Contacts of the helix formed by residues 60 - 78 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I ASN* 3.5 17.9 - - + +
126I VAL 4.6 7.0 - - - +
127I GLY* 4.0 6.1 - - - +
128I PRO* 3.9 35.7 - - + -
58J ASN 3.6 6.7 - - - +
59J THR* 1.4 90.8 - - + +
61J PRO* 1.3 73.6 - - + +
62J LEU* 4.3 7.2 - - + +
63J LYS* 3.1 19.4 + - + +
64J ARG* 3.0 19.1 + - - +
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Residues in contact with PRO 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ARG* 3.7 16.2 - - + +
125I ASN* 3.3 20.9 - - + +
59J THR 3.5 3.8 - - - +
60J PRO* 1.3 82.0 - - + +
62J LEU* 1.3 61.9 + - - +
64J ARG* 3.3 26.5 + - - +
65J ALA* 2.9 25.5 + - - +
114J ALA* 4.5 3.5 - - + +
115J PRO* 4.1 23.0 - - + +
118J LEU* 4.0 25.1 - - + -
164J VAL 4.9 0.7 - - - +
446L TYR* 5.4 2.7 - - - +
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Residues in contact with LEU 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I VAL 4.4 11.0 - - - +
60J PRO* 3.1 7.4 - - + -
61J PRO* 1.3 81.1 - - - +
63J LYS* 1.3 57.4 + - + +
65J ALA* 3.2 6.1 + - + +
66J ARG* 3.1 46.8 + - - +
69J PHE* 6.3 1.1 - - + -
115J PRO* 3.9 12.8 - - + +
106L GLU* 3.8 23.3 - - + +
109L GLU* 3.3 27.8 - - + +
444L VAL* 3.8 25.6 - - + -
446L TYR* 3.9 22.8 + - + +
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Residues in contact with LYS 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J TRP* 5.1 1.2 - - + -
59J THR* 4.0 20.5 - - + +
60J PRO* 3.1 21.0 + - + +
62J LEU* 1.3 76.9 - - - +
64J ARG* 1.3 63.6 + - - +
66J ARG* 3.4 28.5 + - - +
67J VAL* 3.7 10.7 + - - +
70J ARG* 5.5 1.7 + - - +
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Residues in contact with ARG 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ARG* 4.8 5.1 - - - +
56J TRP* 3.2 62.9 + - + +
57J ARG 3.3 14.6 + - - -
59J THR* 3.0 31.3 + - + +
60J PRO 3.0 16.8 + - - +
61J PRO* 3.6 19.0 - - - +
63J LYS* 1.3 76.3 - - - +
65J ALA* 1.3 61.7 + - - +
67J VAL* 3.3 19.6 - - - +
68J MET* 3.9 4.5 + - - +
118J LEU* 3.6 17.0 - - - +
138J PRO* 4.6 3.2 - - - +
163J ILE* 4.0 1.9 - - - +
164J VAL* 2.9 39.9 + - + +
165J CYS 3.5 12.1 + - - -
166J GLY* 3.4 14.5 - - - +
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Residues in contact with ALA 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J PRO 2.9 17.3 + - - +
62J LEU* 3.2 7.6 + - + +
64J ARG* 1.3 71.4 - - - +
66J ARG* 1.3 60.3 + - - +
67J VAL 3.1 2.2 - - - -
68J MET* 2.8 23.4 + - - +
69J PHE* 2.9 19.3 + - + -
111J ALA 4.2 0.4 - - - +
112J CYS* 3.4 28.9 - - - +
114J ALA* 4.4 3.8 - - + -
115J PRO* 4.6 4.0 - - + -
164J VAL* 3.5 17.0 - - + +
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Residues in contact with ARG 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J LEU* 3.1 34.2 + - - +
63J LYS* 3.6 20.9 - - + +
64J ARG 3.3 0.6 - - - -
65J ALA* 1.3 75.6 - - - +
67J VAL* 1.3 61.5 + - - +
69J PHE* 3.3 13.2 + - + +
70J ARG* 3.2 51.2 + - - +
72L LYS* 5.5 4.3 - - - +
102L GLN* 4.2 22.4 - - - +
105L ILE* 5.5 0.2 - - - +
106L GLU* 3.4 24.9 + - - +
109L GLU* 2.6 50.8 + - - +
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Residues in contact with VAL 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J TRP* 4.0 19.1 - - + -
63J LYS 3.7 10.1 + - - +
64J ARG 3.3 13.7 - - - +
66J ARG* 1.3 78.3 - - - +
68J MET* 1.3 65.3 + - - +
70J ARG* 3.4 15.6 + - - +
71J PHE* 2.9 25.6 + - - +
163J ILE* 6.3 0.2 - - + -
188J LEU* 4.7 5.8 - - + +
191J ALA* 3.6 12.5 - - + +
192J GLY 4.4 11.4 - - - +
193J LEU* 3.8 38.6 - - + +
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Residues in contact with MET 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J ARG 4.1 9.4 - - - +
65J ALA* 2.8 10.1 + - - +
67J VAL* 1.3 84.0 - - - +
69J PHE* 1.3 66.0 + - - +
71J PHE* 3.5 30.7 - - + -
72J LYS* 2.9 21.1 + - - +
108J VAL* 3.3 19.1 - - + +
111J ALA* 4.2 13.7 - - + -
112J CYS* 3.6 16.9 - - - +
159J PHE* 5.6 0.9 - - + -
160J PRO* 3.5 44.2 - - + +
163J ILE* 5.1 11.0 - - - -
164J VAL* 4.2 12.1 - - + -
188J LEU* 4.8 7.4 - - + -
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Residues in contact with PHE 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J LEU* 6.3 0.7 - - + -
