Contacts of the helix formed by residues 44 - 52 (chain B) in PDB entry 4IXU
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 HIS 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B GLY* 2.8 20.8 + - - +
43B GLU* 1.3 96.7 + - + +
45B GLY* 1.3 65.7 + - - +
46B PRO* 3.4 2.0 - - - -
47B ALA* 3.4 13.3 + - + +
48B ALA* 3.0 21.7 + - - +
299B PRO* 3.9 15.2 - - + +
300B GLN* 3.2 33.2 + - + -
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Residues in contact with GLY 45 (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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42B VAL 3.0 6.8 + - - -
44B HIS* 1.3 77.1 - - - +
46B PRO* 1.3 69.7 - - - +
48B ALA* 3.1 3.0 + - - +
49B ILE* 3.0 28.1 + - - +
117B GLY 3.5 9.9 - - - -
297B VAL* 3.3 27.7 + - - -
299B PRO* 4.0 6.0 - - - +
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Residues in contact with PRO 46 (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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30B GLY* 4.1 3.1 - - - -
31B ALA 4.0 8.1 - - - +
32B PRO* 4.1 11.7 - - + -
43B GLU 3.4 14.1 - - - +
44B HIS 3.6 0.7 - - - -
45B GLY* 1.3 89.2 - - - +
47B ALA* 1.3 62.6 + - - +
49B ILE* 3.2 3.5 + - + +
50B ARG* 3.0 29.2 + - - +
70B ASP* 3.8 22.0 - - - +
116B LEU* 3.4 44.7 - - + +
117B GLY 3.2 13.0 - - - +
118B GLY 3.8 1.8 - - - +
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Residues in contact with ALA 47 (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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43B GLU 5.3 0.4 + - - +
44B HIS* 3.4 15.9 + - + +
45B GLY 3.3 0.6 - - - -
46B PRO* 1.3 79.0 - - - +
48B ALA* 1.3 57.8 + - - +
50B ARG* 3.3 11.3 + - - +
51B GLU* 2.9 48.5 + - - +
70B ASP* 4.3 9.4 + - - +
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Residues in contact with ALA 48 (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 HIS 3.0 14.0 + - - +
45B GLY* 3.1 10.0 + - - +
47B ALA* 1.3 77.9 - - - +
49B ILE* 1.3 61.7 + - - +
51B GLU* 3.3 12.5 + - - +
52B ALA* 3.1 17.0 + - - +
297B VAL* 4.6 5.2 - - + -
299B PRO* 4.0 22.4 - - + -
308B ALA* 5.7 1.3 - - + +
312B ALA* 3.5 24.3 - - + +
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Residues in contact with ILE 49 (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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45B GLY 3.0 20.5 + - - +
46B PRO 3.8 3.6 - - - +
48B ALA* 1.3 73.4 - - - +
50B ARG* 1.3 68.5 + - - +
52B ALA* 3.1 13.1 + - - -
54B LEU* 3.6 23.7 + - + -
116B LEU* 4.2 21.3 - - + -
117B GLY 4.4 3.8 - - - +
294B LEU* 4.0 21.8 - - + +
297B VAL* 4.2 15.9 - - + -
312B ALA* 4.4 3.6 - - - +
315B ALA* 3.9 25.6 - - + -
316B VAL* 3.4 29.8 - - + +
319B ILE* 4.2 7.0 - - + -
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Residues in contact with ARG 50 (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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28B VAL* 4.1 11.6 - - - +
30B GLY* 3.9 9.7 - - - +
46B PRO 3.0 21.4 + - - +
47B ALA* 3.6 8.1 - - - +
49B ILE* 1.3 76.3 - - - +
51B GLU* 1.3 57.4 + - + +
53B GLY* 3.0 20.6 + - - -
54B LEU* 3.7 10.2 + - + +
55B MET* 4.5 21.2 + - + +
67B ASP* 2.4 45.8 + - - -
69B GLY* 3.3 26.5 + - - -
70B ASP* 3.2 19.3 + - - -
116B LEU* 4.2 11.9 - - + +
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Residues in contact with GLU 51 (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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47B ALA* 2.9 33.2 + - - +
48B ALA* 3.7 10.4 - - - +
50B ARG* 1.3 77.4 - - + +
52B ALA* 1.3 57.1 + - - +
53B GLY* 3.1 4.2 + - - -
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Residues in contact with ALA 52 (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 ALA 3.1 12.7 + - - +
49B ILE 3.5 9.6 - - - +
50B ARG 3.1 0.8 - - - -
51B GLU* 1.3 75.9 - - - +
53B GLY* 1.3 58.4 + - - +
54B LEU 3.6 1.1 - - - -
57B ARG* 5.2 4.0 + - - +
312B ALA* 3.8 16.8 - - + +
313B ASN* 3.5 25.1 - - - +
316B VAL* 3.6 22.3 - - + +
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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