Contacts of the helix formed by residues 82 - 95 (chain A) in PDB entry 2CX9
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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26A VAL* 3.7 18.6 - - + -
30A ALA* 3.6 12.2 - - - +
33A ARG* 2.7 36.2 + - - +
78A ILE* 2.8 18.8 + - - +
79A ALA 3.7 2.0 + - - -
81A TYR* 1.3 76.0 - - - +
83A GLY* 1.3 61.9 + - - +
84A ALA* 3.1 14.1 + - - +
85A LEU* 2.7 39.3 + - + +
86A ALA* 3.1 17.7 + - - +
212A ALA* 5.7 0.2 - - - +
357A ARG* 5.0 2.7 - - - +
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Residues in contact with GLY 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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79A ALA 4.0 4.5 + - - -
82A ASP* 1.3 72.9 + - - +
84A ALA* 1.3 62.0 + - - +
86A ALA* 3.1 8.2 + - - +
87A LEU 2.9 19.9 + - - -
210A LEU* 3.3 11.2 - - - +
255A MET* 3.5 6.9 - - - +
259A LEU* 4.2 20.0 - - - +
357A ARG* 5.5 1.2 - - - +
361A ASP* 3.6 20.3 + - - -
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Residues in contact with ALA 84 (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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82A ASP* 3.1 9.0 + - - +
83A GLY* 1.3 76.2 - - - +
85A LEU* 1.3 57.1 + - + +
87A LEU* 3.4 4.1 + - - +
88A THR* 2.8 31.5 + - - -
210A LEU* 3.4 25.1 - - - +
211A THR 4.7 0.2 - - - +
212A ALA* 4.0 13.5 - - + +
213A SER* 3.7 31.0 + - - +
361A ASP* 4.3 2.0 + - - -
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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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26A VAL* 4.1 23.6 - - + -
33A ARG* 4.4 0.7 - - - +
39A PHE* 6.3 0.2 - - + -
40A PRO* 3.8 26.0 - - + -
43A LEU* 3.7 35.0 - - + -
44A VAL* 4.7 11.4 - - + -
47A LEU* 4.0 21.1 - - + -
53A PHE* 5.7 0.2 - - + -
78A ILE* 3.7 15.3 - - + -
82A ASP* 2.7 24.6 + - - +
84A ALA* 1.3 69.6 - - - +
86A ALA* 1.3 66.1 + - - +
88A THR* 3.2 13.4 + - + +
89A VAL* 2.9 29.8 + - + +
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Residues in contact with ALA 86 (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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75A VAL* 4.0 10.5 - - + +
78A ILE* 3.3 10.5 - - + +
79A ALA* 3.5 42.8 - - + +
82A ASP 3.1 5.6 + - - +
83A GLY 3.1 8.5 + - - +
85A LEU* 1.3 76.5 - - - +
87A LEU* 1.3 56.4 + - - +
89A VAL* 3.2 4.3 + - - +
90A ALA* 2.8 34.0 + - - +
255A MET* 4.1 9.6 - - + -
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Residues in contact with LEU 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 GLY 2.9 12.2 + - - +
84A ALA* 3.7 7.9 - - - +
86A ALA* 1.3 76.8 - - - +
88A THR* 1.3 63.7 + - - +
90A ALA* 4.5 1.6 - - - -
91A SER* 2.9 35.8 + - - +
160A THR* 4.3 17.5 - - + +
207A LYS* 6.0 1.3 - - - -
210A LEU* 3.9 20.9 - - + -
213A SER* 3.2 22.7 - - - +
215A THR* 5.6 2.0 - - - +
252A ILE* 4.3 16.4 - - + -
255A MET* 3.7 25.5 - - + -
364A LEU* 4.3 13.0 - - + -
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Residues in contact with THR 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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39A PHE* 4.1 30.6 - - + -
44A VAL* 4.8 4.0 - - + -
53A PHE* 4.3 19.5 - - + -
84A ALA 2.8 20.9 + - - -
85A LEU* 3.4 16.6 - - + +
87A LEU* 1.3 76.4 - - - +
89A VAL* 1.3 62.2 + - - +
91A SER* 3.3 1.9 + - - -
92A HIS* 3.1 27.4 + - + +
122A LEU* 5.0 1.1 - - + -
160A THR* 4.7 0.2 - - - -
161A GLN* 3.4 28.1 + - + +
212A ALA 5.0 0.7 + - - -
213A SER* 4.1 8.3 + - - -
