Contacts of the helix formed by residues 60 - 78 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN 3.6 6.7 - - - +
59A THR* 1.3 92.8 - - + +
61A PRO* 1.3 70.9 - - + +
62A LEU* 4.3 6.7 - - + +
63A LYS* 3.0 19.1 + - + +
64A ARG* 2.9 19.6 + - - +
125D ASN* 3.5 17.3 - - + +
126D VAL 4.6 7.2 - - - +
127D GLY* 4.0 4.3 - - - +
128D PRO* 3.9 38.8 - - + -
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR 3.5 5.3 - - - +
60A PRO* 1.3 82.7 - - + +
62A LEU* 1.3 61.8 + - - +
64A ARG* 3.8 26.3 - - + +
65A ALA* 2.9 26.7 + - - +
114A ALA* 4.5 2.3 - - + +
115A PRO* 4.1 24.9 - - + +
118A LEU* 4.2 21.3 - - + -
164A VAL 4.9 1.3 - - - +
446C TYR* 5.1 4.0 - - + +
124D ARG* 3.8 17.7 - - - +
125D ASN* 3.4 18.6 - - + +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 3.1 6.6 - - + +
61A PRO* 1.3 79.8 - - - +
63A LYS* 1.3 63.0 + - - +
65A ALA* 3.2 4.7 + - + +
66A ARG* 3.1 42.7 + - - +
115A PRO* 4.2 13.0 - - + -
106C GLU* 4.1 18.2 - - + +
109C GLU* 3.1 28.9 - - + +
444C VAL* 3.6 15.3 - - + -
445C ALA* 6.2 1.1 - - + -
446C TYR* 3.5 38.5 + - + +
125D ASN 5.4 0.2 + - - -
126D VAL 4.1 11.7 - - - +
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 5.0 2.6 - - + -
59A THR* 3.8 20.7 - - + +
60A PRO* 3.0 20.3 + - + +
62A LEU* 1.3 77.2 - - - +
64A ARG* 1.3 65.7 + - - +
65A ALA 3.4 0.2 + - - -
66A ARG* 3.4 24.9 + - + +
67A VAL* 3.7 12.3 + - - +
70A ARG* 5.3 2.7 + - - +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 3.4 59.8 + - + +
57A ARG 3.3 19.2 + - - -
59A THR* 2.6 36.5 + - + -
60A PRO 2.9 16.0 + - - +
61A PRO* 3.8 18.4 - - - +
62A LEU 3.3 0.2 - - - -
63A LYS* 1.3 77.5 - - - +
65A ALA* 1.3 60.8 + - - +
67A VAL* 3.2 20.1 + - - +
68A MET* 3.8 4.0 + - - +
118A LEU* 3.7 19.2 - - - +
138A PRO* 5.2 0.6 - - - +
163A ILE* 3.9 0.6 - - - +
164A VAL* 2.6 40.4 + - + +
165A CYS 3.5 13.3 + - - -
166A GLY* 3.4 10.9 - - - +
124D ARG* 4.7 7.7 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PRO 2.9 19.5 + - - +
62A LEU* 3.2 7.2 + - + +
64A ARG* 1.3 71.8 - - - +
66A ARG* 1.3 60.8 + - - +
67A VAL 3.1 2.0 - - - -
68A MET* 2.8 22.7 + - - +
69A PHE* 3.0 19.3 + - + -
111A ALA 4.3 0.2 - - - +
112A CYS* 3.2 28.2 - - - +
115A PRO* 4.5 7.0 - - + -
164A VAL* 3.6 17.9 - - + +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.1 39.3 + - - +
63A LYS* 3.7 16.7 - - + +
64A ARG 3.3 0.6 - - - -
65A ALA* 1.3 73.1 - - - +
67A VAL* 1.3 66.2 + - - +
69A PHE* 3.6 14.9 - - + +
70A ARG* 3.1 52.1 + - - +
72C LYS* 4.9 8.7 - - - +
76C GLU* 5.8 1.5 + - - -
102C GLN* 3.8 25.5 - - - +
106C GLU* 3.5 24.4 + - - +
109C GLU* 2.4 48.6 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 4.1 17.7 - - + -
63A LYS 3.7 9.6 + - - +
64A ARG 3.3 13.7 - - - +
65A ALA 3.1 0.8 - - - -
66A ARG* 1.3 78.7 - - - +
68A MET* 1.3 62.9 + - - +
70A ARG* 3.3 12.7 + - - +
71A PHE* 2.9 25.8 + - - +
163A ILE* 6.2 0.2 - - + -
188A LEU* 4.4 10.3 - - + -
191A ALA* 3.6 19.6 - - + +
192A GLY 4.0 17.0 - - - +
193A LEU* 3.9 30.1 - - + +
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG 4.3 2.9 - - - +
65A ALA 2.8 9.9 + - - +
67A VAL* 1.3 81.9 - - - +
69A PHE* 1.3 58.7 + - - +
71A PHE* 3.3 34.8 - - + -
72A LYS* 2.8 24.4 + - - +
108A VAL* 3.2 24.7 - - + +
111A ALA* 4.2 7.2 - - + -
112A CYS* 3.6 16.8 - - - +
159A PHE* 6.1 0.2 - - - -
160A PRO* 3.6 40.8 - - + +
163A ILE* 5.0 12.3 - - - -
164A VAL* 4.1 23.3 - - + -
188A LEU* 4.7 10.3 - - + -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.0 23.7 + - + -
