3.2 41.4 - + - -
72E LYS* 3.7 34.8 - - + +
109E GLU* 3.9 44.9 - - + -
112E CYS* 4.0 9.9 - - + -
62G LEU* 6.2 1.3 - - + -
65G ALA* 2.8 24.8 + - + -
66G ARG* 3.2 17.7 + - + +
68G MET* 1.3 77.3 - - - +
70G ARG* 1.3 60.5 + - + +
72G LYS* 3.4 15.2 - - - +
73G GLU* 3.6 14.8 + - - +
112G CYS* 3.5 33.6 - - + -
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Residues in contact with ARG 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS* 6.0 1.8 - - - +
63G LYS* 5.3 2.2 + - - +
66G ARG* 3.0 36.5 + - - +
67G VAL* 3.4 33.8 - - - +
69G PHE* 1.3 74.0 - - + +
71G PHE* 1.3 65.2 + - - +
73G GLU* 3.1 32.1 + - - +
74G LEU* 3.2 17.2 + - + +
190G GLU 5.4 0.9 - - - -
191G ALA* 2.9 45.7 + - + +
192G GLY* 4.4 4.5 + - - -
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Residues in contact with PHE 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G VAL 2.8 17.3 + - - +
68G MET* 3.4 28.5 - - + +
70G ARG* 1.3 76.0 - - - +
72G LYS* 1.3 61.9 + - - +
74G LEU* 3.2 4.0 + - + +
75G LEU* 3.0 54.2 + - + +
108G VAL* 3.8 11.4 - - + -
156G LEU* 3.6 29.4 - - + -
159G PHE* 4.1 12.8 - + - -
184G ILE* 3.2 28.3 - - + -
187G LEU* 4.0 11.2 - - + -
188G LEU* 3.3 34.1 - - + -
191G ALA* 3.7 6.6 - - + +
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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
----------------------------------------------------------
66E ARG* 5.3 5.5 - - - +
69E PHE* 3.7 45.4 - - + +
70E ARG* 6.2 1.4 - - - +
68G MET 2.9 11.8 + - - +
69G PHE* 3.4 13.0 - - - +
71G PHE* 1.3 75.8 - - - +
73G GLU* 1.3 63.0 + - + +
75G LEU* 3.5 8.7 + - - +
76G GLU* 2.8 57.2 + - - +
105G ILE* 4.1 13.6 - - + +
108G VAL* 4.0 12.2 - - + +
109G GLU* 3.0 41.5 + - + -
112G CYS* 5.2 0.4 - - - -
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Residues in contact with GLU 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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72E LYS* 6.1 0.5 - - - +
73E GLU* 2.6 49.0 - - - +
76E GLU* 5.4 0.9 - - - +
69G PHE* 3.6 13.0 + - - +
70G ARG* 3.1 24.6 + - - +
72G LYS* 1.3 79.3 - - + +
74G LEU* 1.3 54.3 + - + +
76G GLU* 3.0 12.6 + - - +
77G GLN* 2.7 53.2 + - - +
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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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70G ARG* 3.2 17.5 + - + +
71G PHE* 3.7 4.9 - - - +
73G GLU* 1.3 81.5 - - + +
75G LEU* 1.3 58.3 + - - +
77G GLN* 4.1 17.5 - - - +
78G HIS* 2.8 47.1 + - - +
187G LEU* 3.6 41.3 - - + +
190G GLU* 3.2 34.3 - - + +
191G ALA* 3.7 23.6 - - + +
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Residues in contact with LEU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PHE* 3.0 59.5 + - + +
72G LYS* 3.7 6.3 - - - +
74G LEU* 1.3 75.5 - - - +
76G GLU* 1.3 61.5 + - - +
78G HIS 3.7 1.4 + - - -
79G ALA* 3.3 23.4 + - - +
82G ILE* 4.0 5.7 - - + +
101G LEU* 3.9 13.9 - - + +
105G ILE* 4.0 25.4 - - + -
108G VAL* 3.8 18.6 - - + -
156G LEU* 4.4 10.5 - - + -
184G ILE* 3.7 31.4 - - + -
187G LEU* 4.1 7.6 - - + -
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Residues in contact with GLU 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ARG* 5.6 3.1 - - - -
72G LYS* 2.8 47.2 + - - +
73G GLU* 3.0 13.9 + - - +
75G LEU* 1.3 75.4 - - - +
77G GLN* 1.3 65.4 + - - +
78G HIS 3.5 0.3 + - - -
79G ALA* 3.5 17.1 - - - +
102G GLN* 4.9 6.1 + - - +
105G ILE* 4.0 24.8 - - + +
109G GLU* 4.7 1.2 - - - +
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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
----------------------------------------------------------
73E GLU* 5.5 1.2 + - - -
73G GLU* 2.7 42.1 + - - +
74G LEU* 3.6 19.6 - - - +
76G GLU* 1.3 74.6 - - - +
78G HIS* 1.3 68.5 + - + +
79G ALA 3.4 2.8 + - - -
80G ASP 5.1 0.3 + - - -
81G GLU* 4.1 7.1 - - - +
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Residues in contact with HIS 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LEU* 2.8 41.0 + - + +
75G LEU 3.7 2.7 - - - -
76G GLU 3.3 0.2 - - - -
77G GLN* 1.3 84.9 + - + +
79G ALA* 1.3 62.9 + - - +
80G ASP 3.3 2.6 + - - -
81G GLU* 3.3 22.1 + - - +
82G ILE* 3.0 23.6 + - + +
183G TYR* 2.9 34.7 + - + +
187G LEU* 3.7 29.2 - - + +
190G GLU* 4.8 4.9 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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