Contacts of the helix formed by residues 60 - 78 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ASN 3.7 4.9 - - - +
59I THR* 1.3 92.6 - - + +
61I PRO* 1.4 65.3 - - + +
62I LEU* 3.1 5.2 - - + +
63I LYS* 2.9 34.8 + - + +
64I ARG* 3.0 10.8 + - - +
125J ASN* 3.4 18.4 - - + +
126J VAL 4.5 8.5 - - - +
127J GLY* 4.0 3.6 - - - +
128J PRO* 3.9 39.5 - - + -
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Residues in contact with PRO 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I THR 3.8 4.9 - - - +
60I PRO* 1.4 82.8 - - + +
62I LEU* 1.3 52.2 + - - +
64I ARG* 3.5 26.8 + - - +
65I ALA* 2.8 35.2 + - - +
114I ALA* 4.4 3.4 - - + +
115I PRO* 4.0 24.9 - - + +
118I LEU* 4.0 22.4 - - + -
164I VAL 4.9 0.9 - - - +
124J ARG* 3.8 18.8 - - + +
125J ASN* 3.4 19.1 - - + +
446K TYR* 5.3 3.6 - - - +
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Residues in contact with LEU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I PRO* 3.1 6.6 - - + +
61I PRO* 1.3 78.7 - - - +
63I LYS* 1.3 57.1 + - - +
65I ALA* 3.4 5.8 + - + +
66I ARG* 3.2 46.3 + - - +
69I PHE* 5.9 0.4 - - + -
115I PRO* 4.0 11.8 - - + +
126J VAL 4.1 15.0 - - - +
106K GLU* 4.2 19.3 - - + +
109K GLU* 3.4 26.9 - - + +
444K VAL* 3.7 29.6 - - + -
445K ALA* 6.3 1.3 - - + -
446K TYR* 3.9 19.4 + - + +
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Residues in contact with LYS 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TRP* 5.5 0.7 - - + -
59I THR* 3.9 20.9 - - + +
60I PRO* 2.9 20.9 + - + +
62I LEU* 1.3 76.1 - - - +
64I ARG* 1.3 64.9 + - - +
66I ARG* 3.1 31.6 + - + +
67I VAL* 3.6 9.8 + - - +
70I ARG* 5.3 2.6 + - - +
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Residues in contact with ARG 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TRP* 3.2 57.1 + - + +
57I ARG 3.1 21.2 + - - -
59I THR* 3.0 32.9 + - + +
60I PRO 3.0 12.8 + - - +
61I PRO* 3.6 19.8 - - - +
63I LYS* 1.3 74.1 - - - +
65I ALA* 1.3 63.3 + - - +
67I VAL* 3.3 20.3 + - - +
68I MET* 3.9 3.8 + - - +
118I LEU* 3.5 22.2 - - - +
138I PRO* 4.7 1.6 - - - +
163I ILE* 3.8 1.9 - - - +
164I VAL* 2.8 40.7 + - + +
165I CYS 3.8 6.9 + - - -
166I GLY* 3.5 11.5 - - - +
124J ARG* 4.6 6.9 - - - +
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Residues in contact with ALA 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I PRO 2.8 21.5 + - - +
62I LEU* 3.6 9.9 - - + +
63I LYS 3.2 0.2 - - - -
64I ARG* 1.3 73.4 - - - +
66I ARG* 1.3 56.5 + - - +
68I MET* 2.9 22.6 + - - +
69I PHE* 3.0 18.9 + - + -
112I CYS* 3.3 29.6 - - - +
114I ALA* 4.4 3.8 - - + -
115I PRO* 4.4 2.9 - - + -
164I VAL* 3.6 16.5 - - + +
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Residues in contact with ARG 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I LEU* 3.2 34.4 + - - +
63I LYS* 3.1 21.5 + - + +
65I ALA* 1.3 73.3 - - - +
67I VAL* 1.3 63.4 + - - +
69I PHE* 3.4 16.1 + - + +
70I ARG* 3.1 49.5 + - - +
72K LYS* 5.0 8.3 - - - +
76K GLU* 5.7 1.1 - - - -
102K GLN* 4.0 22.1 - - - +
106K GLU* 3.7 19.8 + - - +
109K GLU* 2.6 49.8 + - - +
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Residues in contact with VAL 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TRP* 4.1 18.2 - - + -
63I LYS 3.6 8.3 + - - +
64I ARG 3.4 13.2 - - - +
65I ALA 3.2 0.6 - - - -
66I ARG* 1.3 77.9 - - - +
68I MET* 1.3 56.4 + - - +
70I ARG* 3.3 14.3 + - - +
71I PHE* 2.7 32.1 + - - +
163I ILE* 6.3 0.2 - - + -
188I LEU* 3.9 24.2 - - + -
191I ALA* 3.6 12.6 - - - +
192I GLY 4.0 18.2 - - - +
193I LEU* 4.0 20.2 - - + +
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Residues in contact with MET 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I ARG 4.2 2.2 - - - +
65I ALA 2.9 10.7 + - - +
67I VAL* 1.3 86.4 - - - +
69I PHE* 1.3 61.5 + - - +
71I PHE* 3.4 33.9 - - + -
72I LYS* 2.9 30.1 + - - +
108I VAL* 3.3 17.1 - - + +
111I ALA* 4.2 8.7 - - + -
112I CYS* 3.6 15.7 - - - +
159I PHE* 5.6 0.7 - - + -
160I PRO* 3.6 39.7 - - + +
163I ILE* 5.2 11.2 - - - -
164I VAL* 4.1 23.3 - - + -
188I LEU* 4.6 5.6 - - + -