66A ARG* 3.6 18.4 - - + +
68A MET* 1.3 78.2 - - - +
70A ARG* 1.3 58.8 + - + +
72A LYS* 3.2 20.7 - - - +
73A GLU* 3.6 12.5 - - - +
112A CYS* 3.4 32.0 - - + -
69C PHE* 3.3 39.5 - + - -
72C LYS* 3.8 33.4 - - + +
109C GLU* 3.9 43.5 - - + -
112C CYS* 4.0 7.9 - - + -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 5.3 2.8 + - - +
66A ARG* 3.1 46.0 + - - +
67A VAL* 3.7 14.9 - - - +
69A PHE* 1.3 76.7 - - + +
71A PHE* 1.3 65.2 + - - +
73A GLU* 3.3 12.1 + - - +
74A LEU* 3.3 23.6 + - + +
190A GLU 5.3 1.6 - - - -
191A ALA* 3.0 41.8 + - + +
192A GLY* 4.3 6.2 + - - -
72C LYS* 6.2 1.3 - - - +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL 2.9 18.0 + - - +
68A MET* 3.3 32.3 - - + +
70A ARG* 1.3 74.7 - - - +
72A LYS* 1.3 63.8 + - - +
73A GLU 3.1 0.3 + - - -
74A LEU* 3.1 3.6 + - + -
75A LEU* 3.1 54.4 + - + +
108A VAL* 4.0 7.9 - - + -
156A LEU* 3.7 28.9 - - + -
159A PHE* 4.2 11.7 - + - -
184A ILE* 3.4 27.6 - - + -
187A LEU* 4.1 11.9 - - + -
188A LEU* 3.3 33.4 - - + -
191A ALA* 3.6 5.3 - - + +
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET 2.8 15.4 + - - +
69A PHE* 3.2 16.8 - - - +
71A PHE* 1.3 72.5 - - - +
73A GLU* 1.3 71.1 + - - +
75A LEU* 3.5 6.8 + - - +
76A GLU* 3.1 56.5 + - - +
105A ILE* 3.8 17.0 - - + +
108A VAL* 4.0 13.6 - - + +
109A GLU* 2.9 33.1 + - + +
112A CYS* 5.1 0.2 - - - -
66C ARG* 4.4 9.1 + - - +
69C PHE* 3.4 46.5 - - + +
70C ARG* 6.2 1.0 - - - +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE 3.6 15.1 - - - +
70A ARG* 3.4 11.0 - - - +
72A LYS* 1.3 93.3 - - - +
74A LEU* 1.3 62.1 + - + +
76A GLU* 3.1 14.5 + - - +
77A GLN* 2.8 50.2 + - - +
69C PHE* 5.4 0.3 - - - +
73C GLU* 2.3 46.3 - - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ARG 3.4 9.9 - - - +
71A PHE* 3.1 8.0 + - + +
73A GLU* 1.3 80.5 - - + +
75A LEU* 1.3 58.3 + - - +
77A GLN* 4.1 18.2 - - - +
78A HIS* 2.8 49.2 + - + +
187A LEU* 3.0 43.0 - - + +
190A GLU* 3.8 28.9 - - + +
191A ALA* 3.7 25.8 - - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.1 59.5 + - + +
72A LYS* 3.7 5.4 - - - +
74A LEU* 1.3 78.1 - - - +
76A GLU* 1.3 56.5 + - - +
78A HIS 3.5 2.1 + - - -
79A ALA* 3.1 27.4 + - - +
82A ILE* 3.7 10.1 - - + +
101A LEU* 3.9 8.4 - - + +
105A ILE* 4.0 25.1 - - + -
108A VAL* 4.0 17.0 - - + -
156A LEU* 4.5 11.4 - - + -
184A ILE* 4.0 20.0 - - + -
187A LEU* 4.0 14.4 - - + -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.1 47.2 + - - +
73A GLU* 3.1 17.4 + - - +
75A LEU* 1.3 75.4 - - - +
77A GLN* 1.3 64.8 + - + +
79A ALA* 3.3 20.6 + - - +
102A GLN* 5.1 5.9 + - - +
105A ILE* 3.9 23.8 - - + +
109A GLU* 4.7 0.7 - - - +
66C ARG* 5.6 2.1 - - - -
70C ARG* 6.2 0.2 - - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLU* 2.8 39.4 + - - +
74A LEU* 3.6 20.7 - - - +
76A GLU* 1.3 79.0 - - + +
78A HIS* 1.3 68.1 + - + +
79A ALA 3.3 2.1 + - - -
80A ASP 5.2 0.7 + - - -
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 2.8 44.2 + - - +
75A LEU 3.5 3.1 - - - -
76A GLU 3.3 0.2 - - - -
77A GLN* 1.3 83.1 + - + +
79A ALA* 1.3 63.9 + - - +
80A ASP 3.3 2.9 - - - -
81A GLU* 3.2 8.1 + - + +
82A ILE* 3.0 26.5 + - + +
183A TYR* 3.1 35.3 + - + +
187A LEU* 3.5 26.4 - - + +
190A GLU* 4.6 5.5 + - - -
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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
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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