Contacts of the helix formed by residues 60 - 78 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F ASN 3.5 6.3 - - - +
59F THR* 1.3 91.1 - - + +
61F PRO* 1.3 72.2 - - + +
62F LEU* 4.3 6.3 - - + +
63F LYS* 2.9 29.1 + - + +
64F ARG* 3.1 10.6 + - - +
125G ASN* 3.5 17.7 - - + +
126G VAL 4.3 8.5 - - - +
127G GLY* 3.9 2.9 - - - +
128G PRO* 3.9 37.9 - - + -
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Residues in contact with PRO 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F THR 3.8 5.2 - - - +
60F PRO* 1.3 81.7 - - + +
62F LEU* 1.3 60.8 + - - +
64F ARG* 3.5 25.9 + - - +
65F ALA* 2.9 25.1 + - - +
114F ALA* 4.5 3.1 - - + +
115F PRO* 4.0 24.3 - - + +
118F LEU* 3.9 26.2 - - + -
164F VAL 5.0 0.7 - - - +
124G ARG* 3.7 20.6 - - + +
125G ASN* 3.3 19.3 - - + +
446H TYR* 5.3 2.7 - - - +
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F PRO* 3.0 3.9 + - + +
61F PRO* 1.3 77.6 - - - +
63F LYS* 1.3 65.9 + - - +
65F ALA* 3.1 7.5 + - + +
66F ARG* 3.0 44.8 + - + +
69F PHE* 6.4 0.7 - - + -
115F PRO* 4.0 11.1 - - + +
125G ASN 5.3 0.2 + - - -
126G VAL 4.1 14.4 - - - +
106H GLU* 4.1 17.5 - - + +
109H GLU* 3.2 28.0 - - + +
444H VAL* 3.9 13.5 - - + -
446H TYR* 3.7 37.7 + - + +
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F TRP* 6.0 1.1 - - + -
59F THR* 3.6 20.6 - - + -
60F PRO* 2.9 23.2 + - + +
62F LEU* 1.3 77.7 - - - +
64F ARG* 1.3 64.1 + - - +
66F ARG* 3.1 29.9 + - + +
67F VAL* 3.6 8.9 + - + +
70F ARG* 5.4 0.5 + - - -
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Residues in contact with ARG 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F TRP* 3.3 54.3 + - + +
57F ARG 3.0 19.8 + - - -
59F THR* 3.0 40.1 + - + +
60F PRO 3.1 5.7 + - - +
61F PRO* 3.7 17.3 - - - +
63F LYS* 1.3 75.5 - - - +
65F ALA* 1.3 62.3 + - - +
67F VAL* 3.3 20.4 - - - +
68F MET* 3.8 4.0 + - - +
118F LEU* 3.6 19.0 - - - +
138F PRO* 4.7 3.6 - - - +
163F ILE* 3.8 3.3 - - - +
164F VAL* 2.7 40.9 + - + +
165F CYS 3.5 12.1 + - - -
166F GLY* 3.3 12.8 - - - +
124G ARG* 4.8 5.3 - - - +
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Residues in contact with ALA 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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61F PRO 2.9 18.8 + - - +
62F LEU* 3.4 9.9 - - + +
64F ARG* 1.3 77.6 - - - +
66F ARG* 1.3 53.2 + - + +
68F MET* 2.8 26.8 + - - +
69F PHE* 3.1 17.2 + - + -
111F ALA 4.4 0.7 - - - +
112F CYS* 3.4 25.9 - - - +
115F PRO* 4.4 7.4 - - + -
164F VAL* 3.5 18.3 - - + +
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Residues in contact with ARG 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU* 3.0 39.4 + - + +
63F LYS* 3.1 14.9 + - + +
65F ALA* 1.3 75.1 - - + +
67F VAL* 1.3 61.8 + - - +
69F PHE* 3.3 15.4 + - + +
70F ARG* 3.2 48.5 + - - +
72H LYS* 5.1 6.2 + - - +
76H GLU* 5.9 0.9 + - - -
102H GLN* 4.0 22.0 + - - +
105H ILE* 5.3 0.4 - - - +
106H GLU* 3.5 25.7 + - - +
109H GLU* 2.5 48.8 + - - +
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Residues in contact with VAL 67 (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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56F TRP* 4.1 19.7 - - + -
63F LYS* 3.6 8.9 + - + +
64F ARG 3.3 14.1 - - - +
65F ALA 3.1 0.4 - - - -
66F ARG* 1.3 77.9 - - - +
68F MET* 1.3 62.4 + - + +
70F ARG* 3.3 17.4 + - - +
71F PHE* 2.9 24.3 + - - +
188F LEU* 4.4 10.1 - - + -
191F ALA* 3.5 14.4 - - + +
192F GLY 4.5 13.7 - - - +
193F LEU* 4.0 33.9 - - + +
194F PRO* 5.3 0.2 - - + -
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Residues in contact with MET 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F ARG 4.1 2.9 - - - +
65F ALA 2.8 15.2 + - - +
67F VAL* 1.3 76.1 - - - +
69F PHE* 1.3 60.1 + - - +
71F PHE* 3.5 29.2 - - + -
72F LYS* 3.0 23.6 + - - +
108F VAL* 3.3 23.4 - - + +
111F ALA* 4.4 4.7 - - + -
112F CYS* 3.7 15.1 - - - +
160F PRO* 3.5 43.1 - - + +
163F ILE* 4.8 13.9 - - - -
164F VAL* 4.1 24.7 - - + -
188F LEU* 4.5 14.1 - - + -
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Residues in contact with PHE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU* 6.4 0.4 - - + -
65F ALA* 3.1 23.3 + - + -
66F ARG* 3.4 17.9 - - + +
68F MET* 1.3 77.1 - - - +
70F ARG* 1.3 61.7 + - + +
72F LYS* 3.4 18.2 - - - +
73F GLU* 3.4 13.2 + - - +
