Contacts of the helix formed by residues 52 - 63 (chain B) in PDB entry 1IAO
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 GLU 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 5.2 0.5 - - - -
51B THR* 1.3 75.7 - - - +
53B LEU* 1.3 61.8 + - + +
54B GLY 2.8 6.8 + - - -
55B ARG* 3.0 39.5 + - - +
56B PRO* 3.6 4.2 - - - +
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Residues in contact with LEU 53 (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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73A LEU* 3.8 12.3 - - + -
76A ARG* 2.8 59.7 + - + +
77A SER* 3.7 26.2 - - - +
32B TYR* 4.1 23.3 - - + -
35B GLU* 3.5 29.8 - - - +
37B TYR* 3.7 14.9 - - + -
51B THR* 3.2 8.3 + - - +
52B GLU* 1.3 81.3 + - + +
54B GLY* 1.3 57.7 + - - +
56B PRO* 3.6 1.3 - - - +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.1 29.0 + - - +
38B VAL* 3.6 14.5 - - - +
49B ALA* 3.4 7.9 - - - +
51B THR 2.9 4.8 + - - -
52B GLU 2.8 3.2 + - - -
53B LEU* 1.3 78.8 - - - +
55B ARG* 1.3 64.0 + - - +
56B PRO* 3.0 5.9 - - - -
57B ASP* 3.2 11.1 + - - -
58B ALA 3.2 9.9 + - - -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.3 17.0 - - + +
51B THR 3.9 3.1 + - - +
52B GLU* 3.0 35.5 - - - +
54B GLY* 1.3 73.5 - - - +
56B PRO* 1.3 67.2 - - + +
58B ALA* 3.8 2.3 + - - +
59B GLU* 3.4 24.8 + - - +
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Residues in contact with PRO 56 (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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76A ARG* 3.8 30.5 - - - +
52B GLU 3.6 4.3 - - - +
53B LEU 3.6 8.7 - - - +
54B GLY 3.1 6.5 - - - -
55B ARG* 1.3 92.7 - - + +
57B ASP* 1.3 66.3 + - - +
58B ALA 3.2 1.7 + - - -
59B GLU* 3.3 6.6 + - + +
60B TYR* 3.0 25.8 + - - +
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Residues in contact with ASP 57 (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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73A LEU* 4.1 1.6 - - - +
76A ARG* 3.2 31.5 + - - -
37B TYR* 3.2 33.4 - - - -
38B VAL* 3.6 5.5 - - + +
54B GLY 3.2 6.3 + - - +
56B PRO* 1.3 75.7 - - - +
58B ALA* 1.3 58.0 + - - +
60B TYR* 4.4 5.6 - - - -
61B TRP* 2.9 70.7 + - + +
332B ALA* 4.0 12.5 - - - +
333B GLU 5.1 1.2 + - - -
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Residues in contact with ALA 58 (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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38B VAL* 4.0 6.4 - - + +
47B TYR* 4.1 24.0 - - - +
48B ARG* 4.3 0.4 - - - -
49B ALA* 3.9 23.6 - - + +
54B GLY 3.2 13.3 + - - +
55B ARG 4.0 4.3 - - - +
56B PRO 3.2 0.8 - - - -
57B ASP* 1.3 76.8 - - - +
59B GLU* 1.3 65.9 + - - +
62B ASN* 3.0 34.2 + - - +
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Residues in contact with GLU 59 (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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55B ARG 3.4 16.0 + - - +
56B PRO* 3.3 6.0 + - + +
58B ALA* 1.3 80.5 - - - +
60B TYR* 1.3 57.8 + - - +
62B ASN* 4.5 3.3 - - - +
63B SER* 2.8 23.2 + - - -
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Residues in contact with TYR 60 (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 PRO 3.0 19.4 + - - +
57B ASP* 3.8 4.0 - - - +
59B GLU* 1.3 76.2 - - - +
61B TRP* 1.3 80.3 + + - +
63B SER* 2.4 30.7 + - - -
64B GLN* 3.0 46.4 + - + +
67B ILE* 4.9 3.9 - - + +
331B HIS 3.7 12.8 - - - -
332B ALA* 4.0 1.5 + - - -
333B GLU* 3.4 66.6 - - + +
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Residues in contact with TRP 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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69A ASN* 4.7 3.1 - - - -
30B TYR* 3.6 48.2 - + + -
37B TYR* 5.5 0.4 - + - -
38B VAL* 4.4 4.9 - - + -
47B TYR* 3.2 46.4 - + + -
57B ASP* 2.9 49.7 + - + +
60B TYR* 1.3 87.8 - + - +
62B ASN* 1.3 62.4 + - - +
64B GLN* 3.2 24.7 + - - +
67B ILE* 3.6 26.2 - - + -
68B LEU* 3.5 11.4 + - - +
330B ALA* 3.5 20.6 - - + +
331B HIS 2.7 32.3 + - - -
332B ALA* 4.0 7.6 - - + +
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Residues in contact with ASN 62 (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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46B GLU* 3.7 24.1 + - - +
47B TYR* 2.9 56.2 + - - +
58B ALA* 3.0 24.6 + - - +
59B GLU* 4.5 4.0 - - - +
61B TRP* 1.3 77.3 - - - +
63B SER* 1.3 59.3 + - - +
64B GLN 3.7 0.5 + - - -
65B PRO* 4.9 0.9 - - - +
68B LEU* 3.3 28.8 - - + +
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Residues in contact with SER 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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59B GLU 2.8 16.0 + - - -
60B TYR* 2.4 28.8 + - - -
62B ASN* 1.3 78.5 - - - +
64B GLN* 1.3 62.4 + - - +
65B PRO* 2.7 22.0 - - - +
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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