Contacts of the helix formed by residues 60 - 78 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ASN* 3.4 16.2 - - + +
126E VAL 4.5 8.1 - - - +
127E GLY* 4.0 3.6 - - - +
128E PRO* 3.9 37.7 - - + -
58H ASN 3.6 5.8 - - - +
59H THR* 1.3 91.2 - - + +
61H PRO* 1.4 62.3 - - + +
62H LEU* 4.3 5.2 - - + +
63H LYS* 2.8 42.2 + - + +
64H ARG* 3.1 10.4 + - - +
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Residues in contact with PRO 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ARG* 3.7 19.3 - - + +
125E ASN* 3.3 18.2 - - + +
446F TYR* 5.2 4.5 - - - +
59H THR 3.5 5.6 - - - +
60H PRO* 1.4 81.8 - - + +
62H LEU* 1.3 61.6 + - - +
64H ARG* 4.0 26.3 - - - +
65H ALA* 3.1 24.8 + - - +
114H ALA* 4.3 2.9 - - + +
115H PRO* 3.9 25.7 - - + +
118H LEU* 4.1 23.3 - - + -
164H VAL 5.0 0.7 - - - +
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Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E VAL 4.5 13.0 - - - +
106F GLU* 3.5 22.2 - - + +
109F GLU* 3.3 29.4 - - + +
444F VAL* 3.5 30.5 - - + -
445F ALA* 6.5 0.9 - - + -
446F TYR* 3.9 18.9 + - + +
60H PRO* 3.1 6.7 - - + +
61H PRO* 1.3 79.3 - - - +
63H LYS* 1.3 63.6 + - - +
65H ALA* 3.3 6.0 + - + +
66H ARG* 3.1 39.2 + - - +
69H PHE* 6.4 0.2 - - + -
115H PRO* 3.9 12.5 - - + +
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Residues in contact with LYS 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TRP* 5.3 1.1 - - + -
59H THR* 3.9 21.2 - - + +
60H PRO* 2.8 27.6 + - + +
62H LEU* 1.3 73.1 - - - +
64H ARG* 1.3 64.7 + - - +
66H ARG* 3.2 29.6 + - + +
67H VAL* 3.6 8.9 + - - +
70H ARG* 5.4 1.9 + - - +
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Residues in contact with ARG 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ARG* 4.8 5.3 - - - +
56H TRP* 3.3 62.0 + - + +
57H ARG 3.3 20.0 + - - -
59H THR* 3.1 28.7 + - + -
60H PRO 3.1 10.8 + - - +
61H PRO* 4.0 17.6 - - - +
63H LYS* 1.3 76.4 - - - +
65H ALA* 1.3 61.5 + - - +
67H VAL* 3.0 22.3 + - - +
68H MET* 3.8 3.5 + - - +
118H LEU* 3.6 18.2 - - - +
138H PRO* 4.7 3.2 - - - +
163H ILE 3.8 1.1 - - - -
164H VAL* 2.9 38.3 + - + +
165H CYS 3.3 14.3 + - - -
166H GLY* 3.2 14.5 - - - +
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Residues in contact with ALA 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H PRO 3.1 20.1 + - - +
62H LEU* 3.7 7.6 - - + +
63H LYS 3.2 0.4 - - - -
64H ARG* 1.3 72.5 - - - +
66H ARG* 1.3 60.0 + - - +
68H MET* 3.0 20.6 + - - +
69H PHE* 3.0 20.8 + - + -
111H ALA 4.3 0.2 - - - +
112H CYS* 3.4 27.9 - - - +
115H PRO* 4.5 7.2 - - + -
164H VAL* 3.6 18.6 - - + +
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Residues in contact with ARG 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LYS* 4.7 6.7 - - - +
102F GLN* 4.0 25.1 - - - +
105F ILE* 5.4 0.8 - - - +
106F GLU* 3.1 27.9 + - - +
109F GLU* 2.6 52.5 + - - +
62H LEU* 3.1 30.2 + - - +
63H LYS* 3.2 19.8 + - + +
65H ALA* 1.3 75.6 - - - +
67H VAL* 1.3 62.3 + - - +
69H PHE* 3.5 11.3 + - + +
70H ARG* 3.3 48.6 + - - +
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Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TRP* 4.2 14.1 - - + -
63H LYS 3.6 7.4 + - - +
64H ARG 3.0 14.8 + - - +
66H ARG* 1.3 78.0 - - - +
68H MET* 1.3 61.5 + - - +
70H ARG* 3.3 18.7 + - - +
71H PHE* 2.8 26.2 + - - +
163H ILE* 6.3 0.2 - - + -
188H LEU* 4.1 10.8 - - + -
191H ALA* 3.6 21.5 - - + +
192H GLY 4.1 4.7 - - - +
193H LEU* 3.8 42.0 - - + +
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Residues in contact with MET 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ARG 4.3 2.7 - - - +
65H ALA 3.0 7.7 + - - +
67H VAL* 1.3 80.4 - - - +
69H PHE* 1.3 60.0 + - - +
71H PHE* 3.6 27.6 - - + -
72H LYS* 3.0 23.4 + - - +
108H VAL* 3.1 26.5 - - + +
111H ALA* 4.4 2.9 - - + -
112H CYS* 3.5 15.8 - - - +
159H PHE* 5.6 0.4 - - + -
160H PRO* 3.4 42.2 - - + +
163H ILE* 5.1 11.9 - - - -
164H VAL* 4.1 27.8 - - + -
188H LEU* 4.4 16.4 - - + -
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Residues in contact with PHE 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F PHE* 3.3 38.3 - + - -
72F LYS* 3.7 39.7 - - + +
109F GLU* 3.8 44.9 - - + -
