Contacts of the helix formed by residues 93 - 113 (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 ILE 93 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L LYS* 1.3 77.0 - - - +
94L ALA* 1.3 79.1 + - + +
95L HIS* 3.3 33.7 - - + +
96L ASP* 2.8 20.5 + - - +
97L ALA* 3.1 8.3 + - - -
311L GLY 4.3 1.1 - - - +
313L SER* 4.0 21.1 - - - +
315L ASP 4.5 1.6 - - - +
316L SER* 3.8 26.7 - - - -
317L GLY 3.9 4.0 - - - +
318L ASN* 3.2 34.3 - - + +
319L ASP 4.5 0.2 - - - +
320L PHE* 3.9 29.8 - - - +
321L GLY* 3.9 4.9 - - - +
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Residues in contact with ALA 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L CYS* 4.2 10.8 + - + -
92L LYS 3.9 0.8 + - - -
93L ILE* 1.3 80.3 - - + +
95L HIS* 1.3 57.3 + - - +
97L ALA* 3.9 6.0 - - - +
98L MET* 2.8 37.5 + - + +
313L SER* 4.9 7.1 + - - +
316L SER* 4.3 14.8 - - - +
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Residues in contact with HIS 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L ILE* 2.9 25.9 + - + +
94L ALA* 1.3 76.8 - - - +
96L ASP* 1.3 87.7 + - - +
98L MET* 3.5 5.9 + - - +
99L GLY* 2.9 25.1 + - - -
317L GLY* 5.5 1.0 + - - -
318L ASN 3.4 14.4 - - - -
319L ASP* 3.3 33.0 + - - -
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Residues in contact with ASP 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L LYS* 3.8 23.5 + - + +
93L ILE 2.8 17.4 + - - +
95L HIS* 1.3 96.1 + - - +
97L ALA* 1.3 56.9 + - - +
99L GLY* 3.1 3.3 + - - -
100L GLU* 2.9 28.2 + - - +
274L GLY* 4.5 2.8 - - - -
275L SER* 3.1 37.0 + - - +
279L ARG* 4.2 10.0 + - - -
319L ASP 3.9 13.0 - - - +
320L PHE* 4.9 2.8 - - - -
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Residues in contact with ALA 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L CYS* 3.5 38.7 - - + +
86L ILE* 3.9 23.5 - - + +
92L LYS* 3.6 13.9 - - + +
93L ILE 3.1 10.7 + - - +
94L ALA* 3.9 4.5 - - - +
96L ASP* 1.3 76.7 - - - +
98L MET* 1.3 55.5 + - - +
100L GLU* 3.4 6.0 + - - +
101L LEU* 2.9 29.1 + - - +
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Residues in contact with MET 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L ALA* 3.9 28.3 - - + +
80L ASP* 5.2 6.1 - - - +
83L CYS* 3.3 22.0 - - - -
94L ALA* 2.8 25.1 + - + +
95L HIS* 3.8 5.8 - - - +
97L ALA* 1.3 69.1 - - - +
99L GLY* 1.3 54.3 + - - +
101L LEU* 3.0 10.7 + - + +
102L GLN* 2.7 53.2 + - - +
105L ILE* 6.0 1.3 - - + -
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Residues in contact with GLY 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L HIS 2.9 18.0 + - - -
96L ASP* 3.1 4.0 + - - -
98L MET* 1.3 71.3 - - - +
100L GLU* 1.3 61.7 + - - +
102L GLN* 3.3 7.5 + - - +
103L ARG* 3.2 33.8 + - - +
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Residues in contact with GLU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ILE* 4.0 8.9 - - + +
92L LYS* 2.9 28.2 + - - +
96L ASP 2.9 11.6 + - - +
97L ALA 3.5 7.9 - - - +
99L GLY* 1.3 76.0 - - - +
101L LEU* 1.3 64.8 + - - +
103L ARG* 3.5 2.7 + - - +
104L GLY* 3.1 18.4 + - - -
150L PHE* 3.0 34.6 - - + -
151L PRO* 3.2 6.9 - - - +
152L VAL* 2.8 36.8 + - + -
153L MET* 3.1 29.9 + - + +
