Contacts of the helix formed by residues 77 - 90 (chain H) 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 LEU 77 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43H ILE* 3.9 22.9 - - + -
47H ILE* 3.9 17.9 - - + +
55H VAL* 4.2 10.1 - - + -
59H LEU* 4.1 13.7 - - + -
72H LEU 3.0 13.6 + - - +
73H ILE* 3.4 22.2 - - + +
76H ALA* 1.3 76.8 - - - +
78H MET* 1.3 62.0 + - - +
79H VAL 3.5 0.2 - - - -
81H MET* 3.1 28.7 + - - +
104H ALA 5.7 0.4 - - - +
105H MET* 4.0 18.7 - - + +
108H GLY* 3.2 33.2 - - - +
109H ILE* 3.7 18.4 - - + +
112H CYS* 4.5 2.7 - - - -
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Residues in contact with MET 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ILE* 2.9 26.6 + - + +
74H ASP* 3.5 32.7 + - - +
77H LEU* 1.3 79.7 - - + +
79H VAL* 1.3 60.2 + - + +
81H MET* 3.9 3.1 - - - +
82H GLY* 3.1 21.5 + - - -
105H MET* 5.2 8.1 - - - +
109H ILE* 6.5 1.1 - - + -
123H LYS* 4.7 9.4 - - - -
148H ARG 5.5 0.2 - - - +
149H ALA 4.0 14.5 - - - +
150H ASN 3.6 24.7 - - - +
151H GLY* 3.7 21.1 - - - -
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU 5.8 0.9 - - - +
35H PRO* 3.9 36.3 - - + -
40H ILE* 4.8 0.7 - - + -
74H ASP 4.0 11.8 + - - +
75H ASP* 3.5 24.5 - - - +
77H LEU 3.5 1.0 - - - +
78H MET* 1.3 75.8 - - - +
80H GLY* 1.3 61.0 + - - +
82H GLY* 3.1 15.9 + - - -
83H VAL* 3.3 16.0 + - + +
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Residues in contact with GLY 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H ALA* 3.7 36.1 - - - +
47H ILE* 3.5 17.6 - - - +
76H ALA 3.8 11.8 + - - -
77H LEU 4.5 0.2 - - - -
79H VAL* 1.3 79.8 - - - +
81H MET* 1.3 58.7 - - - +
83H VAL* 3.7 12.4 + - - +
84H VAL* 3.6 11.8 - - - +
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Residues in contact with MET 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 3.8 10.0 - - - +
77H LEU 3.1 22.4 + - - +
78H MET* 4.0 5.8 - - - +
79H VAL 3.2 0.6 - - - -
80H GLY* 1.3 73.9 - - - +
82H GLY* 1.3 60.0 + - - +
83H VAL 3.2 0.4 - - - -
84H VAL* 3.2 16.8 + - + +
85H ILE* 3.1 34.4 + - + +
98H VAL* 3.9 9.6 - - + +
101H SER* 3.6 26.9 - - - +
102H ALA* 3.5 24.7 - - + +
105H MET* 3.7 19.5 - - + -
149H ALA* 3.6 44.6 - - + +
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Residues in contact with GLY 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H MET 3.1 13.9 + - - -
79H VAL* 3.1 10.2 + - - -
81H MET* 1.3 74.9 - - - +
83H VAL* 1.3 58.0 + - - +
85H ILE* 4.0 11.8 - - - +
86H ARG* 3.1 30.0 + - - +
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Residues in contact with VAL 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ALA* 4.2 16.8 - - + +
33H LEU* 4.1 35.7 - - + +
34H TYR* 4.3 21.3 - - + -
35H PRO* 4.9 3.8 - - + -
48H PHE* 4.8 3.6 - - + -
79H VAL* 3.3 16.8 - - + +
80H GLY* 3.7 14.1 - - - +
81H MET 3.2 0.2 - - - -
82H GLY* 1.3 77.6 - - - +
84H VAL* 1.3 58.0 + - + +
86H ARG* 3.4 4.9 + - - +
87H LEU* 2.9 53.3 + - + +
