Contacts of the helix formed by residues 72 - 86 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P ARG* 4.0 1.8 + - - -
71P VAL* 1.3 71.8 - - - +
73P LEU* 1.3 66.9 + - - +
74P ARG* 3.7 39.9 - - + -
75P GLY* 3.0 38.5 + - - -
76P VAL* 3.1 14.2 + - - +
97P GLY 3.8 17.9 - - - -
98P VAL* 4.2 11.9 - - + -
99P GLY 5.3 1.3 - - - -
100P ILE* 5.0 7.2 - - + -
226P PHE* 3.9 19.8 - + + -
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Residues in contact with LEU 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P LEU* 4.6 7.4 - - + -
65P LEU* 4.1 30.1 - - + -
71P VAL 2.6 14.1 + - - +
72P PHE* 1.3 71.3 - - - +
74P ARG* 1.3 64.5 + - - +
76P VAL* 2.9 21.5 + - + +
77P ILE* 3.0 34.7 + - + +
229P ALA* 5.8 0.2 - - + -
233P LEU* 4.7 7.6 - - + -
300P PHE 5.9 0.4 - - - +
302P VAL* 3.5 41.3 - - + -
305P TYR* 5.3 6.5 - - + -
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Residues in contact with ARG 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P PHE* 3.4 29.2 - - + -
73P LEU* 1.3 80.3 - - - +
75P GLY* 1.3 57.4 + - - +
77P ILE* 3.4 10.3 + - - +
78P ALA* 2.9 30.4 + - + +
96P GLN* 2.8 31.6 + - - +
97P GLY* 4.2 8.5 + - - -
98P VAL* 4.0 11.8 - - + +
297P VAL* 4.4 20.2 - - + -
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Residues in contact with GLY 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P PHE* 3.0 36.2 + - - -
74P ARG* 1.3 80.1 - - - +
76P VAL* 1.3 60.6 + - - +
78P ALA* 3.8 1.2 - - - +
79P GLU* 3.0 25.6 + - - +
98P VAL* 4.0 17.4 - - - +
100P ILE* 4.5 0.2 - - - +
226P PHE* 3.9 8.5 - - - -
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Residues in contact with VAL 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P LEU* 5.3 0.4 - - + -
71P VAL* 4.3 8.7 - - + -
72P PHE 3.1 16.1 + - - +
73P LEU* 2.9 12.2 + - + +
75P GLY* 1.3 77.6 - - - +
77P ILE* 1.3 61.6 + - - +
79P GLU* 3.4 5.4 + - - +
80P LEU* 3.0 22.3 + - - +
226P PHE* 3.5 38.8 - - + +
229P ALA* 4.0 9.0 - - + -
230P SER* 3.6 37.8 + - - +
233P LEU* 3.9 14.6 - - + -
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Residues in contact with ILE 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P LEU* 3.0 36.4 + - + +
74P ARG* 3.8 9.6 - - - +
76P VAL* 1.3 76.5 - - - +
78P ALA* 1.3 64.1 + - - +
80P LEU* 3.1 6.9 + - - +
81P LEU* 3.0 25.8 + - + +
233P LEU* 4.0 21.1 - - + -
297P VAL* 4.1 25.1 - - + +
300P PHE* 3.6 58.8 - - + +
302P VAL* 5.2 0.7 - - + -
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Residues in contact with ALA 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P ARG* 2.9 20.1 + - + +
75P GLY 3.8 3.8 - - - +
77P ILE* 1.3 76.9 - - - +
79P GLU* 1.3 64.2 + - - +
81P LEU* 3.4 3.6 + - - +
82P TRP* 3.0 23.2 + - - +
93P LEU* 3.7 7.2 - - + +
96P GLN* 3.7 31.5 - - - +
98P VAL* 3.9 17.5 - - + -
297P VAL* 4.7 8.9 - - + +
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Residues in contact with GLU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P GLY 3.0 17.0 + - - +
76P VAL* 3.7 4.8 - - - +
78P ALA* 1.3 76.9 - - - +
80P LEU* 1.3 56.7 + - - +
82P TRP* 3.0 16.0 - - + +
83P PHE* 2.9 58.5 + - + -
93P LEU* 4.0 8.0 - - + +
98P VAL* 5.6 0.2 - - + -
100P ILE* 3.5 23.1 - - + +
101P TRP* 2.8 27.4 + - - +
188P HIS* 5.4 1.5 + - - -
226P PHE* 4.2 16.3 - - - +
230P SER* 4.7 8.0 + - - -