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Residues in contact with LEU 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L LEU* 3.9 13.7 - - + +
79L ALA* 3.6 44.9 - - + +
82L ILE* 4.1 26.7 - - + -
83L CYS* 4.7 0.7 - - - -
97L ALA 2.9 17.8 + - - +
98L MET* 3.0 13.7 + - + +
100L GLU* 1.3 77.2 - - - +
102L GLN* 1.3 57.2 + - - +
104L GLY* 3.3 1.0 + - - -
105L ILE* 2.9 52.8 + - + +
152L VAL* 4.0 24.7 - - + -
156L LEU* 4.9 1.8 - - + -
184L ILE* 4.4 3.6 - - + -
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Residues in contact with GLN 102 (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* 4.2 25.3 - - - +
76L GLU* 5.4 4.4 + - - +
98L MET* 2.7 35.1 + - - +
99L GLY* 3.7 7.9 - - - +
100L GLU 3.2 0.4 - - - -
101L LEU* 1.3 73.4 - - - +
103L ARG* 1.3 64.6 + - + +
105L ILE* 3.0 32.2 + - - +
106L GLU* 3.0 25.3 + - - +
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Residues in contact with ARG 103 (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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99L GLY 3.2 19.0 + - - +
100L GLU* 5.4 0.8 - - - +
102L GLN* 1.3 76.5 - - + +
104L GLY* 1.3 63.7 + - - +
106L GLU* 3.1 31.7 + - - +
107L ASN* 3.2 17.5 + - - +
150L PHE* 4.5 12.1 - - - -
153L MET* 3.2 47.3 - - - +
157L TRP* 5.3 0.6 - - - -
279L ARG* 6.0 4.2 - - - +
280L CYS* 6.4 0.2 - - - -
440L LEU* 6.4 0.2 - - - +
442L VAL* 3.7 41.9 - - - +
443L PRO 5.9 0.9 - - - -
445L ALA* 5.1 0.2 - - - +
449L PHE* 6.0 0.6 - - - -
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Residues in contact with GLY 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L GLU 3.1 15.7 + - - -
101L LEU 3.6 4.5 - - - -
102L GLN 3.2 0.2 - - - -
103L ARG* 1.3 77.0 - - - +
105L ILE* 1.3 60.2 + - - +
107L ASN* 3.3 21.2 + - - +
108L VAL* 3.3 10.0 + - - +
153L MET* 3.9 7.5 - - - +
156L LEU* 3.6 34.3 - - - +
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Residues in contact with ILE 105 (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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72L LYS* 4.2 24.9 - - + -
75L LEU* 3.8 32.3 - - + -
76L GLU* 4.2 25.6 - - + +
79L ALA* 6.1 0.2 - - + -
98L MET* 6.0 1.3 - - + -
101L LEU* 2.9 41.8 + - + +
102L GLN* 3.0 25.5 + - - +
104L GLY* 1.3 74.8 - - - +
106L GLU* 1.3 51.4 + - - +
108L VAL* 2.8 13.0 + - - +
109L GLU* 2.7 43.2 + - - +
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Residues in contact with GLU 106 (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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62J LEU* 3.8 17.6 - - + +
66J ARG* 3.4 23.8 + - - +
102L GLN* 3.0 24.2 + - + +
103L ARG* 3.1 23.2 + - - +
105L ILE* 1.3 72.7 - - - +
107L ASN* 1.3 64.6 + - - +
109L GLU* 3.3 22.8 + - - +
110L TYR* 3.1 17.0 + - - +
444L VAL* 3.7 19.5 - - + +
445L ALA* 3.0 23.8 + - + +
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Residues in contact with ASN 107 (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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103L ARG* 3.2 18.4 + - - +
104L GLY* 3.5 11.1 - - - +
105L ILE 3.2 0.2 - - - -
106L GLU* 1.3 75.5 - - - +
108L VAL* 1.3 61.6 + - - +
110L TYR* 3.4 4.1 + - - +
111L ALA* 3.1 24.0 + - - +
156L LEU 3.2 25.8 - - - +
