Contacts of the helix formed by residues 60 - 68 (chain B) in PDB entry 2POD
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 GLN 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B GLU* 4.2 6.4 - - - +
57B ASP* 3.4 37.3 + - + +
58B PRO 3.2 1.8 - - - -
59B LEU* 1.3 75.1 - - + +
61B ILE* 1.3 56.5 + - - +
62B ASP 3.5 1.6 - - - -
63B ARG* 2.9 43.7 + - + -
64B HIS* 3.0 36.9 + - - +
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Residues in contact with ILE 61 (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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58B PRO 3.4 18.6 - - - +
59B LEU 2.9 13.6 + - - +
60B GLN* 1.3 68.7 - - - +
62B ASP* 1.3 66.7 + - - +
64B HIS* 3.4 2.1 + - - +
65B ALA* 3.1 24.3 + - - +
88B ASP* 3.7 8.1 - - - +
91B LEU* 3.5 38.2 - - + +
92B TRP* 3.4 42.4 - - + +
95B PHE* 3.7 24.0 - - + -
301B SER* 3.2 22.2 - - - +
304B ARG* 4.9 0.2 - - - +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 1.3 77.3 - - - +
63B ARG* 1.3 62.8 + - - +
65B ALA* 3.7 5.4 + - - +
66B LYS* 3.3 21.5 + - - +
301B SER* 4.1 2.8 + - - -
304B ARG* 2.8 41.3 + - - -
305B LYS* 3.2 22.6 + - - +
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Residues in contact with ARG 63 (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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56B GLU* 2.8 35.2 + - - -
60B GLN* 2.9 41.3 + - + +
62B ASP* 1.3 78.0 - - - +
64B HIS* 1.3 61.6 + - - +
66B LYS* 3.5 7.1 + - - +
67B ARG* 3.0 53.0 + - + +
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Residues in contact with HIS 64 (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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3B ILE* 5.4 0.4 - - + -
53B LEU* 3.8 23.3 - - + -
56B GLU* 3.2 37.1 - - + +
57B ASP 2.6 31.2 + - - -
58B PRO* 4.5 2.7 - - + -
60B GLN* 3.0 27.7 + - - +
61B ILE 4.0 2.9 - - - +
63B ARG* 1.3 87.6 - - - +
65B ALA* 1.3 54.7 + - - +
67B ARG* 3.1 23.1 + - - +
68B LEU* 2.7 42.3 + - + +
91B LEU* 4.1 22.0 - - + -
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Residues in contact with ALA 65 (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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61B ILE 3.1 17.5 + - - +
62B ASP* 3.9 6.3 - - - +
64B HIS* 1.3 76.2 - - - +
66B LYS* 1.3 60.6 + - - +
68B LEU* 3.7 6.7 + - - +
69B SER* 3.3 20.4 + - - -
84B ASN* 5.6 0.6 + - - -
88B ASP* 4.4 6.9 + - + +
91B LEU* 5.8 0.4 - - - +
298B GLY 5.3 4.3 - - - +
301B SER* 4.2 22.2 - - - +
302B GLU* 5.6 6.5 - - + +
305B LYS* 6.2 1.1 - - - +
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Residues in contact with LYS 66 (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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186A ASP* 4.0 41.0 + - - +
188A TYR* 4.4 14.1 + - - -
224A ASN* 5.3 1.8 - - - +
248A ARG* 6.4 1.8 - - - -
62B ASP 3.3 12.2 + - - +
63B ARG* 3.7 8.7 - - - +
64B HIS 3.2 0.6 - - - -
65B ALA* 1.3 77.9 - - - +
67B ARG* 1.3 63.1 + - + +
69B SER* 3.4 24.8 + - - +
276B TRP* 6.1 5.2 - - + -
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Residues in contact with ARG 67 (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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48B TRP* 3.5 7.1 - - - -
52B ARG* 2.8 93.3 + - - +
53B LEU* 4.7 2.0 - - - +
56B GLU* 3.5 17.0 + - - -
63B ARG* 3.0 54.0 + - + +
64B HIS* 3.1 29.6 + - - +
66B LYS* 1.3 77.3 - - + +
68B LEU* 1.3 62.3 + - + +
69B SER 3.5 3.8 + - - +
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Residues in contact with LEU 68 (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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44B TYR* 3.4 8.7 + - - -
48B TRP* 3.4 9.3 - - + -
49B ALA* 3.7 33.7 - - + +
52B ARG* 3.8 18.6 - - + -
53B LEU* 4.3 19.7 - - + -
64B HIS* 2.7 25.6 + - + +
65B ALA* 4.0 5.4 - - - +
67B ARG* 1.3 71.4 - - + +
69B SER* 1.3 58.8 + - - +
70B GLY 3.1 7.4 + - - -
84B ASN* 2.9 46.4 + - + +
87B LEU* 4.0 27.4 - - + -
91B LEU* 6.2 1.6 - - + -
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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