Contacts of the helix formed by residues 76 - 91 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40L ILE* 3.8 15.5 - - + -
43L ILE* 3.7 43.4 - - + +
44L ALA* 4.3 4.7 + - - +
47L ILE* 4.4 0.5 - - - +
59L LEU* 4.9 2.0 - - + -
72L LEU* 2.8 31.0 + - + +
75L ASP* 1.3 76.2 - - - +
77L LEU* 1.3 59.7 + - - +
78L MET 3.7 0.2 - - - -
79L VAL* 4.5 0.4 - - - +
80L GLY* 3.1 24.2 + - - -
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Residues in contact with LEU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ILE* 4.1 8.3 - - + -
47L ILE* 3.7 27.6 - - + +
55L VAL* 3.9 17.5 - - + -
59L LEU* 4.3 11.0 - - + -
72L LEU 3.3 8.5 + - - +
73L ILE* 3.5 22.9 - - + +
76L ALA* 1.3 75.5 - - - +
78L MET* 1.3 60.1 + - + +
79L VAL 3.2 0.2 - - - -
80L GLY* 3.5 0.9 + - - -
81L MET* 2.9 31.1 + - - +
105L MET* 4.1 19.8 - - + +
108L GLY* 3.6 29.6 - - - +
109L ILE* 3.7 19.5 - - + +
112L CYS* 4.4 4.5 - - - -
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Residues in contact with MET 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L ILE* 2.8 30.5 + - + +
74L ASP* 3.8 26.2 - - - +
77L LEU* 1.3 74.1 - - + +
79L VAL* 1.3 59.9 + - - +
81L MET* 4.2 3.4 - - - +
82L GLY* 3.3 19.7 + - - -
85L ILE* 5.5 0.2 - - - +
105L MET* 5.0 10.8 - - - +
109L ILE* 5.7 1.6 - - + -
123L LYS* 5.9 2.9 - - + -
148L ARG 4.4 5.4 - - - +
149L ALA 3.8 18.4 - - - +
150L ASN 4.1 3.4 - - - +
151L GLY* 3.6 36.1 - - - +
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Residues in contact with VAL 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L PRO* 3.7 31.9 - - + -
74L ASP 3.3 22.7 - - - +
75L ASP* 3.3 24.5 - - - +
76L ALA* 3.9 1.2 + - - +
77L LEU 3.2 0.4 - - - -
78L MET* 1.3 78.7 - - - +
80L GLY* 1.3 64.7 + - - +
82L GLY* 3.3 9.7 + - - -
83L VAL* 3.4 16.3 + - + +
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Residues in contact with GLY 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L ALA* 3.7 32.7 - - - +
47L ILE* 3.6 14.1 - - - +
48L PHE* 5.5 0.5 - - - +
76L ALA 3.1 18.8 + - - -
77L LEU 3.9 0.7 - - - -
79L VAL* 1.3 74.5 - - - +
81L MET* 1.3 61.6 + - - +
83L VAL* 3.3 20.9 + - - +
84L VAL* 3.4 6.1 + - - +
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Residues in contact with MET 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ILE* 3.6 6.5 - - + +
77L LEU 2.9 20.0 + - - +
78L MET* 4.2 7.4 - - - +
80L GLY* 1.3 73.6 - - - +
82L GLY* 1.3 58.6 + - - +
84L VAL* 2.9 23.2 + - + +
85L ILE* 2.8 35.9 + - + +
98L VAL* 3.9 28.7 - - + +
101L SER* 3.8 26.2 - - - +
102L ALA* 4.0 13.0 - - + +
105L MET* 4.1 21.8 - - - +
149L ALA* 3.7 37.2 - - + +
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Residues in contact with GLY 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L MET 3.3 15.2 + - - -
79L VAL* 3.3 6.0 + - - -
80L GLY 3.3 1.0 - - - -
81L MET* 1.3 77.7 - - - +
83L VAL* 1.3 56.9 + - - +
85L ILE* 3.6 15.2 - - - +
86L ARG* 3.1 27.5 + - - +
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Residues in contact with VAL 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ALA* 4.3 13.7 - - + +
33L LEU* 3.8 43.3 - - + +
34L TYR* 4.6 15.7 - - + +
35L PRO* 4.7 5.8 - - + -
48L PHE* 4.8 3.8 - - + -
79L VAL* 3.4 14.3 + - + +
80L GLY* 3.3 10.3 + - - +
81L MET 3.1 0.4 - - - -
82L GLY* 1.3 73.4 - - - +
84L VAL* 1.3 61.4 + - + +
86L ARG* 3.3 5.5 + - - +
