Contacts of the helix formed by residues 72 - 86 (chain L) in PDB entry 2AAZ
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 PHE 72 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ARG* 4.0 2.2 + - - -
71L VAL* 1.3 69.5 - - - +
73L LEU* 1.3 65.8 + - - +
74L ARG* 3.7 40.8 - - + -
75L GLY* 3.0 36.7 + - - -
76L VAL* 3.1 16.7 + - - +
97L GLY 3.8 17.5 - - - -
98L VAL* 4.2 11.9 - - + -
99L GLY 5.3 1.3 - - - -
100L ILE* 5.0 7.0 - - + -
226L PHE* 3.9 18.7 - + + -
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Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L LEU* 4.6 7.6 - - + -
65L LEU* 4.1 29.8 - - + -
71L VAL 2.6 13.3 + - - +
72L PHE* 1.3 71.1 - - - +
74L ARG* 1.3 65.0 + - - +
76L VAL* 2.9 20.8 + - + +
77L ILE* 3.0 34.6 + - + +
229L ALA* 5.8 0.2 - - + -
233L LEU* 4.7 8.1 - - + -
300L PHE 5.9 0.7 - - - +
302L VAL* 3.5 40.8 - - + -
305L TYR* 5.3 6.3 - - + -
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Residues in contact with ARG 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L PHE* 3.4 28.9 - - + -
73L LEU* 1.3 80.8 - - - +
75L GLY* 1.3 56.7 + - - +
77L ILE* 3.5 8.4 + - - +
78L ALA* 2.9 31.1 + - + +
96L GLN* 2.8 31.8 + - - +
97L GLY* 4.2 8.1 + - - -
98L VAL* 4.0 12.4 - - + +
297L VAL* 4.4 21.4 - - + +
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Residues in contact with GLY 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L PHE* 3.0 36.2 + - - -
74L ARG* 1.3 81.0 - - - +
76L VAL* 1.3 61.6 + - - +
78L ALA* 3.8 1.0 - - - +
79L GLU* 3.0 25.6 + - - +
98L VAL* 4.0 17.2 - - - +
100L ILE* 4.5 0.2 - - - +
226L PHE* 3.9 8.7 - - - -
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Residues in contact with VAL 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L LEU* 5.2 0.7 - - + -
71L VAL* 4.3 9.0 - - + -
72L PHE 3.1 16.8 + - - +
73L LEU* 2.9 12.0 + - + +
75L GLY* 1.3 77.5 - - - +
77L ILE* 1.3 63.5 + - - +
79L GLU* 3.7 4.9 - - - +
80L LEU* 3.0 22.9 + - - +
226L PHE* 3.5 40.8 - - + +
229L ALA* 4.0 9.2 - - + -
230L SER* 3.6 37.0 + - - +
233L LEU* 3.9 13.5 - - + -
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Residues in contact with ILE 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 LEU* 3.0 36.2 + - + +
74L ARG* 3.8 9.6 - - - +
76L VAL* 1.3 76.1 - - - +
78L ALA* 1.3 62.9 + - - +
80L LEU* 3.1 7.3 + - - +
81L LEU* 3.0 33.7 + - + +
233L LEU* 4.0 20.6 - - + -
297L VAL* 4.1 19.1 - - + +
300L PHE* 3.6 58.3 - - + +
302L VAL* 5.2 0.9 - - + -
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Residues in contact with ALA 78 (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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74L ARG* 2.9 20.1 + - + +
75L GLY 3.8 3.4 - - - +
77L ILE* 1.3 79.3 - - - +
79L GLU* 1.3 63.6 + - - +
81L LEU* 3.4 4.2 + - - +
82L TRP* 3.0 23.4 + - - +
93L LEU* 3.7 7.6 - - + +
96L GLN* 3.7 30.7 - - - +
98L VAL* 3.9 17.7 - - + -
297L VAL* 4.7 8.5 - - + +
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Residues in contact with GLU 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L GLY 3.0 18.7 + - - +
76L VAL* 3.7 4.7 - - - +
78L ALA* 1.3 75.8 - - - +
80L LEU* 1.3 57.2 + - - +
82L TRP* 3.1 15.5 - - + +
83L PHE* 2.9 59.8 + - + -
93L LEU* 4.0 7.5 - - + +
100L ILE* 3.6 22.5 - - + +
101L TRP* 2.9 27.8 + - + +
188L HIS* 5.3 1.3 + - - -
226L PHE* 4.2 16.0 - - - +
230L SER* 4.7 8.3 + - - -
500L UMP 5.5 2.4 - - - +
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Residues in contact with LEU 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L VAL 3.0 13.7 + - - +
