Contacts of the helix formed by residues 72 - 86 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ARG 4.0 1.8 + - - -
71I VAL* 1.3 73.2 - - - +
73I LEU* 1.3 66.4 + - - +
74I ARG* 3.7 40.6 - - + -
75I GLY* 3.0 37.7 + - - -
76I VAL* 3.1 14.4 + - - +
97I GLY 3.8 17.9 - - - -
98I VAL* 4.2 11.7 - - + -
99I GLY 5.3 1.6 - - - -
100I ILE* 5.0 6.7 - - + -
226I PHE* 3.8 18.7 - + + -
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Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 4.6 7.4 - - + -
65I LEU* 4.1 30.5 - - + -
71I VAL 2.7 13.8 + - - +
72I PHE* 1.3 71.6 - - - +
74I ARG* 1.3 65.5 + - - +
76I VAL* 2.9 21.7 + - + +
77I ILE* 3.0 34.3 + - + +
229I ALA* 5.8 0.2 - - + -
233I LEU* 4.7 7.6 - - + -
300I PHE 5.9 0.4 - - - +
302I VAL* 3.5 40.6 - - + -
305I TYR* 5.3 6.5 - - + -
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Residues in contact with ARG 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I PHE* 3.4 29.5 - - + -
73I LEU* 1.3 80.5 - - - +
75I GLY* 1.3 57.7 + - - +
77I ILE* 3.8 8.9 - - - +
78I ALA* 2.9 30.6 + - + +
96I GLN* 2.8 30.8 + - - +
97I GLY* 4.2 8.5 + - - -
98I VAL* 4.0 12.2 - - + +
297I VAL* 4.5 20.3 - - + +
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Residues in contact with GLY 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I PHE* 3.0 35.5 + - - -
74I ARG* 1.3 80.9 - - - +
76I VAL* 1.3 60.6 + - - +
78I ALA* 3.8 1.2 - - - +
79I GLU* 3.0 26.0 + - - +
98I VAL* 4.0 17.5 - - - +
100I ILE* 4.5 0.2 - - - +
226I PHE* 3.9 8.6 - - - -
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Residues in contact with VAL 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I LEU* 5.3 0.4 - - + -
71I VAL* 4.3 7.6 - - + -
72I PHE 3.1 16.5 + - - +
73I LEU* 2.9 11.8 + - + +
75I GLY* 1.3 77.4 - - - +
77I ILE* 1.3 63.4 + - - +
79I GLU* 3.4 5.6 + - - +
80I LEU* 3.0 22.3 + - - +
226I PHE* 3.5 41.3 - - + +
229I ALA* 4.0 8.5 - - + -
230I SER* 3.6 37.1 + - - +
233I LEU* 3.9 14.1 - - + -
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Residues in contact with ILE 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I LEU* 3.0 36.0 + - + +
74I ARG* 3.8 8.7 - - - +
76I VAL* 1.3 75.7 - - - +
78I ALA* 1.3 63.9 + - - +
80I LEU* 3.1 7.9 + - - +
81I LEU* 3.0 32.9 + - + +
233I LEU* 4.0 21.1 - - + -
297I VAL* 4.1 20.0 - - + +
300I PHE* 3.6 56.8 - - + +
302I VAL* 5.3 0.7 - - + -
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Residues in contact with ALA 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I ARG* 2.9 20.1 + - + +
75I GLY 3.8 3.6 - - - +
77I ILE* 1.3 77.1 - - - +
79I GLU* 1.3 62.8 + - - +
81I LEU* 3.4 3.8 + - - +
82I TRP* 3.0 22.9 + - - +
93I LEU* 3.7 6.4 - - + +
96I GLN* 3.7 31.4 - - - +
98I VAL* 3.8 17.9 - - + -
297I VAL* 4.8 8.7 - - + +
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Residues in contact with GLU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I GLY 3.0 17.9 + - - +
76I VAL* 3.7 4.6 - - - +
78I ALA* 1.3 76.6 - - - +
80I LEU* 1.3 57.3 + - - +
82I TRP* 3.0 15.3 - - + +
83I PHE* 2.9 59.1 + - + -
93I LEU* 4.0 7.5 - - + +
100I ILE* 3.5 22.9 - - + +
101I TRP* 2.9 27.3 + - + +
188I HIS* 5.7 0.4 - - - -
226I PHE* 4.2 16.8 - - - +
227I ASN* 6.0 0.2 + - - -
