Contacts of the helix formed by residues 60 - 78 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K ASN* 3.5 17.9 - - + +
126K VAL 4.6 7.0 - - - +
127K GLY* 4.1 2.7 - - - -
128K PRO* 3.9 38.8 - - + -
58L ASN 3.7 5.2 - - - +
59L THR* 1.3 92.6 - - + +
61L PRO* 1.3 71.3 - - + +
62L LEU* 4.3 6.1 - - + +
63L LYS* 3.0 28.7 + - + +
64L ARG* 3.0 10.8 + - - +
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Residues in contact with PRO 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446J TYR* 5.5 4.3 - - - +
124K ARG* 3.8 17.9 - - + +
125K ASN* 3.3 20.2 - - + +
59L THR 3.9 4.5 - - - +
60L PRO* 1.3 81.6 - - + +
62L LEU* 1.3 53.0 + - - +
64L ARG* 3.2 26.7 + - + +
65L ALA* 2.7 36.0 + - - +
114L ALA* 4.7 3.3 - - + +
115L PRO* 4.1 23.4 - - + +
118L LEU* 4.1 24.7 - - + -
164L VAL 5.0 0.9 - - - +
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Residues in contact with LEU 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J GLU* 4.0 18.8 - - + +
109J GLU* 3.6 24.2 - - + +
444J VAL* 3.8 15.0 - - + -
446J TYR* 3.7 40.1 + - + +
125K ASN 5.4 0.2 + - - -
126K VAL 4.0 13.2 - - - +
60L PRO* 3.1 6.9 - - + -
61L PRO* 1.3 79.6 - - - +
63L LYS* 1.3 61.4 + - - +
65L ALA* 3.2 5.9 + - + +
66L ARG* 3.1 42.6 + - - +
69L PHE* 6.6 0.2 - - + -
115L PRO* 4.1 10.2 - - + +
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Residues in contact with LYS 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L TRP* 4.9 2.1 - - + -
59L THR* 3.8 20.3 - - + +
60L PRO* 3.0 21.9 + - + +
62L LEU* 1.3 76.3 - - - +
64L ARG* 1.3 66.5 + - - +
66L ARG* 3.4 22.2 + - + +
67L VAL* 3.6 13.7 + - + +
70L ARG* 5.4 1.4 + - - +
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Residues in contact with ARG 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K ARG* 4.5 6.9 - - - +
56L TRP* 3.2 62.9 + - + +
57L ARG 3.2 11.9 + - - -
59L THR* 2.9 38.2 + - + -
60L PRO 3.0 17.2 + - - +
61L PRO* 3.2 18.6 + - - +
63L LYS* 1.3 75.8 - - - +
65L ALA* 1.3 62.6 + - - +
67L VAL* 3.2 21.3 + - - +
68L MET* 3.8 4.3 + - - +
118L LEU* 3.6 18.0 - - - +
138L PRO* 4.8 2.4 - - - +
163L ILE 3.8 0.2 - - - -
164L VAL* 2.7 41.1 + - + +
165L CYS 3.5 13.3 + - - -
166L GLY* 3.4 11.9 - - - +
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Residues in contact with ALA 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L PRO 2.7 17.7 + - - +
62L LEU* 3.6 7.9 - - + +
64L ARG* 1.3 74.9 - - - +
66L ARG* 1.3 59.9 + - - +
68L MET* 2.9 21.3 + - - +
69L PHE* 3.0 19.2 + - + -
111L ALA 4.3 0.4 - - - +
112L CYS* 3.2 30.0 - - - +
115L PRO* 4.4 9.4 - - + -
164L VAL* 3.7 14.8 - - + +
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Residues in contact with ARG 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J LYS* 4.4 10.0 + - - +
76J GLU* 5.8 0.7 - - - -
102J GLN* 4.3 21.3 - - - +
105J ILE* 5.5 0.4 - - - +
106J GLU* 3.5 26.1 + - - +
109J GLU* 2.5 52.9 + - - +
62L LEU* 3.1 35.8 + - - +
63L LYS* 3.8 14.1 - - + +
64L ARG 3.3 0.4 - - - -
65L ALA* 1.3 74.3 - - - +
67L VAL* 1.3 65.3 - - - +
69L PHE* 3.3 12.3 + - + +
70L ARG* 3.2 46.6 + - - +
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Residues in contact with VAL 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L TRP* 4.2 16.2 - - + -
63L LYS* 3.6 10.1 + - + +
64L ARG 3.2 14.0 + - - +
66L ARG* 1.3 77.5 - - - +
68L MET* 1.3 59.3 + - - +
70L ARG* 3.3 21.2 + - - +
71L PHE* 2.9 25.3 + - - +
188L LEU* 4.3 9.9 - - + -
191L ALA* 3.7 19.1 - - + +
192L GLY 4.3 13.0 - - - +
193L LEU* 4.0 31.9 - - + +
194L PRO* 5.3 0.2 - - + -
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Residues in contact with MET 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L ARG 4.2 3.1 - - - +
65L ALA 2.9 8.6 + - - +
67L VAL* 1.3 78.6 - - - +
69L PHE* 1.3 60.8 + - - +
71L PHE* 3.4 33.2 - - + -
72L LYS* 2.9 24.8 + - - +
108L VAL* 3.2 21.8 - - + +
111L ALA* 4.4 5.4 - - + -
112L CYS* 3.5 16.9 - - - +
159L PHE* 5.9 0.2 - - + -
160L PRO* 3.7 39.5 - - + +
163L ILE* 5.3 9.2 - - - -
164L VAL* 4.0 29.6 - - + -
188L LEU* 4.3 15.5 - - + -
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Residues in contact with PHE 69 (chain L).
