Contacts of the helix formed by residues 68 - 77 (chain B) in PDB entry 2I10
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 ARG 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 2.9 49.1 + - - +
61B LEU* 3.6 36.3 - - - +
62B ASP* 2.9 30.6 + - - +
65B MSE 3.5 20.0 + - - +
66B CYS 3.2 4.9 + - - +
67B GLU* 1.3 74.4 - - - +
69B THR* 1.3 78.8 + - + +
70B LEU* 3.5 2.0 - - + +
71B GLN* 3.3 25.3 + - - +
72B LEU* 3.1 20.4 + - - +
88B PHE* 5.1 1.2 - - - -
92B ARG* 4.1 18.2 - - - +
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B MSE 5.1 0.6 - - - +
67B GLU 3.2 6.5 + - - -
68B ARG* 1.3 87.0 - - - +
70B LEU* 1.3 62.0 + - + +
72B LEU* 3.3 6.5 + - - +
73B GLU* 2.9 54.0 + - - +
131B GLN* 6.1 4.2 - - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.5 2.7 - - + +
69B THR* 1.3 83.1 - - + +
71B GLN* 1.3 82.3 + - - +
73B GLU* 3.9 7.4 - - + +
74B GLU* 2.9 44.6 + - + +
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP* 4.9 4.8 + - - +
68B ARG* 3.3 31.0 + - - +
69B THR 3.3 0.4 - - - -
70B LEU* 1.3 103.6 - - - +
72B LEU* 1.3 65.2 + - - +
74B GLU* 3.2 25.6 + - - +
75B ALA* 3.1 23.6 + - - +
88B PHE* 4.2 6.6 - - + -
92B ARG* 3.7 28.3 - - - +
95B VAL* 5.8 2.2 - - + -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLU 4.9 7.0 - - - +
68B ARG 3.1 17.2 + - - +
69B THR* 3.7 6.1 - - - +
71B GLN* 1.3 76.3 - - - +
73B GLU* 1.3 58.7 + - + +
75B ALA* 3.1 5.5 + - - +
76B MSE 2.9 44.2 + - + +
88B PHE* 3.6 43.8 - - + -
131B GLN* 5.1 0.4 - - + -
132B MSE 3.6 39.5 - - + +
135B THR* 3.9 24.7 - - + +
136B VAL* 4.4 11.2 - - + -
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B THR* 2.9 37.4 + - - +
70B LEU* 3.9 7.2 - - + +
72B LEU* 1.3 76.6 - - + +
74B GLU* 1.3 62.0 + - - +
76B MSE 3.1 18.1 + - + +
77B VAL* 3.5 18.6 + - - +
135B THR* 4.9 15.7 + - + +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 2.9 34.4 + - + +
71B GLN* 3.2 40.8 + - - +
72B LEU 3.3 0.2 - - - -
73B GLU* 1.3 76.1 - - - +
75B ALA* 1.3 62.8 + - + +
77B VAL* 3.6 16.8 + - - +
78B ARG* 4.5 5.5 + - - -
87B ASP* 4.6 5.9 - - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLN 3.1 14.9 + - - +
72B LEU 3.1 8.3 + - - +
74B GLU* 1.3 79.0 - - + +
76B MSE 1.3 65.7 + - + +
77B VAL 3.1 1.7 + - - -
78B ARG* 3.2 21.5 + - - +
84B ALA* 3.4 23.3 - - - +
87B ASP* 4.0 13.5 - - + +
88B PHE* 3.7 27.1 - - + +
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Residues in contact with MSE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 2.9 33.6 + - + +
73B GLU* 3.1 8.2 + - + +
75B ALA* 1.3 83.5 - - + +
77B VAL* 1.3 59.2 + - + +
78B ARG 3.2 0.8 + - - +
84B ALA* 3.7 30.5 - - + +
85B VAL* 4.3 9.4 - - + +
88B PHE* 4.3 5.4 - - + -
135B THR* 3.7 31.2 - - + +
136B VAL* 4.4 14.4 - - + -
139B ARG* 2.9 60.3 + - + -
142B LYS* 5.8 1.0 - - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU 3.5 14.6 - - - +
74B GLU* 3.8 11.9 - - - +
75B ALA 3.1 1.4 + - - -
76B MSE 1.3 73.8 - - + +
78B ARG* 1.3 68.2 + - - +
79B PRO* 3.6 2.4 - - - +
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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