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Residues in contact with VAL 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 4.4 2.5 - - + -
48H PHE* 3.6 27.6 - - + +
80H GLY 3.6 15.7 - - - +
81H MET* 3.2 15.0 + - + +
83H VAL* 1.3 75.3 - - - +
85H ILE* 1.3 57.2 + - - +
87H LEU* 3.4 0.7 + - - -
88H TYR* 2.9 27.9 + - - +
93H ILE* 3.4 25.7 - - + +
98H VAL* 3.7 17.3 - - + -
101H SER* 3.4 38.8 - - - +
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Residues in contact with ILE 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H MET 5.8 0.2 - - - +
81H MET* 3.1 27.9 + - + +
82H GLY* 4.2 8.1 - - - +
84H VAL* 1.3 75.5 - - - +
86H ARG* 1.3 60.6 + - - +
88H TYR* 3.4 6.7 + - + +
89H ASP* 2.8 40.5 + - - +
98H VAL* 5.2 7.6 - - + -
146H LEU* 4.7 15.9 - - + -
149H ALA* 3.1 46.4 - - + +
150H ASN* 4.1 23.6 - - - +
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Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 3.5 45.8 - - + +
82H GLY 3.1 21.4 + - - +
83H VAL* 3.6 4.3 - - - +
85H ILE* 1.3 76.6 - - - +
87H LEU* 1.3 60.3 + - - +
89H ASP* 3.3 15.0 + - - +
90H GLU* 2.9 39.1 + - - +
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Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PRO 4.3 1.3 - - - +
29H ALA* 3.8 18.8 - - + +
30H ALA* 3.8 20.2 - - + +
33H LEU* 3.7 22.9 - - + -
48H PHE* 3.3 34.3 - - + -
83H VAL* 2.9 23.2 + - + +
84H VAL 3.9 3.1 - - - +
86H ARG* 1.3 73.0 - - - +
88H TYR* 1.3 63.3 + - - +
89H ASP 3.4 0.2 - - - -
90H GLU* 3.8 13.6 + - - +
91H GLY 3.2 2.9 + - - -
92H VAL* 3.1 53.1 + - + +
93H ILE* 3.4 10.2 + - + -
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Residues in contact with TYR 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236G LYS* 2.7 54.3 + - - +
237G ASN* 2.9 20.7 + - - -
84H VAL 2.9 17.5 + - - +
85H ILE* 3.5 8.1 - - + +
86H ARG 3.2 0.2 - - - -
87H LEU* 1.3 78.5 - - - +
89H ASP* 1.3 63.2 + - - +
91H GLY* 3.3 6.1 + - - -
93H ILE* 3.7 16.6 - - - +
95H LEU* 3.3 36.8 - - + +
98H VAL* 3.3 26.9 - - + -
142H ILE* 5.1 4.9 - - - +
146H LEU* 4.8 20.0 - - + -
230H GLU* 4.3 10.4 + - - -
231H ALA* 6.0 0.7 - - - +
232H ALA* 4.5 18.6 - - + -
500H B13 5.4 0.7 + - - -
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Residues in contact with ASP 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236G LYS* 3.3 14.9 + - - +
85H ILE* 2.8 29.5 + - - +
86H ARG* 3.3 9.4 + - - +
88H TYR* 1.3 84.8 - - - +
90H GLU* 1.3 65.0 + - + +
146H LEU* 5.7 0.7 - - - +
232H ALA* 5.2 11.6 - - - +
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Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H LYS* 3.8 30.8 + - - +
29H ALA* 5.8 0.5 - - - +
33H LEU* 5.2 1.7 - - - +
86H ARG* 2.9 50.6 + - - +
87H LEU* 4.1 20.7 - - - +
88H TYR 3.3 0.4 - - - -
89H ASP* 1.3 78.7 - - + +
91H GLY* 1.3 59.8 + - - +
92H VAL* 3.5 9.0 - - + +
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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