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* 3.4 38.8 - + - -
72J LYS* 3.8 33.4 - - + +
109J GLU* 3.9 44.0 - - + -
112J CYS* 4.2 9.4 - - + -
65L ALA* 3.0 25.1 + - + -
66L ARG* 3.4 18.8 - - + +
68L MET* 1.3 77.4 - - - +
70L ARG* 1.3 61.9 + - + +
72L LYS* 3.4 17.7 - - - +
73L GLU* 3.6 12.7 + - - +
112L CYS* 3.4 32.0 - - + -
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Residues in contact with ARG 70 (chain L).
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* 6.2 0.9 - - - +
63L LYS* 5.5 1.6 + - - +
66L ARG* 3.2 35.0 + - - +
67L VAL* 3.7 28.3 - - - +
69L PHE* 1.3 72.6 - - + +
71L PHE* 1.3 61.5 + - - +
72L LYS 3.0 1.6 - - - -
73L GLU* 2.8 36.7 + - - +
74L LEU* 3.1 15.6 + - + +
190L GLU 5.6 0.2 - - - -
191L ALA* 2.9 44.2 + - + +
192L GLY* 4.3 5.1 + - - -
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Residues in contact with PHE 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L VAL 2.9 18.2 + - - +
68L MET* 3.4 28.0 - - + +
70L ARG* 1.3 77.9 - - - +
72L LYS* 1.3 59.1 + - - +
74L LEU* 3.6 2.7 + - + +
75L LEU* 3.2 48.1 + - + +
108L VAL* 3.7 11.0 - - + -
156L LEU* 3.5 30.3 - - + -
159L PHE* 4.2 11.4 - + - -
184L ILE* 3.4 28.0 - - + -
187L LEU* 3.9 9.4 - - + -
188L LEU* 3.3 42.0 - - + -
191L ALA* 3.6 6.9 - - + +
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Residues in contact with LYS 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ARG* 5.5 5.1 - - - +
69J PHE* 3.7 45.5 - - + +
70J ARG* 5.9 2.8 - - - +
68L MET 2.9 14.2 + - - +
69L PHE* 3.4 12.8 - - - +
71L PHE* 1.3 76.8 - - - +
73L GLU* 1.3 64.9 + - + +
75L LEU* 3.4 8.7 + - - +
76L GLU* 2.8 52.8 + - - +
105L ILE* 4.2 11.2 - - + +
108L VAL* 4.0 11.9 - - + +
109L GLU* 3.1 38.3 + - + -
112L CYS* 5.3 0.9 - - - -
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Residues in contact with GLU 73 (chain L).
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* 2.8 46.1 - - - +
69L PHE 3.6 11.2 + - - +
70L ARG* 2.8 26.6 + - - +
72L LYS* 1.3 77.6 - - + +
74L LEU* 1.3 56.5 + - + +
76L GLU* 3.0 15.2 + - - +
77L GLN* 2.8 48.9 + - - +
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Residues in contact with LEU 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ARG* 3.1 12.0 + - + +
71L PHE* 4.0 4.7 - - - +
72L LYS 3.3 0.2 - - - -
73L GLU* 1.3 75.1 - - + +
75L LEU* 1.3 66.1 + - - +
77L GLN* 3.7 25.4 - - - +
78L HIS* 2.9 41.3 + - + +
187L LEU* 3.4 35.4 - - + +
190L GLU* 3.9 31.0 - - + +
191L ALA* 3.8 23.3 - - + +
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Residues in contact with LEU 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L PHE* 3.2 50.3 + - + +
72L LYS* 3.7 7.0 - - - +
74L LEU* 1.3 78.4 - - - +
76L GLU* 1.3 61.7 + - - +
78L HIS 3.6 1.4 + - - -
79L ALA* 3.3 23.7 + - - +
82L ILE* 4.0 8.8 - - + +
101L LEU* 3.9 10.2 - - + +
105L ILE* 3.8 29.8 - - + -
108L VAL* 3.9 16.2 - - + -
156L LEU* 4.3 9.2 - - + -
184L ILE* 3.5 36.6 - - + -
187L LEU* 4.3 3.8 - - + -
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Residues in contact with GLU 76 (chain L).
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* 5.4 1.7 - - - +
72L LYS* 2.8 47.5 + - - +
73L GLU* 3.0 17.7 + - - +
75L LEU* 1.3 75.5 - - - +
77L GLN* 1.3 67.8 + - - +
79L ALA* 3.5 16.9 - - - +
102L GLN* 5.4 4.8 + - - +
105L ILE* 4.2 21.1 - - + +
109L GLU* 5.0 0.5 - - - +
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Residues in contact with GLN 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L GLU* 2.8 28.4 + - + +
74L LEU* 3.7 26.4 - - - +
76L GLU* 1.3 74.2 - - + +
78L HIS* 1.3 71.6 + - + +
79L ALA* 3.2 5.4 + - - +
80L ASP* 4.7 1.4 + - - -
81L GLU* 4.2 4.0 - - - +
190L GLU* 5.4 0.3 - - - +
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Residues in contact with HIS 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L LEU* 2.9 32.9 + - + +
75L LEU 3.6 3.6 - - - -
77L GLN* 1.3 88.8 + - + +
79L ALA* 1.3 62.9 + - - +
80L ASP 3.3 2.5 - - - -
81L GLU* 3.4 22.7 + - - +
82L ILE* 3.0 25.3 + - + +
183L TYR* 2.7 36.1 + + + +
187L LEU* 3.7 24.4 - - + +
190L GLU* 4.5 12.6 + - - -
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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