87L LEU* 2.9 49.8 + - + +
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Residues in contact with VAL 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ILE* 4.3 3.1 - - + -
48L PHE* 3.9 29.2 - - + -
80L GLY 3.4 9.2 + - - +
81L MET* 2.9 20.6 + - + +
83L VAL* 1.3 80.6 - - - +
85L ILE* 1.3 56.4 + - - +
87L LEU* 4.7 2.0 - - - -
88L TYR* 3.0 28.4 + - - +
93L ILE* 3.6 15.2 - - + +
98L VAL* 3.9 24.5 - - + -
101L SER* 3.4 36.8 - - - +
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Residues in contact with ILE 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L MET* 2.8 34.9 + - + +
82L GLY* 3.6 11.4 - - - +
83L VAL 3.2 0.2 - - - -
84L VAL* 1.3 75.0 - - + +
86L ARG* 1.3 65.8 + - - +
88L TYR* 3.3 6.6 + - + +
89L ASP* 3.0 39.2 + - - +
98L VAL* 5.6 3.1 - - + -
146L LEU* 4.5 16.2 - - + -
149L ALA* 3.1 46.0 - - + +
150L ASN* 3.9 20.9 - - - +
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Residues in contact with ARG 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L LEU* 3.4 45.1 - - + +
82L GLY 3.1 19.1 + - - +
83L VAL* 3.5 5.2 - - - +
85L ILE* 1.3 76.5 - - - +
87L LEU* 1.3 64.3 + - - +
89L ASP* 3.0 10.4 + - - +
90L GLU* 2.6 49.6 + - - +
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Residues in contact with LEU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PRO 4.4 1.3 - - - +
29L ALA* 3.9 15.7 - - + -
30L ALA 4.0 15.9 - - - +
33L LEU* 3.9 20.0 - - + -
48L PHE* 3.7 30.3 - - + -
83L VAL* 2.9 29.7 + - + +
84L VAL* 4.0 1.3 - - - +
86L ARG* 1.3 76.1 - - - +
88L TYR* 1.3 56.9 + - - +
90L GLU* 3.2 17.5 + - - +
91L GLY 3.0 22.3 + - - -
92L VAL* 3.1 40.9 + - + -
93L ILE* 4.0 10.5 - - + -
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Residues in contact with TYR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K LYS* 3.4 42.3 + - - +
237K ASN* 2.5 24.3 + - - -
84L VAL 3.0 18.6 + - - +
85L ILE* 3.6 7.4 - - - +
87L LEU* 1.3 74.9 - - - +
89L ASP* 1.3 70.4 + - - +
91L GLY* 3.2 9.4 + - - -
93L ILE* 3.5 20.6 - - + +
94L PHE 3.8 7.9 - - - -
95L LEU* 3.4 32.4 - - + +
98L VAL* 3.6 18.6 - - + -
142L ILE* 5.1 4.9 - - + +
146L LEU* 4.5 30.7 - - + -
230L GLU* 5.3 2.9 + - - -
232L ALA* 5.5 9.4 - - + -
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Residues in contact with ASP 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K LYS* 3.6 14.2 + - - +
85L ILE* 3.0 31.1 + - - +
86L ARG* 3.0 11.1 + - - +
88L TYR* 1.3 81.8 - - - +
90L GLU* 1.3 62.3 + - + +
91L GLY 3.4 0.5 + - - -
146L LEU* 6.5 0.7 - - - -
232L ALA* 4.4 17.8 - - - +
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Residues in contact with GLU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LYS* 3.5 32.1 + - - +
33L LEU* 5.5 0.9 - - - +
86L ARG* 2.6 52.3 + - - +
87L LEU* 3.6 20.4 - - - +
88L TYR 3.2 0.6 - - - -
89L ASP* 1.3 76.3 - - + +
91L GLY* 1.3 61.1 + - - +
92L VAL* 3.4 13.6 - - + +
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Residues in contact with GLY 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K LYS* 3.9 20.0 - - - +
87L LEU 3.0 4.0 + - - -
88L TYR 3.2 12.7 + - - -
89L ASP 3.2 0.6 - - - -
90L GLU* 1.3 78.8 - - - +
92L VAL* 1.3 61.8 + - - +
93L ILE 3.5 5.4 - - - +
94L PHE* 4.3 13.0 - - - -
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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