Contacts of the helix formed by residues 76 - 90 (chain D) in PDB entry 2I2X
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 ALA 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ILE* 3.7 14.9 - - + +
43D ILE* 3.6 41.3 - - + +
44D ALA 4.6 2.1 + - - -
47D ILE* 5.0 0.3 - - - +
59D LEU* 4.9 1.3 - - + -
72D LEU* 2.9 26.5 + - + +
75D ASP* 1.3 80.7 - - - +
77D LEU* 1.3 59.9 + - - +
78D MET 3.6 0.4 - - - -
79D VAL* 4.0 2.2 - - - +
80D GLY* 3.1 24.6 + - - -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 3.8 11.2 - - + -
47D ILE* 3.7 27.3 - - + +
55D VAL* 3.8 17.3 - - + -
59D LEU* 4.1 8.7 - - + -
72D LEU 3.0 14.9 + - - +
73D ILE* 3.2 18.6 - - + +
76D ALA* 1.3 75.7 - - - +
78D MET* 1.3 60.0 + - + +
80D GLY* 3.4 1.6 + - - -
81D MET* 2.9 28.9 + - - +
105D MET* 4.0 19.5 - - + +
108D GLY* 3.4 33.7 - - - +
109D ILE* 3.5 18.8 - - + +
112D CYS* 4.5 2.7 - - - -
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Residues in contact with MET 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE* 2.7 28.4 + - + +
74D ASP* 3.9 26.7 - - + +
77D LEU* 1.3 72.4 - - + +
79D VAL* 1.3 60.8 + - - +
81D MET* 3.9 7.9 - - + -
82D GLY* 3.3 18.6 + - - -
85D ILE* 5.6 1.3 - - + -
105D MET* 4.7 8.5 - - - +
109D ILE* 6.1 2.5 - - + -
123D LYS* 4.8 4.7 - - - +
148D ARG 4.4 4.9 - - - +
149D ALA 4.0 12.3 - - - +
150D ASN* 3.4 30.1 - - - +
151D GLY* 3.7 20.9 - - - +
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Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PRO* 3.7 36.8 - - + -
40D ILE* 4.6 3.1 - - + -
44D ALA* 5.0 0.4 - - + -
74D ASP 3.7 11.3 + - - +
75D ASP* 3.6 26.0 - - - +
76D ALA 3.7 2.2 + - - +
77D LEU 3.2 0.4 - - - -
78D MET* 1.3 79.1 - - - +
80D GLY* 1.3 64.9 + - - +
82D GLY* 3.1 11.2 + - - -
83D VAL* 3.3 15.1 + - + +
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Residues in contact with GLY 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ALA* 3.7 34.6 - - - +
47D ILE* 3.8 16.1 - - - +
76D ALA 3.1 12.5 + - - -
77D LEU 3.8 2.5 - - - -
79D VAL* 1.3 77.5 - - - +
81D MET* 1.3 60.2 + - - +
83D VAL* 3.2 22.2 + - - +
84D VAL* 3.4 5.0 + - - +
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.8 19.6 - - - +
77D LEU 2.9 17.3 + - - +
78D MET* 4.1 10.1 - - - +
80D GLY* 1.3 72.4 - - - +
82D GLY* 1.3 58.1 + - - +
83D VAL 3.1 2.2 - - - -
84D VAL* 3.1 29.7 + - + +
85D ILE* 3.0 36.4 + - + +
98D VAL* 4.0 6.7 - - + +
101D SER* 3.9 10.3 - - - +
102D ALA* 3.9 20.0 - - + +
105D MET* 3.9 23.8 - - - +
149D ALA* 3.3 45.3 - - + +
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 3.3 12.1 + - - -
79D VAL* 3.1 8.8 + - - -
81D MET* 1.3 78.2 - - - +
83D VAL* 1.3 60.2 + - - +
85D ILE* 4.1 10.2 - - - +
86D ARG* 3.3 23.4 + - - +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA* 4.5 5.6 - - + -