65J ALA* 2.9 26.5 + - + -
66J ARG* 3.5 17.3 - - + +
68J MET* 1.3 76.3 - - - +
70J ARG* 1.3 63.0 + - + +
72J LYS* 3.2 19.0 - - - +
73J GLU* 3.6 12.3 + - - +
112J CYS* 3.6 35.6 - - + -
69L PHE* 3.4 37.0 - + - -
72L LYS* 3.7 39.7 - - + +
109L GLU* 3.9 42.8 - - + -
112L CYS* 4.4 6.7 - - + -
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Residues in contact with ARG 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J LYS* 5.5 2.2 + - - +
66J ARG* 3.2 48.7 + - - +
67J VAL* 3.7 10.5 - - - +
69J PHE* 1.3 76.8 - - + +
71J PHE* 1.3 63.6 + - - +
73J GLU* 3.3 24.7 + - - +
74J LEU* 3.2 25.2 + - + +
190J GLU 5.6 0.9 - - - -
191J ALA* 2.9 51.2 + - + +
192J GLY* 4.3 6.0 - - - -
72L LYS* 5.9 2.9 - - - +
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Residues in contact with PHE 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J VAL 2.9 17.7 + - - +
68J MET* 3.3 28.9 + - + +
70J ARG* 1.3 72.3 - - - +
72J LYS* 1.3 64.6 + - - +
74J LEU* 3.2 3.6 + - + +
75J LEU* 3.1 52.3 + - + +
108J VAL* 3.8 13.5 - - + -
156J LEU* 3.5 30.7 - - + -
159J PHE* 4.1 13.2 - + - -
184J ILE* 3.2 28.0 - - + -
187J LEU* 4.0 8.7 - - + -
188J LEU* 3.2 36.6 - - + -
191J ALA* 3.5 6.6 - - + +
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Residues in contact with LYS 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J MET 2.9 13.1 + - - +
69J PHE* 3.2 14.4 - - - +
71J PHE* 1.3 76.7 - - - +
73J GLU* 1.3 63.7 + - + +
75J LEU* 3.4 9.1 + - - +
76J GLU* 3.1 51.9 + - - +
105J ILE* 3.8 14.4 - - + +
108J VAL* 4.1 11.4 - - + +
109J GLU* 3.1 41.5 + - + -
112J CYS* 5.2 1.1 - - - -
66L ARG* 4.4 10.7 - - - +
69L PHE* 3.8 40.7 - - + +
70L ARG* 6.2 1.0 - - - +
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Residues in contact with GLU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J PHE 3.8 8.2 - - - +
70J ARG* 3.3 30.6 + - - +
71J PHE 3.3 0.6 - - - -
72J LYS* 1.3 82.7 - - + +
74J LEU* 1.3 61.9 + - + +
76J GLU* 3.2 12.7 + - - +
77J GLN* 2.9 49.2 + - - +
73L GLU* 2.8 42.9 - - - +
76L GLU* 5.4 2.1 - - - +
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Residues in contact with LEU 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J ARG* 3.4 9.2 - - + +
71J PHE* 3.2 8.4 + - - +
73J GLU* 1.3 81.6 - - + +
75J LEU* 1.3 58.9 + - - +
77J GLN* 3.9 20.0 - - - +
78J HIS* 2.8 49.4 + - + +
187J LEU* 3.3 39.9 - - + +
190J GLU* 3.7 30.3 - - + +
191J ALA* 3.5 29.4 - - + +
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Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J PHE* 3.1 59.1 + - + +
72J LYS* 3.7 7.0 - - - +
73J GLU 3.2 0.2 - - - -
74J LEU* 1.3 75.8 - - - +
76J GLU* 1.3 58.8 + - - +
78J HIS 3.5 1.6 - - - -
79J ALA* 3.1 28.2 + - - +
82J ILE* 4.0 6.8 - - + +
101J LEU* 3.9 11.7 - - + +
105J ILE* 3.7 29.8 - - + -
108J VAL* 4.1 13.7 - - + -
156J LEU* 4.4 11.4 - - + -
184J ILE* 3.8 17.5 - - + -
187J LEU* 3.7 13.5 - - + -
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Residues in contact with GLU 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J LYS* 3.1 49.1 + - - +
73J GLU* 3.2 13.1 + - - +
75J LEU* 1.3 75.6 - - - +
77J GLN* 1.3 64.3 + - + +
79J ALA* 3.3 20.3 - - - +
102J GLN* 5.4 4.3 + - - +
105J ILE* 3.9 23.2 - - + +
109J GLU* 4.8 0.3 - - - +
66L ARG* 5.8 0.7 - - - -
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Residues in contact with GLN 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J GLU* 2.9 38.8 + - - +
74J LEU* 3.8 20.5 - - - +
76J GLU* 1.3 77.7 - - + +
78J HIS* 1.3 66.0 + - + +
79J ALA 3.3 4.0 + - - -
80J ASP* 4.9 1.7 + - - +
81J GLU* 4.2 6.8 - - - +
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Residues in contact with HIS 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J LEU* 2.8 41.9 + - + +
75J LEU 3.5 3.6 - - - -
77J GLN* 1.3 80.4 + - + +
79J ALA* 1.3 62.5 + - - +
80J ASP 3.4 3.1 + - - -
81J GLU* 3.4 18.9 + - - +
82J ILE* 3.1 27.4 + - + +
183J TYR* 3.1 36.4 + - + +
187J LEU* 3.3 25.5 - - + +
190J GLU* 4.4 11.6 + - - -
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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