Contacts of the helix formed by residues 82 - 96 (chain A) in PDB entry 6AF6
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 ASP 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ALA* 4.2 8.0 - - + +
31A ARG* 2.9 40.5 + - - +
32A ILE* 4.1 14.3 - - + +
36A ILE 4.8 0.7 - - - +
37A LEU* 5.9 0.2 - - - -
38A SER 5.8 0.5 + - - -
80A SER* 3.1 14.8 + - - +
81A ARG* 1.3 74.3 - - - +
83A ILE* 1.3 61.8 + - - +
84A GLY 3.8 0.2 + - - -
85A LEU* 3.2 27.2 + - + +
86A SER* 3.1 22.0 + - - -
208A ASN* 2.9 31.3 + - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLY* 5.9 3.4 - - - +
80A SER 4.9 4.0 - - - +
81A ARG 2.9 11.6 + - - +
82A ASP* 1.3 70.5 - - - +
84A GLY* 1.3 61.8 + - - +
86A SER* 4.1 6.1 - - - -
87A PHE* 2.7 29.7 + - + +
206A LEU* 3.9 8.3 - - + -
251A LEU* 4.2 25.6 - - + +
252A PHE* 3.8 19.1 - - + -
255A GLY* 5.9 3.4 - - - -
354A HIS* 5.8 0.2 - - - +
357A ASN* 2.9 42.6 - - + +
358A MET* 3.3 31.6 - - + -
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.9 0.4 - - - -
82A ASP* 3.2 3.2 + - - -
83A ILE* 1.3 83.3 - - - +
85A LEU* 1.4 60.6 + - - +
87A PHE* 3.4 0.8 + - - +
88A SER* 3.0 24.1 + - - -
206A LEU* 4.3 12.1 - - - +
208A ASN* 3.3 22.0 + - - -
209A CYS* 3.6 22.3 - - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.0 31.0 - - + -
31A ARG* 4.3 2.2 - - - +
37A LEU* 4.1 20.6 - - + -
38A SER 4.2 4.5 - - - +
41A LEU* 4.2 18.2 - - + -
42A TRP* 3.4 47.6 - - + +
82A ASP* 3.2 36.7 + - + +
84A GLY* 1.4 75.1 - - - +
86A SER* 1.4 63.7 + - - +
88A SER* 3.2 4.2 + - - -
89A LEU* 3.0 26.9 + - + +
208A ASN* 4.1 4.2 + - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 5.1 1.7 - - - +
76A LEU* 3.4 33.4 + - - +
77A GLY* 5.6 0.2 - - - -
80A SER* 4.7 4.3 + - - -
82A ASP 3.1 15.2 + - - -
83A ILE* 3.6 9.5 - - - -
85A LEU* 1.4 77.4 - - - +
87A PHE* 1.3 64.2 + - - +
89A LEU* 3.3 7.2 + - - +
90A CYS* 2.9 27.9 + - - -
251A LEU* 3.6 27.8 - - - -
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 2.7 21.4 + - + +
84A GLY* 3.8 6.1 - - - +
86A SER* 1.3 73.6 - - - +
88A SER* 1.3 55.8 + - - +
90A CYS* 3.3 2.4 + - - +
91A ALA* 2.9 30.9 + - + +
160A THR* 3.7 26.2 - - + -
206A LEU* 4.1 16.2 - - + -
209A CYS* 3.7 17.7 - - - -
248A LEU* 3.8 24.2 - - + -
251A LEU* 3.9 9.8 - - + +
252A PHE* 4.4 6.3 - + - -
364A PHE* 3.2 54.1 - + - -
501A FAD 4.0 15.3 - + + -
505A PRO* 4.1 11.2 - - + -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.6 18.5 - - - +
42A TRP* 2.8 25.0 + - - -
84A GLY 3.0 14.1 + - - -
85A LEU 3.2 8.7 + - - -
87A PHE* 1.3 77.9 - - - +
89A LEU* 1.3 60.8 + - - +
91A ALA 3.4 0.2 + - - -
92A HIS* 3.1 13.2 + - - +
160A THR* 4.5 2.2 - - - -
161A ASN* 2.6 46.3 + - - +
164A ILE* 4.4 0.5 - - - +
209A CYS* 3.8 10.3 - - - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.1 4.5 - - + -
42A TRP* 3.6 48.7 - - + +
45A ALA* 3.5 23.3 - - + -
46A ALA* 3.9 18.8 - - + +
50A PHE* 4.6 18.1 - - + +
51A ALA* 5.3 3.7 - - + +
76A LEU* 4.8 7.0 - - + -
85A LEU* 3.0 26.9 + - + +