157L TRP* 3.2 25.8 + - - -
160L PRO* 4.6 2.2 - - - +
161L MET* 5.6 1.2 - - - +
445L ALA* 3.5 15.7 + - - +
463L TYR* 3.5 39.1 - - + +
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Residues in contact with VAL 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L MET* 3.2 41.3 - - + +
71L PHE* 3.7 26.7 - - + -
72L LYS* 4.0 18.6 - - + +
75L LEU* 3.9 9.6 - - + -
104L GLY 3.3 11.6 + - - +
105L ILE* 2.8 13.0 + - - +
107L ASN* 1.3 75.3 - - - +
109L GLU* 1.3 63.1 + - - +
111L ALA* 3.4 7.3 + - - +
112L CYS* 3.2 20.5 + - - -
156L LEU* 3.9 8.7 - - + -
160L PRO* 4.1 4.9 - - + -
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Residues in contact with GLU 109 (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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62J LEU* 3.3 21.6 - - + +
66J ARG* 2.6 40.1 + - - +
69J PHE* 3.9 26.8 - - + -
112J CYS 5.6 1.1 - - - +
113J GLY* 6.1 1.4 - - - -
72L LYS* 3.1 37.7 + - + -
76L GLU* 5.0 0.3 - - - +
105L ILE* 2.7 20.4 + - - +
106L GLU* 3.5 19.3 - - - +
107L ASN 3.2 0.2 - - - -
108L VAL* 1.3 73.1 - - - +
110L TYR* 1.3 56.5 + - - +
112L CYS* 2.9 28.2 + - - +
113L GLY 3.8 1.9 + - - -
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Residues in contact with TYR 110 (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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116J GLU* 2.8 38.1 + - + -
106L GLU 3.1 16.3 + - - +
107L ASN* 3.9 4.5 - - - +
109L GLU* 1.3 76.2 - - - +
111L ALA* 1.3 60.2 + - - +
113L GLY* 3.4 10.2 + - - -
117L LEU* 3.2 46.3 - - + +
161L MET* 3.6 15.7 - - + -
445L ALA* 3.3 21.3 - - + +
446L TYR* 3.3 30.5 - + + +
464L GLY* 3.7 24.7 - - - -
465L PRO* 3.6 19.8 - - + +
468L VAL* 4.9 0.4 - - + -
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Residues in contact with ALA 111 (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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68L MET* 4.4 7.4 - - + -
107L ASN 3.1 18.2 + - - +
108L VAL 3.6 6.7 - - - +
109L GLU 3.2 0.2 - - - -
110L TYR* 1.3 73.1 - - - +
112L CYS* 1.3 63.5 + - - +
113L GLY 3.1 2.5 - - - -
114L ALA* 3.0 23.8 + - - +
117L LEU* 5.0 0.2 - - - -
160L PRO* 4.1 30.5 - - + +
161L MET* 4.3 14.8 - - + +
164L VAL* 3.6 15.1 - - + +
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Residues in contact with CYS 112 (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* 4.4 8.3 - - + -
109J GLU 5.6 1.1 - - - +
112J CYS* 6.0 0.2 - - + -
65L ALA* 3.2 25.8 - - - +
68L MET* 3.5 9.4 - - - -
69L PHE* 3.4 67.0 - - + -
72L LYS* 5.3 1.1 - - - -
108L VAL* 3.2 22.3 + - - -
109L GLU* 2.9 15.7 + - - +
111L ALA* 1.3 76.4 - - - +
113L GLY* 1.3 54.1 + - - +
114L ALA 3.3 1.0 + - - -
115L PRO* 4.1 2.4 - - - +
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Residues in contact with GLY 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J GLU 5.9 2.9 - - - -
113J GLY* 5.5 11.2 - - - -
109L GLU 3.8 2.6 + - - -
110L TYR 3.4 9.0 + - - -
111L ALA 3.1 1.6 - - - -
112L CYS* 1.3 76.3 - - - +
114L ALA* 1.3 61.7 + - - -
115L PRO* 3.1 7.4 - - - -
116L GLU* 3.3 16.6 + - - +
117L LEU* 3.4 19.2 + - - +
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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