700P UMP 5.5 2.4 - - - +
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Residues in contact with LEU 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P VAL 3.0 18.7 + - - +
77P ILE* 3.5 4.9 - - - +
79P GLU* 1.3 75.1 + - - +
81P LEU* 1.3 66.2 + - + +
83P PHE* 3.0 17.6 + - + +
84P VAL* 3.0 30.3 + - + +
131P TRP* 4.5 7.4 - - + -
230P SER* 3.6 35.7 - - - +
233P LEU* 3.6 20.2 - - + -
234P LEU* 3.7 27.1 - - + +
237P MET* 3.6 29.2 - - - -
300P PHE* 5.0 3.4 - - + -
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Residues in contact with LEU 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P ILE* 3.0 23.2 + - + +
78P ALA* 4.0 3.8 - - - +
80P LEU* 1.3 76.7 - - + +
82P TRP* 1.3 57.0 + - - +
84P VAL* 3.6 6.7 + - + +
85P SER* 3.0 29.3 + - - -
237P MET* 3.8 19.3 - - + -
292P ILE 5.9 0.2 - - - +
295P PHE* 3.7 30.3 - - + +
296P LYS* 3.7 11.0 - - - +
297P VAL* 3.4 44.2 - - + +
300P PHE* 4.0 9.0 - - + -
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Residues in contact with TRP 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P ALA 3.0 14.1 + - - +
79P GLU* 3.0 14.4 - - + +
81P LEU* 1.3 75.2 - - - +
83P PHE* 1.3 99.5 + + - +
85P SER* 2.6 21.6 + - - -
86P GLY 3.4 3.1 + - - -
87P CYS* 3.4 43.7 + - + +
88P THR* 3.7 24.2 - - - -
89P ASP 3.1 25.4 + - - -
90P ALA* 4.0 5.2 - - - -
92P MET* 4.1 13.0 - - + +
93P LEU* 3.7 25.1 - - + +
96P GLN* 5.9 0.2 - - - +
101P TRP* 3.7 22.2 - + - -
123P LEU* 3.5 24.7 - - + -
126P VAL* 4.7 7.6 - - + -
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Residues in contact with PHE 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P GLU* 2.9 48.0 + - + -
80P LEU* 3.3 15.7 - - + +
82P TRP* 1.3 103.0 - + - +
84P VAL* 1.3 54.4 + - - +
86P GLY* 2.8 22.9 + - - -
87P CYS 5.1 0.4 - - - -
101P TRP* 4.7 0.2 - - - -
127P TYR* 3.4 44.6 - + + -
128P GLY* 3.1 22.0 - - - +
131P TRP* 3.6 34.1 - + + -
132P ARG* 4.5 0.7 - - - +
188P HIS* 3.7 22.0 - + - -
230P SER* 4.4 9.6 - - - -
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Residues in contact with VAL 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P LEU* 3.0 25.3 + - + +
81P LEU* 3.7 10.8 - - + +
83P PHE* 1.3 80.9 - - - +
85P SER* 1.3 59.8 + - - +
86P GLY 3.1 1.0 + - - -
131P TRP* 4.7 4.9 - - + -
132P ARG* 2.7 32.3 + - - +
153P LEU* 3.8 28.5 - - + -
234P LEU* 4.6 8.1 - - + -
237P MET* 4.3 19.1 - - + -
292P ILE* 3.4 26.2 - - + +
293P ASP* 3.8 11.4 - - - +
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Residues in contact with SER 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P LEU 3.0 13.4 + - - -
82P TRP* 2.6 24.7 + - - -
84P VAL* 1.3 76.7 - - - +
86P GLY* 1.3 57.6 + - - +
87P CYS* 3.1 19.2 + - - +
132P ARG* 4.7 2.1 - - - +
133P HIS* 5.2 3.6 + - - -
293P ASP* 4.7 5.4 - - - -
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Residues in contact with GLY 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P PHE 2.8 10.4 + - - -
84P VAL 3.0 1.2 - - - -
85P SER* 1.3 78.4 + - - +
87P CYS* 1.3 63.7 + - - +
88P THR* 3.8 3.8 + - - +
128P GLY 3.3 26.0 - - - -
129P PHE* 3.6 18.5 + - - +
132P ARG* 4.1 9.2 - - - -
133P HIS* 4.8 9.0 - - - -
145P TYR* 5.9 1.4 - - - -
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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