230I SER* 4.8 8.0 + - - -
350I UMP 5.3 4.1 - - - +
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I VAL 3.0 18.1 + - - +
77I ILE* 3.1 5.4 + - - +
79I GLU* 1.3 73.1 - - - +
81I LEU* 1.3 65.4 + - - +
82I TRP 3.0 1.6 - - - -
83I PHE* 3.0 18.7 + - + +
84I VAL* 3.0 30.4 + - + +
131I TRP* 4.5 6.7 - - + -
230I SER* 3.6 36.8 + - - +
233I LEU* 3.6 20.0 - - + -
234I LEU* 3.7 26.5 - - + +
237I MET* 3.6 30.5 - - - -
300I PHE* 5.1 3.1 - - + -
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I ILE* 3.0 23.5 + - + +
78I ALA* 4.0 3.6 - - - +
80I LEU* 1.3 77.5 - - + +
82I TRP* 1.3 56.3 + - - +
84I VAL* 3.7 7.1 - - + +
85I SER* 3.0 28.4 + - - -
237I MET* 3.8 19.1 - - + -
292I ILE 5.9 0.2 - - - +
295I PHE* 3.8 30.3 - - + +
296I LYS* 3.7 10.5 - - - -
297I VAL* 3.5 44.6 - - + +
300I PHE* 4.1 8.7 - - + -
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Residues in contact with TRP 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ALA 3.0 14.8 + - - +
79I GLU* 3.0 15.7 - - + +
81I LEU* 1.3 76.3 - - - +
83I PHE* 1.3 99.1 + + - +
85I SER* 2.6 22.4 + - - -
86I GLY 3.4 2.9 + - - -
87I CYS* 3.4 42.9 + - + +
88I THR* 3.7 22.7 - - - -
89I ASP 3.2 25.4 + - - -
90I ALA* 4.0 5.6 - - - -
92I MET* 4.0 12.8 - - + +
93I LEU* 3.7 24.6 - - + +
96I GLN* 5.9 0.4 - - - +
101I TRP* 3.8 22.7 - + - -
123I LEU* 3.5 25.4 - - + -
126I VAL* 4.7 7.6 - - + -
127I TYR* 5.4 0.4 - + - -
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Residues in contact with PHE 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I GLU* 2.9 48.7 + - + -
80I LEU* 3.3 15.7 - - + +
82I TRP* 1.3 103.8 - + - +
84I VAL* 1.3 55.1 + - - +
86I GLY* 2.8 22.7 + - - -
87I CYS 5.1 0.2 - - - -
101I TRP* 4.8 0.2 - - - -
127I TYR* 3.4 44.0 - + + -
128I GLY* 3.1 22.3 - - - +
131I TRP* 3.5 34.9 - + + -
132I ARG* 4.5 0.7 - - - +
188I HIS* 3.8 21.5 - + - -
230I SER* 4.5 9.4 - - - -
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Residues in contact with VAL 84 (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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80I LEU* 3.0 27.1 + - + +
81I LEU* 3.7 8.7 - - + +
83I PHE* 1.3 80.4 - - - +
85I SER* 1.3 60.0 + - - +
86I GLY 3.1 1.2 + - - -
131I TRP* 4.4 6.0 - - + -
132I ARG* 2.6 31.9 + - - +
153I LEU* 3.9 27.1 - - + -
234I LEU* 4.6 7.2 - - + -
237I MET* 4.3 18.8 - - + -
292I ILE* 3.4 26.2 - - + +
293I ASP* 3.8 12.1 - - - +
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Residues in contact with SER 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU 3.0 14.0 + - - -
82I TRP* 2.6 24.4 + - - -
84I VAL* 1.3 76.7 - - - +
86I GLY* 1.3 59.2 + - - +
87I CYS* 3.1 18.9 + - - +
132I ARG* 4.7 2.3 - - - +
133I HIS* 5.2 3.5 + - - -
293I ASP* 4.7 5.6 - - - -
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Residues in contact with GLY 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I PHE 2.8 10.8 + - - -
84I VAL 3.0 1.4 - - - -
85I SER* 1.3 78.0 + - - +
87I CYS* 1.3 63.1 + - - +
88I THR* 3.9 3.3 - - - +
128I GLY 3.3 25.8 - - - -
129I PHE* 3.6 18.5 + - - +
132I ARG* 4.1 9.6 - - - -
133I HIS* 4.7 9.4 - - - -
145I TYR* 5.9 1.9 - - - -
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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