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Residues in contact with PHE 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I ALA* 3.0 26.5 + - + -
66I ARG* 3.4 20.0 - - + +
67I VAL 3.3 0.2 - - - -
68I MET* 1.3 77.3 - - - +
70I ARG* 1.3 60.9 + - + +
72I LYS* 3.5 14.8 - - - +
73I GLU* 3.6 16.7 + - - +
112I CYS* 3.5 32.7 - - + -
69K PHE* 3.3 36.3 - + - -
72K LYS* 3.5 40.6 - - + +
109K GLU* 3.9 41.7 - - + -
112K CYS* 4.0 7.4 - - + -
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Residues in contact with ARG 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LYS* 5.3 2.4 + - - +
66I ARG* 3.1 42.5 + - - +
67I VAL* 3.7 14.4 - - - +
69I PHE* 1.3 74.7 - - + +
71I PHE* 1.3 64.6 + - - +
72I LYS 3.2 0.2 - - - -
73I GLU* 3.5 21.9 - - - +
74I LEU* 3.3 26.1 + - + +
190I GLU 5.1 2.2 - - - -
191I ALA* 2.9 52.1 + - + +
192I GLY* 4.3 6.3 + - - -
72K LYS* 6.2 1.1 - - - +
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Residues in contact with PHE 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I VAL 2.7 22.2 + - - +
68I MET* 3.4 29.2 - - + +
70I ARG* 1.3 74.2 - - - +
72I LYS* 1.3 56.2 + - - +
74I LEU* 3.2 2.6 + - + +
75I LEU* 2.9 54.4 + - + +
108I VAL* 3.9 10.3 - - + -
156I LEU* 3.7 26.0 - - + -
159I PHE* 4.0 22.4 - + - -
184I ILE* 3.3 28.5 - - + -
187I LEU* 3.9 14.6 - - + -
188I LEU* 3.6 28.3 - - + -
191I ALA* 3.5 7.1 - - + +
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Residues in contact with LYS 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I MET 2.9 18.7 + - - +
69I PHE* 3.5 8.7 - - - +
71I PHE* 1.3 77.8 - - - +
73I GLU* 1.3 61.5 + - + +
75I LEU* 3.7 7.4 + - - +
76I GLU* 3.2 54.4 + - - +
105I ILE* 3.8 15.5 - - + +
108I VAL* 4.0 13.2 - - + -
109I GLU* 3.3 34.3 + - + +
112I CYS* 5.2 0.4 - - - -
66K ARG* 4.7 7.1 - - - +
69K PHE* 3.4 45.8 - - + +
70K ARG* 6.0 1.4 - - - +
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Residues in contact with GLU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I PHE* 3.8 16.6 - - - +
70I ARG* 3.5 23.7 + - - +
72I LYS* 1.3 80.4 - - + +
74I LEU* 1.3 61.1 + - + +
76I GLU* 3.3 10.9 + - - +
77I GLN* 2.9 50.5 + - - +
72K LYS* 5.8 1.9 + - - -
73K GLU* 3.1 46.3 - - - +
76K GLU* 5.2 3.5 - - - +
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ARG* 3.3 15.5 + - + +
71I PHE* 3.2 8.8 + - - +
73I GLU* 1.3 79.1 - - + +
75I LEU* 1.3 66.2 + - - +
77I GLN* 3.5 22.9 - - - +
78I HIS* 3.0 37.4 + - - +
187I LEU* 3.2 43.2 - - + +
190I GLU* 3.7 32.1 - - + +
191I ALA* 3.7 20.0 - - + +
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I PHE* 2.9 50.9 + - + +
72I LYS* 3.8 6.5 - - - +
74I LEU* 1.3 76.9 - - - +
76I GLU* 1.3 63.1 + - - +
78I HIS 3.7 1.7 - - - -
79I ALA* 3.3 22.0 + - - +
82I ILE* 4.0 8.0 - - + +
101I LEU* 3.9 12.1 - - + +
105I ILE* 3.9 27.8 - - + -
108I VAL* 3.9 17.9 - - + -
156I LEU* 4.4 11.7 - - + -
184I ILE* 3.9 28.0 - - + -
187I LEU* 3.9 12.1 - - + -
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Residues in contact with GLU 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LYS* 3.2 42.2 + - - +
73I GLU* 3.6 11.7 - - - +
74I LEU 3.2 0.4 - - - -
75I LEU* 1.3 80.2 - - - +
77I GLN* 1.3 62.0 + - + +
79I ALA* 3.3 20.4 + - - +
102I GLN* 5.0 7.8 + - - +
105I ILE* 3.9 21.7 - - + +
109I GLU* 4.8 0.9 - - - +
66K ARG* 5.7 2.9 - - - -
70K ARG* 6.0 0.3 + - - -
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Residues in contact with GLN 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I GLU* 2.9 39.5 + - - +
74I LEU* 3.5 23.4 - - - +
76I GLU* 1.3 79.0 - - + +
78I HIS* 1.3 67.8 + - + +
79I ALA 3.3 2.1 + - - -
80I ASP 5.2 0.2 + - - -
81I GLU* 4.5 5.5 - - - +
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Residues in contact with HIS 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I LEU* 3.0 36.5 + - + +
75I LEU 3.7 3.6 - - - -
77I GLN* 1.3 86.7 + - + +
79I ALA* 1.3 64.2 + - - +
80I ASP 3.3 2.5 - - - -
81I GLU* 3.4 20.6 + - - +
82I ILE* 3.1 27.1 + - + +
183I TYR* 2.9 34.4 + - + +
187I LEU* 3.5 23.1 - - + +
190I GLU* 4.7 6.4 + - - -
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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