77L ILE* 3.5 8.5 - - - +
79L GLU* 1.3 73.1 + - - +
81L LEU* 1.3 66.0 + - + +
82L TRP 3.0 1.8 - - - -
83L PHE* 3.0 19.0 + - + +
84L VAL* 3.0 29.4 + - + +
131L TRP* 4.5 7.0 - - + -
230L SER* 3.6 34.8 - - - +
233L LEU* 3.6 19.7 - - + -
234L LEU* 3.6 26.7 - - + +
237L MET* 3.5 30.1 - - - -
300L PHE* 5.1 3.6 - - + -
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Residues in contact with LEU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L ILE* 3.0 23.2 + - + +
78L ALA* 4.0 3.8 - - - +
80L LEU* 1.3 76.2 - - + +
82L TRP* 1.3 56.9 + - - +
84L VAL* 3.6 7.4 + - + +
85L SER* 3.0 28.4 + - - -
237L MET* 3.7 29.4 - - + -
292L ILE 5.9 0.4 - - - +
295L PHE* 3.7 19.1 - - + +
296L LYS* 3.7 11.2 - - - +
297L VAL* 3.5 43.7 - - + +
300L PHE* 4.0 9.2 - - + -
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Residues in contact with TRP 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L ALA 3.0 14.5 + - - +
79L GLU* 3.1 15.0 - - + +
80L LEU 3.0 0.2 - - - -
81L LEU* 1.3 75.7 - - - +
83L PHE* 1.3 98.0 - + - +
85L SER* 2.6 22.5 + - - -
86L GLY 3.4 3.1 + - - -
87L CYS* 3.4 42.5 + - + +
88L THR* 3.7 23.6 - - - -
89L ASP 3.1 25.7 + - - -
90L ALA* 4.0 5.2 - - - -
92L MET* 4.1 12.8 - - + +
93L LEU* 3.7 25.3 - - + +
96L GLN* 5.9 0.7 - - - +
101L TRP* 3.7 22.4 - + - -
123L LEU* 3.5 25.6 - - + -
126L VAL* 4.7 7.6 - - + -
127L TYR* 5.3 0.4 - + - -
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Residues in contact with PHE 83 (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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79L GLU* 2.9 51.2 + - + -
80L LEU* 3.3 16.4 - - + +
82L TRP* 1.3 102.1 - + - +
84L VAL* 1.3 54.6 + - - +
86L GLY* 2.8 23.2 + - - -
87L CYS 5.7 0.2 - - - -
101L TRP* 4.7 0.2 - - - -
127L TYR* 3.4 44.9 - + + -
128L GLY* 3.1 22.1 - - - +
131L TRP* 3.5 35.1 - + + -
132L ARG* 4.5 0.9 - - - +
188L HIS* 3.7 22.4 - + - -
230L SER* 4.4 9.6 - - - -
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Residues in contact with VAL 84 (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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80L LEU* 3.0 27.1 + - + +
81L LEU* 3.7 9.0 - - + +
82L TRP 3.3 0.2 - - - -
83L PHE* 1.3 80.3 - - - +
85L SER* 1.3 59.5 + - - +
86L GLY 3.1 1.2 + - - -
131L TRP* 4.6 5.6 - - + -
132L ARG* 2.6 32.3 + - - +
153L LEU* 3.8 28.9 - - + -
234L LEU* 4.6 7.6 - - + -
237L MET* 4.3 18.8 - - + -
292L ILE* 3.4 26.2 - - + +
293L ASP* 3.8 11.9 - - - +
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Residues in contact with SER 85 (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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81L LEU 3.0 14.6 + - - -
82L TRP* 2.6 24.3 + - - -
84L VAL* 1.3 76.2 - - - +
86L GLY* 1.3 59.0 + - - +
87L CYS* 3.1 19.2 + - - +
132L ARG* 4.6 2.8 - - - +
133L HIS* 5.2 3.8 + - - -
293L ASP* 4.7 6.1 - - - -
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Residues in contact with GLY 86 (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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83L PHE 2.8 10.2 + - - -
84L VAL 3.0 1.4 - - - -
85L SER* 1.3 79.3 + - - +
87L CYS* 1.3 62.5 + - - +
88L THR* 3.8 3.8 + - - +
128L GLY 3.2 25.8 - - - -
129L PHE* 3.6 18.1 + - - +
132L ARG* 4.0 9.6 - - - -
133L HIS* 4.7 8.8 - - - -
145L TYR* 5.9 1.6 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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