112F CYS* 3.5 34.5 - - + -
69H PHE* 3.3 38.3 - + - -
72H LYS* 3.7 39.7 - - + +
109H GLU* 4.0 41.5 - - + -
112H CYS* 4.0 7.0 - - + -
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Residues in contact with ARG 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 ARG* 3.2 41.3 + - - +
67F VAL* 3.5 22.5 - - - +
68F MET 3.3 0.2 - - - -
69F PHE* 1.3 74.1 - - + +
71F PHE* 1.3 66.8 + - - +
73F GLU* 3.1 25.3 - - - +
74F LEU* 3.0 25.4 + - + +
190F GLU 5.5 0.7 - - - -
191F ALA* 2.9 45.3 + - + +
192F GLY* 4.5 4.2 - - - -
72H LYS* 6.0 1.8 - - - +
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Residues in contact with PHE 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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67F VAL 2.9 17.9 + - - +
68F MET* 3.5 30.5 - - + +
70F ARG* 1.3 75.4 - - - +
72F LYS* 1.3 57.1 + - - +
74F LEU* 3.2 3.6 + - + +
75F LEU* 3.1 56.1 + - + +
108F VAL* 4.1 9.2 - - + -
156F LEU* 3.7 29.2 - - + -
159F PHE* 4.1 13.9 - + - -
184F ILE* 3.2 29.2 - - + -
187F LEU* 4.0 12.1 - - + -
188F LEU* 3.4 34.8 - - + -
191F ALA* 3.7 5.6 - - + +
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Residues in contact with LYS 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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68F MET 3.0 12.8 + - - +
69F PHE* 3.4 11.7 - - - +
71F PHE* 1.3 74.4 - - - +
73F GLU* 1.3 65.9 + - - +
75F LEU* 3.6 7.1 + - - +
76F GLU* 2.9 53.0 + - - +
105F ILE* 3.7 19.0 - - + +
108F VAL* 4.1 11.8 - - + +
109F GLU* 2.9 34.1 + - + +
66H ARG* 4.7 8.9 - - - +
69H PHE* 3.7 47.3 - - + +
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Residues in contact with GLU 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 PHE* 3.4 9.2 + - - +
70F ARG* 3.1 28.4 + - - +
72F LYS* 1.3 80.1 - - - +
74F LEU* 1.3 60.7 + - + +
76F GLU* 3.4 11.6 + - - +
77F GLN* 3.0 48.4 + - - +
72H LYS* 5.9 0.7 + - - -
73H GLU* 3.1 50.9 - - + +
76H GLU* 5.5 2.1 - - - +
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Residues in contact with LEU 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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70F ARG* 3.0 15.1 + - + +
71F PHE* 3.2 7.2 + - - +
73F GLU* 1.3 80.4 - - + +
75F LEU* 1.3 66.8 + - - +
77F GLN* 3.4 18.3 + - - +
78F HIS* 3.0 40.1 + - + +
187F LEU* 3.4 44.0 - - + +
190F GLU* 3.9 28.9 - - + +
191F ALA* 3.6 24.5 - - + +
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Residues in contact with LEU 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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71F PHE* 3.1 47.3 + - + +
72F LYS* 4.0 7.4 - - - +
74F LEU* 1.3 79.6 - - - +
76F GLU* 1.3 63.4 + - - +
78F HIS 3.2 3.8 + - - +
79F ALA* 3.2 20.4 + - - +
82F ILE* 4.0 8.8 - - + +
101F LEU* 4.3 8.1 - - + +
105F ILE* 3.8 32.8 - - + -
108F VAL* 4.0 24.9 - - + -
156F LEU* 4.6 9.6 - - + -
184F ILE* 4.1 18.8 - - + -
187F LEU* 4.1 12.6 - - + -
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Residues in contact with GLU 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 LYS* 2.9 50.7 + - - +
73F GLU* 3.5 12.7 - - - +
75F LEU* 1.3 78.4 - - - +
77F GLN* 1.3 62.0 + - + +
79F ALA* 3.2 20.9 - - - +
102F GLN* 5.5 5.3 + - - +
105F ILE* 3.8 20.5 - - + +
70H ARG* 6.1 1.0 - - - +
73H GLU* 5.5 2.4 - - - +
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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 GLU* 3.0 43.6 + - - +
74F LEU* 3.7 19.9 - - - +
75F LEU 3.2 0.2 - - - -
76F GLU* 1.3 76.9 - - + +
78F HIS* 1.3 71.1 + - + +
79F ALA 3.2 3.7 + - - -
80F ASP* 5.0 1.2 + - - -
81F GLU* 4.0 5.5 - - - +
73H GLU* 5.7 1.2 + - - -
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Residues in contact with HIS 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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74F LEU* 3.0 36.2 + - + +
75F LEU 3.3 4.5 - - - +
77F GLN* 1.3 87.6 + - + +
79F ALA* 1.3 59.1 + - - -
81F GLU* 3.4 23.0 + - - +
82F ILE* 3.1 26.0 + - - +
183F TYR* 3.2 35.0 + - + +
187F LEU* 3.5 28.9 - - + +
190F GLU* 4.9 7.4 + - - -
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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
------------------------------------------------------------
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