112F CYS* 3.8 7.4 - - + -
62H LEU* 6.4 0.2 - - + -
65H ALA* 3.0 29.1 + - + -
66H ARG* 3.5 13.5 - - + +
68H MET* 1.3 77.0 - - - +
70H ARG* 1.3 62.7 + - + +
72H LYS* 3.3 17.5 + - - +
73H GLU* 3.5 12.6 + - - +
112H CYS* 3.4 33.0 - - + -
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Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 6.1 1.1 - - - +
63H LYS* 5.4 2.0 + - - +
66H ARG* 3.3 44.2 + - - +
67H VAL* 3.7 19.0 - - - +
69H PHE* 1.3 74.5 - - + +
71H PHE* 1.3 64.6 + - - +
73H GLU* 3.2 15.5 + - - +
74H LEU* 3.1 28.9 + - + +
190H GLU 5.3 1.8 - - - -
191H ALA* 2.7 44.1 + - + +
192H GLY* 4.3 5.5 - - - -
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Residues in contact with PHE 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H VAL 2.8 18.3 + - - +
68H MET* 3.6 28.5 - - + +
70H ARG* 1.3 78.6 - - - +
72H LYS* 1.3 60.2 + - - +
74H LEU* 3.3 3.0 + - + +
75H LEU* 3.1 54.4 + - + +
108H VAL* 3.8 10.5 - - + -
156H LEU* 3.7 28.0 - - + -
159H PHE* 4.1 17.0 - + - -
184H ILE* 3.3 28.0 - - + -
187H LEU* 3.9 12.6 - - + -
188H LEU* 3.5 30.3 - - + -
191H ALA* 3.7 5.3 - - + +
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Residues in contact with LYS 72 (chain H).
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* 5.1 8.1 + - - +
69F PHE* 3.7 47.7 - - + +
70F ARG* 6.0 2.2 - - - +
73F GLU* 5.9 0.8 + - - -
68H MET 3.0 14.5 + - - +
69H PHE 3.4 10.1 - - - +
70H ARG 3.2 0.4 - - - -
71H PHE* 1.3 76.8 - - - +
73H GLU* 1.3 63.6 + - + +
75H LEU* 3.5 7.8 + - - +
76H GLU* 2.8 50.5 + - - +
105H ILE* 4.0 13.5 - - + +
108H VAL* 3.9 12.5 - - + +
109H GLU* 3.0 39.8 + - + -
112H CYS* 5.1 0.4 - - - -
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Residues in contact with GLU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F GLU* 3.1 47.3 - - + +
76F GLU* 5.5 2.4 - - - +
77F GLN* 5.7 1.2 + - - -
69H PHE 3.5 10.5 + - - +
70H ARG* 3.2 16.6 + - - +
72H LYS* 1.3 80.7 - - + +
74H LEU* 1.3 59.1 + - + +
76H GLU* 3.0 12.3 + - - +
77H GLN* 2.9 54.3 + - - +
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ARG* 3.1 18.3 + - + +
71H PHE* 3.6 6.5 - - - +
72H LYS 3.3 0.2 - - - -
73H GLU* 1.3 80.1 - - + +
75H LEU* 1.3 62.5 + - - +
77H GLN* 3.4 21.2 + - - +
78H HIS* 3.0 39.0 + - - +
187H LEU* 3.3 40.4 - - + +
190H GLU* 4.0 30.3 - - + +
191H ALA* 3.6 24.5 - - + +
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Residues in contact with LEU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H PHE* 3.1 57.8 + - + +
72H LYS* 3.7 6.7 - - - +
74H LEU* 1.3 75.6 - - - +
76H GLU* 1.3 61.8 + - - +
78H HIS 3.5 2.1 - - - -
79H ALA* 3.3 22.3 + - - +
82H ILE* 3.8 14.6 - - + +
101H LEU* 4.0 10.0 - - + +
105H ILE* 4.0 27.8 - - + -
108H VAL* 4.0 15.0 - - + -
156H LEU* 4.6 8.7 - - + -
184H ILE* 4.0 26.9 - - + -
187H LEU* 4.2 3.8 - - + -
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Residues in contact with GLU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ARG* 5.9 0.5 + - - -
72H LYS* 2.8 52.4 + - - +
73H GLU* 3.0 10.0 + - - +
75H LEU* 1.3 74.7 - - - +
77H GLN* 1.3 67.4 + - + +
79H ALA* 3.3 19.8 - - - +
102H GLN* 5.3 5.1 + - - +
105H ILE* 3.9 26.9 - - + +
109H GLU* 5.0 0.2 - - - +
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Residues in contact with GLN 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H GLU* 2.9 47.0 + - - +
74H LEU* 3.8 21.0 - - - +
76H GLU* 1.3 79.6 - - + +
78H HIS* 1.3 67.7 + - + +
79H ALA 3.3 3.1 + - - -
80H ASP* 4.9 1.2 + - - +
81H GLU* 4.1 6.2 - - - +
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Residues in contact with HIS 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H LEU* 3.0 36.0 + - + +
75H LEU 3.5 3.8 - - - -
76H GLU 3.3 0.2 - - - -
77H GLN* 1.3 84.5 + - + +
79H ALA* 1.3 62.5 + - - +
80H ASP 3.4 2.7 - - - -
81H GLU* 3.4 20.2 + - - +
82H ILE* 3.1 27.4 + - + +
183H TYR* 2.8 37.3 + + + +
187H LEU* 3.6 24.2 - - + +
190H GLU* 4.7 6.9 + - - -
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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) + - + + + + + -
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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