33D LEU* 3.8 39.0 - - + +
34D TYR* 4.2 27.8 - - + +
35D PRO* 5.3 3.1 - - + -
48D PHE* 4.3 17.7 - - + -
79D VAL* 3.3 11.7 + - + +
80D GLY* 3.2 13.9 + - - +
81D MET 3.1 0.4 - - - -
82D GLY* 1.3 75.4 - - - +
84D VAL* 1.3 65.4 + - - +
86D ARG* 3.3 5.8 + - - +
87D LEU* 3.1 33.2 + - + +
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 4.1 3.1 - - + -
48D PHE* 3.8 28.9 - - + +
80D GLY 3.4 8.7 + - - +
81D MET* 3.1 24.2 + - + +
83D VAL* 1.3 76.5 - - - +
85D ILE* 1.3 57.8 + - - +
87D LEU* 3.3 2.1 + - - -
88D TYR* 2.9 28.4 + - - +
93D ILE* 3.6 16.4 - - + +
98D VAL* 3.8 34.3 - - + -
101D SER* 3.4 24.5 - - - +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 5.6 1.6 - - + -
81D MET* 3.0 31.0 + - + +
82D GLY* 4.2 8.1 - - - +
84D VAL* 1.3 76.5 - - + +
86D ARG* 1.3 62.7 + - - +
88D TYR* 3.4 10.0 + - + +
89D ASP* 3.0 35.8 + - - +
98D VAL* 5.6 4.0 - - + -
146D LEU* 5.9 7.4 - - + -
149D ALA* 2.7 38.4 - - + +
150D ASN* 3.5 33.7 - - - +
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Residues in contact with ARG 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.5 47.2 - - + +
82D GLY 3.3 18.4 + - - +
83D VAL 3.4 5.2 - - - +
85D ILE* 1.3 79.0 - - - +
87D LEU* 1.3 59.9 + - + +
89D ASP* 3.0 8.9 + - - +
90D GLU* 2.8 58.3 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PRO 4.2 0.9 - - - +
29D ALA* 3.9 12.6 - - + -
30D ALA* 4.0 22.4 - - + +
33D LEU* 3.9 18.8 - - + -
48D PHE* 3.7 30.1 - - + -
83D VAL* 3.1 18.9 + - + +
84D VAL 3.8 0.7 - - - +
86D ARG* 1.3 80.9 - - + +
88D TYR* 1.3 57.8 + - - +
90D GLU* 3.6 17.4 + - - +
91D GLY 3.0 5.7 + - - -
92D VAL* 3.0 53.0 + - + -
93D ILE* 3.2 17.6 + - + -
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LYS* 3.0 48.7 + - + +
237C ASN* 2.8 22.0 + - - -
84D VAL 2.9 17.0 + - - +
85D ILE* 3.6 8.7 - - + +
87D LEU* 1.3 77.9 - - - +
89D ASP* 1.3 67.4 + - - +
91D GLY* 3.1 6.8 + - - -
93D ILE* 3.6 18.8 - - + +
94D PHE 3.9 7.9 - - - -
95D LEU* 3.6 29.7 - - + +
98D VAL* 3.6 19.1 - - + -
142D ILE* 5.0 5.0 - - - +
146D LEU* 4.1 32.5 - - + -
230D GLU* 4.6 6.3 + - + +
231D ALA* 6.0 1.2 - - - +
232D ALA* 4.8 10.0 + - + +
500D B13 5.6 0.5 + - - -
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LYS* 3.5 15.9 + - - +
85D ILE* 3.0 32.6 + - - +
86D ARG* 3.0 8.5 + - - +
88D TYR* 1.3 81.5 - - - +
90D GLU* 1.3 61.8 + - + +
91D GLY 3.1 1.1 + - - -
232D ALA* 4.1 21.3 - - - +
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 4.2 28.7 + - - +
86D ARG* 2.8 57.7 + - + +
87D LEU* 4.0 9.0 - - - +
89D ASP* 1.3 77.6 - - + +
91D GLY* 1.3 61.7 + - - +
92D VAL* 3.2 20.6 + - + +
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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