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Residues in contact with VAL 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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47A LEU* 4.1 9.6 - - + -
52A VAL* 3.7 25.4 - - + +
53A PHE* 3.9 29.8 - - + -
71A PHE* 4.1 8.7 - - + -
75A VAL* 4.7 4.0 - - + -
78A ILE* 3.7 24.9 - - + -
85A LEU* 2.9 21.0 + - + +
86A ALA 3.6 3.4 - - - +
88A THR* 1.3 74.5 - - - +
90A ALA* 1.3 64.6 + - - +
92A HIS* 3.8 0.3 - - - +
93A ASN* 2.8 46.6 + - - +
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Residues in contact with ALA 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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71A PHE* 4.1 11.2 - - - -
75A VAL* 4.3 20.2 - - + -
86A ALA 2.8 22.1 + - - +
87A LEU* 4.0 4.7 - - - +
89A VAL* 1.3 74.0 - - - +
91A SER* 1.3 58.7 + - - +
93A ASN* 4.0 0.2 - - - +
94A SER* 2.9 36.4 + - - +
248A GLY 5.8 0.2 - - - +
251A GLY* 4.6 16.6 - - - +
252A ILE* 4.6 12.1 - - + -
255A MET* 5.5 1.6 - - - -
369A GLU* 5.5 1.6 - - - +
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Residues in contact with SER 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 LEU* 2.9 29.5 + - - +
88A THR 3.3 1.2 + - - -
90A ALA* 1.3 71.0 - - - +
92A HIS* 1.3 68.4 + - - +
94A SER* 4.8 0.2 - - - -
95A LEU* 2.9 49.5 + - - +
96A ALA 3.8 1.2 + - - -
123A GLY 5.2 0.6 - - - +
160A THR* 3.3 21.9 - - - +
161A GLN* 2.8 27.0 + - - -
252A ILE* 6.2 0.2 - - - -
369A GLU* 5.1 3.8 - - - -
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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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53A PHE* 2.8 57.8 + + + -
88A THR 3.1 17.3 + - - +
89A VAL 3.8 2.0 - - - +
91A SER* 1.3 81.8 + - - +
93A ASN* 1.3 62.0 + - - +
96A ALA* 4.0 1.4 + - - +
97A THR* 2.9 38.6 + - - -
116A LEU* 2.8 27.4 + - + -
121A ALA 3.5 19.5 - - - -
122A LEU* 3.6 8.3 - - + +
123A GLY 3.0 28.1 + - - -
161A GLN* 4.0 11.7 - - + +
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Residues in contact with ASN 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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52A VAL 2.8 23.6 + - - -
53A PHE* 3.5 15.9 - - - +
54A GLY* 3.7 2.1 - - - -
55A ALA* 3.2 26.0 + - - +
56A LEU* 4.3 11.0 + - + +
57A VAL* 5.6 0.2 - - - +
71A PHE* 3.5 24.1 - - + -
89A VAL* 2.8 32.7 + - - +
92A HIS* 1.3 82.6 - - - +
94A SER* 1.3 58.5 + - - +
97A THR* 3.5 9.9 - - - +
98A GLY* 2.8 28.4 + - - -
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Residues in contact with SER 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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56A LEU* 5.8 4.3 - - - +
71A PHE* 3.9 17.5 - - - -
90A ALA* 2.9 24.4 + - - -
91A SER* 4.5 0.4 - - - -
93A ASN* 1.3 73.9 - - - +
95A LEU* 1.3 63.9 + - - +
98A GLY* 3.6 11.2 - - - -
244A VAL* 3.2 19.1 - - - +
247A GLY 4.1 5.6 + - - -
248A GLY* 3.5 33.0 + - - -
251A GLY* 4.8 2.8 - - - -
369A GLU* 4.8 1.6 - - - -
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Residues in contact with LEU 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 SER* 2.9 36.2 + - - +
94A SER* 1.3 73.8 - - - +
96A ALA* 1.3 62.0 + - - +
99A HIS* 2.8 35.2 + - - +
125A TRP* 3.4 53.2 - - + +
160A THR* 5.9 2.5 - - - +
244A VAL* 3.8 20.0 - - + +
245A LEU* 4.7 2.7 - - + -
369A GLU* 4.1 35.7 - - + +
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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