86A SER* 3.6 12.8 - - - +
88A SER* 1.3 78.5 - - - +
90A CYS* 1.3 60.7 + - - +
92A HIS* 3.3 5.9 + - - +
93A LEU* 2.9 27.9 + - - +
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Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 5.6 4.7 - - - -
73A ILE* 3.8 42.2 - - + -
76A LEU* 4.2 13.2 - - - -
86A SER 2.9 21.4 + - - +
87A PHE* 4.0 2.0 - - - +
89A LEU* 1.3 75.4 - - - +
91A ALA* 1.3 60.3 + - - +
93A LEU* 4.2 7.2 - - - -
94A CYS* 2.8 35.9 + - - +
248A LEU* 3.6 27.6 - - + -
251A LEU* 4.6 4.7 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PHE* 2.9 19.8 + - + +
88A SER 3.7 4.5 - - - +
90A CYS* 1.3 74.9 - - - +
92A HIS* 1.3 65.5 + - - +
94A CYS* 5.2 0.4 - - - -
95A ALA* 3.0 28.3 + - - +
96A CYS* 3.8 2.8 + - - -
123A ALA 5.5 0.2 - - - -
160A THR* 3.9 21.8 - - + -
161A ASN* 4.3 2.5 - - - +
248A LEU* 3.8 7.5 - - + +
505A PRO* 3.8 26.5 - - + -
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TRP* 3.5 29.3 - + + -
51A ALA* 3.9 13.9 - - + +
88A SER 3.1 11.6 + - - +
89A LEU* 3.5 8.7 - - + +
91A ALA* 1.3 79.4 - - - +
93A LEU* 1.3 60.2 + - - +
96A CYS* 3.2 11.8 + - - +
97A VAL* 2.9 35.8 + - + +
116A LEU* 2.9 36.4 + - + -
121A LEU 3.3 25.8 - - - -
123A ALA* 3.0 41.6 + - + +
161A ASN* 4.2 1.0 - - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE 3.5 20.6 - - - +
51A ALA* 3.6 27.8 - - - +
52A HIS 3.8 15.0 - - - +
53A GLY* 3.9 5.4 - - - +
69A THR* 4.2 24.5 - - + -
73A ILE* 4.4 11.0 - - + -
89A LEU 2.9 17.2 + - - +
90A CYS* 3.6 5.6 - - - +
92A HIS* 1.3 78.9 - - - +
94A CYS* 1.4 70.9 + - - +
97A VAL* 3.4 10.4 + - + +
98A ILE* 3.0 51.6 + - + +
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Residues in contact with CYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 5.1 0.9 - - - -
90A CYS* 2.8 26.0 + - - +
91A ALA* 4.7 0.4 - - - +
93A LEU* 1.4 90.7 - - - +
95A ALA* 1.3 57.7 + - + +
96A CYS 3.4 0.2 - - - -
98A ILE* 4.0 12.8 - - - +
99A PRO* 3.4 14.7 - - - +
240A SER* 3.6 15.3 - - - +
243A TRP* 3.6 24.9 - - - +
244A ALA* 3.7 27.8 - - + +
247A CYS* 4.6 6.3 - - - -
248A LEU* 4.3 15.7 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.0 14.8 + - - +
94A CYS* 1.3 80.0 - - + +
96A CYS* 1.3 63.2 + - - +
99A PRO* 3.2 15.8 - - - +
125A ASN* 3.5 39.4 + - + +
169A ILE* 4.4 5.2 - - - +
171A TYR* 4.7 0.5 + - - -
240A SER* 4.2 8.3 - - - -
241A MET* 4.2 10.8 - - + -
244A ALA* 5.6 0.7 - - + -
505A PRO* 4.1 17.7 - - - +
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Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 4.3 6.5 - - - -
92A HIS* 3.2 12.1 + - - +
94A CYS 3.4 1.2 - - - -
95A ALA* 1.3 86.2 - - - +
97A VAL* 1.3 69.9 + - + +
98A ILE 3.3 0.9 - - - -
99A PRO* 3.5 3.1 - - - +
100A LEU* 3.2 24.3 + - - +
116A LEU* 5.3 3.1 - - + -
123A ALA* 3.5 30.3 - - + -
124A ALA* 3.4 36.8 - - - -
125A ASN* 3.5 6.7 - - - -
169A ILE* 3.9 15.3 - - + +
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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